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<h3 style="margin-top: 20px; margin-bottom: 10px;">
Alexandre Mestiashvili pushed to branch master at <a href="https://salsa.debian.org/med-team/plip">Debian Med / plip</a>
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
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<ul>
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<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/plip/-/commit/61a583490a13a368fe7d884b087f34060b3cb282">61a58349</a></strong>
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<span> by Alexandre Mestiashvili </span> <i> at 2025-01-10T14:29:38+01:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 2.4.0+dfsg</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/plip/-/commit/bec9fb6d4077f65f64dc5e6ecfdff2fac1f0415d">bec9fb6d</a></strong>
<div>
<span> by Alexandre Mestiashvili </span> <i> at 2025-01-10T14:29:38+01:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/2.4.0+dfsg'
Update to upstream version '2.4.0+dfsg'
with Debian dir 933dcfd2ff88b579a7a7ffedefb57df1f43945d1</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/plip/-/commit/1e768ecf9b40a3e3bfc362c86405cac2d2c80838">1e768ecf</a></strong>
<div>
<span> by Alexandre Mestiashvili </span> <i> at 2025-01-10T14:30:10+01:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update changelog
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/plip/-/commit/ccd9b03ca0f94cf28a9da9f3daafc6507f584c47">ccd9b03c</a></strong>
<div>
<span> by Alexandre Mestiashvili </span> <i> at 2025-01-14T14:48:20+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add patch removing custom build option for broken openbabel pip bindings
See also: https://github.com/openbabel/openbabel/issues/2408
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/plip/-/commit/c087e0d98210878bb0eb44ab54b7f6cd719a2a3f">c087e0d9</a></strong>
<div>
<span> by Alexandre Mestiashvili </span> <i> at 2025-01-14T14:57:24+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/control, bump Standards-Version to 4.7.0
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/plip/-/commit/987142df85e4487ee8693e3417f93cd5d85a962c">987142df</a></strong>
<div>
<span> by Alexandre Mestiashvili </span> <i> at 2025-01-14T15:00:17+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update changelog, prepare for release
</pre>
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
14 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
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<li class="file-stats">
<a href="#3251d7a8143ce2e789f0468513df8f285f842c3a">
CHANGES.txt
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<a href="#baf09939cda3fe56aa57fe83e167d8594afc7d6b">
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debian/patches/setup.patch
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<a href="#e0bdfb93722bb0bccd3faf9d5cbf446297ff47c4">
plip/basic/config.py
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<li class="file-stats">
<a href="#6b5252720edd1a79305a8187c9b25ca0b1651838">
plip/basic/supplemental.py
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<li class="file-stats">
<a href="#7a4c9b79c2f1bb441895d677413efbc1cb536c35">
plip/plipcmd.py
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<li class="file-stats">
<a href="#27a6dfa55905f1bad1286d8de59653dccfc480fb">
plip/structure/detection.py
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<li class="file-stats">
<a href="#b72517a8cd7dbc6709d05fdad49ae468ebf79126">
plip/structure/preparation.py
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<li class="file-stats">
<a href="#2525073c8fbdbd4c496cc540b74b251789f6c700">
plip/test/test_literature_validated.py
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<li class="file-stats">
<a href="#814e5fbe237dcc3e3aabaee96b3a65b231d08b1c">
plip/visualization/visualize.py
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
Changes:
</h4>
<li id="a5cc2925ca8258af241be7e5b0381edf30266302">
<a href="https://salsa.debian.org/med-team/plip/-/compare/9408f2de4e28772642baaea5c38da321a843cb5e...987142df85e4487ee8693e3417f93cd5d85a962c#a5cc2925ca8258af241be7e5b0381edf30266302"><strong style="font-weight: 600;">.gitignore</strong></a>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -48,3 +48,4 @@ target/</td>
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<td class="old_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
48
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC48" class="line" lang="plaintext"># Other</span>
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<td class="old_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
49
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<td class="new_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
49
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC49" class="line" lang="plaintext">*~</span>
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<td class="old_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
50
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC50" class="line" lang="plaintext">.nfs*</span>
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<td class="old_line diff-line-num new" data-linenumber="51" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="51" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
51
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC51" class="line" lang="plaintext">tests/</span></pre></td>
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<td class="new_line diff-line-num" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd"></td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">\ No newline at end of file</td>
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<li id="3251d7a8143ce2e789f0468513df8f285f842c3a">
<a href="https://salsa.debian.org/med-team/plip/-/compare/9408f2de4e28772642baaea5c38da321a843cb5e...987142df85e4487ee8693e3417f93cd5d85a962c#3251d7a8143ce2e789f0468513df8f285f842c3a"><strong style="font-weight: 600;">CHANGES.txt</strong></a>
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<td class="old_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1
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1
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1" class="line" lang="plaintext">Changelog</span>
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2
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2
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2" class="line" lang="plaintext">---------</span>
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<td class="old_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="plaintext"># 2.4.0</span>
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<td class="old_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
4
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4" class="line" lang="plaintext">* new "--chains" flag to enable detection of interactions between protein chains by @PhiCMS and @snbolz</span>
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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
5
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="plaintext">* update setup.py, attempt to fix and install broken python openbabel bindings 3.1.1.1</span>
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6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6" class="line" lang="plaintext">* update Dockerfile</span>
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7
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
8
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC8" class="line" lang="plaintext"># 2.3.1</span>
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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
9
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC9" class="line" lang="plaintext">* fixes in interaction detection with peptide ligands by @kalinni in #153</span>
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<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10" class="line" lang="plaintext">* fix in hydrogen bond acceptor identification by @kalinni in #151</span>
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<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
11
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC11" class="line" lang="plaintext">* fixes in waterbridge detection and filtering by @kalinni in #152</span>
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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
12
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC12" class="line" lang="plaintext">* fix NumPy DeprecationWarning when using numpy.uint32 with negative numbers by @QY0831 in #150</span>
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13
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC13" class="line" lang="plaintext"></span>
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3
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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14" class="line" lang="plaintext"># 2.3.0</span>
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4
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<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC15" class="line" lang="plaintext">* fixes an issue that caused encoding errors to be thrown</span>
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5
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<td class="new_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
16
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC16" class="line" lang="plaintext">* salt bridge interaction improved</span>
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<a href="https://salsa.debian.org/med-team/plip/-/compare/9408f2de4e28772642baaea5c38da321a843cb5e...987142df85e4487ee8693e3417f93cd5d85a962c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong style="font-weight: 600;">debian/changelog</strong></a>
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1
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1" class="line" lang="plaintext">plip (2.4.0+dfsg-1) unstable; urgency=medium</span>
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2
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="plaintext"> * New upstream version 2.4.0+dfsg</span>
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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
4
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4" class="line" lang="plaintext"> * Add patch removing custom build option for broken openbabel pip bindings</span>
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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
5
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="plaintext"> * d/control, bump Standards-Version to 4.7.0</span>
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6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
7
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7" class="line" lang="plaintext"> -- Alexandre Mestiashvili <mestia@debian.org> Tue, 14 Jan 2025 14:58:59 +0100</span>
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8
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC8" class="line" lang="plaintext"></span>
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1
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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
9
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC9" class="line" lang="plaintext">plip (2.3.0+dfsg-2) unstable; urgency=medium</span>
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2
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<a href="https://salsa.debian.org/med-team/plip/-/compare/9408f2de4e28772642baaea5c38da321a843cb5e...987142df85e4487ee8693e3417f93cd5d85a962c#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong style="font-weight: 600;">debian/control</strong></a>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -11,7 +11,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC11" class="line" lang="plaintext"> python3-numpy,</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC12" class="line" lang="plaintext"> python3-openbabel,</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC13" class="line" lang="plaintext"> python3-setuptools</span>
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<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right deletion" style="background-color: #fac5cd;">6.2</span></span>
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14
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right addition" style="background-color: #c7f0d2;">7.0</span></span>
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15
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<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/plip</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC16" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/plip.git</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC17" class="line" lang="plaintext">Homepage: https://projects.biotec.tu-dresden.de/plip-web/plip/</span>
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<a href="https://salsa.debian.org/med-team/plip/-/compare/9408f2de4e28772642baaea5c38da321a843cb5e...987142df85e4487ee8693e3417f93cd5d85a962c#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong style="font-weight: 600;">debian/patches/series</strong></a>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1" class="line" lang="plaintext">revert_imagemagick_changes.patch</span>
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2
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2" class="line" lang="plaintext">setup.patch</span></pre></td>
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<a href="https://salsa.debian.org/med-team/plip/-/compare/9408f2de4e28772642baaea5c38da321a843cb5e...987142df85e4487ee8693e3417f93cd5d85a962c#baf09939cda3fe56aa57fe83e167d8594afc7d6b"><strong style="font-weight: 600;">debian/patches/setup.patch</strong></a>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1" class="line" lang="diff"><span class="p">Description: Do not call custom cmdclass for building openbabel bindings</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2" class="line" lang="diff"><span class="p">Author: Alex Mestiashvili <mestia@debian.org></span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000000; background-color: #ffdddd;">--- plip.orig/setup.py</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="diff"><span class="p">@@ -90,10 +90,10 @@</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6" class="line" lang="diff"> license='GPLv2',</span>
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<a href="https://salsa.debian.org/med-team/plip/-/compare/9408f2de4e28772642baaea5c38da321a843cb5e...987142df85e4487ee8693e3417f93cd5d85a962c#e0bdfb93722bb0bccd3faf9d5cbf446297ff47c4"><strong style="font-weight: 600;">plip/basic/config.py</strong></a>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="python"><span class="n" style="color: #333333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">2.<span class="idiff left right deletion" style="background-color: #fac5cd;">3</span>.0</span><span class="sh" style="color: #dd1144;">'</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2" class="line" lang="python"><span class="n" style="color: #333333;">__maintainer__</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">PharmAI GmbH (2020-2021) - www.pharm.ai - hello@pharm.ai</span><span class="sh" style="color: #dd1144;">'</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3" class="line" lang="python"><span class="n" style="color: #333333;">__citation_information__</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">Adasme,M. et al. PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA. </span><span class="sh" style="color: #dd1144;">"</span> \</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4" class="line" lang="python"> <span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">Nucl. Acids Res. (05 May 2021), gkab294. doi: 10.1093/nar/gkab294</span><span class="sh" style="color: #dd1144;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="25" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -25,12 +25,15 @@ NOFIX = False # Turn off fixing of errors in PDB files</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC25" class="line" lang="python"><span class="n" style="color: #333333;">NOFIXFILE</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999999;">False</span> <span class="c1" style="color: #999988; font-style: italic;"># Turn off writing to files for fixed PDB structures</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC26" class="line" lang="python"><span class="n" style="color: #333333;">PEPTIDES</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span> <span class="c1" style="color: #999988; font-style: italic;"># Definition which chains should be considered as peptide ligands</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC27" class="line" lang="python"><span class="n" style="color: #333333;">INTRA</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999999;">None</span></span>
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28
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC28" class="line" lang="python"><span class="n" style="color: #333333;">RESIDUES</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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28
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<td class="new_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
29
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC29" class="line" lang="python"><span class="n" style="color: #333333;">KEEPMOD</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999999;">False</span></span>
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29
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<td class="new_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
30
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC30" class="line" lang="python"><span class="n" style="color: #333333;">DNARECEPTOR</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999999;">False</span></span>
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30
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<td class="new_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
31
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC31" class="line" lang="python"><span class="n" style="color: #333333;">OUTPUTFILENAME</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">report</span><span class="sh" style="color: #dd1144;">"</span> <span class="c1" style="color: #999988; font-style: italic;"># Naming for the TXT and XML report files</span></span>
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31
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<td class="new_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
32
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC32" class="line" lang="python"><span class="n" style="color: #333333;">NOPDBCANMAP</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999999;">False</span> <span class="c1" style="color: #999988; font-style: italic;"># Skip calculation of mapping canonical atom order: PDB atom order</span></span>
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32
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<td class="new_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
33
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC33" class="line" lang="python"><span class="n" style="color: #333333;">NOHYDRO</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999999;">False</span> <span class="c1" style="color: #999988; font-style: italic;"># Do not add hydrogen bonds (in case already present in the structure)</span></span>
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33
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<td class="new_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
34
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC34" class="line" lang="python"><span class="n" style="color: #333333;">MODEL</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #009999;">1</span> <span class="c1" style="color: #999988; font-style: italic;"># The model to be selected for multi-model structures (default = 1).</span></span>
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<td class="new_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
35
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC35" class="line" lang="python"><span class="n" style="color: #333333;">CHAINS</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999999;">None</span> <span class="c1" style="color: #999988; font-style: italic;"># Define chains for protein-protein interaction detection</span></span>
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36
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC36" class="line" lang="python"></span>
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<td class="new_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
37
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC37" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="35" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
35
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<td class="new_line diff-line-num" data-linenumber="38" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
38
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC38" class="line" lang="python"><span class="c1" style="color: #999988; font-style: italic;"># Configuration file for Protein-Ligand Interaction Profiler (PLIP)</span></span>
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<td class="new_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
39
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC39" class="line" lang="python"><span class="c1" style="color: #999988; font-style: italic;"># Set thresholds for detection of interactions</span></span>
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<li id="6b5252720edd1a79305a8187c9b25ca0b1651838">
<a href="https://salsa.debian.org/med-team/plip/-/compare/9408f2de4e28772642baaea5c38da321a843cb5e...987142df85e4487ee8693e3417f93cd5d85a962c#6b5252720edd1a79305a8187c9b25ca0b1651838"><strong style="font-weight: 600;">plip/basic/supplemental.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="55" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="55" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -55,6 +55,18 @@ def whichchain(atom):</td>
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<td class="new_line diff-line-num" data-linenumber="55" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
55
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">atom</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetResidue</span><span class="p">().</span><span class="nc" style="color: #445588; font-weight: 600;">GetChain</span><span class="p">()</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">atom</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetResidue</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999999;">None</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999999;">None</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC56" class="line" lang="python"></span>
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57
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC57" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
58
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC58" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #990000; font-weight: 600;">residue_belongs_to_receptor</span><span class="p">(</span><span class="n" style="color: #333333;">res</span><span class="p">,</span> <span class="n" style="color: #333333;">config</span><span class="p">):</span></span>
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59
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC59" class="line" lang="python"> <span class="sh" style="color: #dd1144;">"""</span><span class="s" style="color: #dd1144;">tests whether the residue is defined as receptor and is not part of a peptide or residue ligand.</span><span class="sh" style="color: #dd1144;">"""</span></span>
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<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
60
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">CHAINS</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
61
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">CHAINS</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">CHAINS</span><span class="p">[</span><span class="mi" style="color: #009999;">1</span><span class="p">]:</span> <span class="c1" style="color: #999988; font-style: italic;"># if receptor and ligand chains were given</span></span>
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<td class="new_line diff-line-num new" data-linenumber="62" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
62
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">res</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetChain</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">CHAINS</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333333;">res</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetChain</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">CHAINS</span><span class="p">[</span><span class="mi" style="color: #009999;">1</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
63
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC63" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># True if residue is part of receptor chains and not of ligand chains</span></span>
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<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
64
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">CHAINS</span><span class="p">[</span><span class="mi" style="color: #009999;">1</span><span class="p">]:</span> <span class="c1" style="color: #999988; font-style: italic;"># if only ligand chains were given</span></span>
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<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
65
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">res</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetChain</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">CHAINS</span><span class="p">[</span><span class="mi" style="color: #009999;">1</span><span class="p">]</span> <span class="c1" style="color: #999988; font-style: italic;"># True if residue is not part of ligand chains</span></span>
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<td class="new_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
66
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999999;">False</span> <span class="c1" style="color: #999988; font-style: italic;"># if only receptor chains were given or both is empty</span></span>
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<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
67
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">res</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetChain</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">PEPTIDES</span> <span class="c1" style="color: #999988; font-style: italic;"># True if residue is not part of peptide ligand.</span></span>
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68
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC68" class="line" lang="python"></span>
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69
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC69" class="line" lang="python"></span>
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58
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<td class="new_line diff-line-num" data-linenumber="70" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
70
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC70" class="line" lang="python"><span class="c1" style="color: #999988; font-style: italic;">#########################</span></span>
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59
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<td class="new_line diff-line-num" data-linenumber="71" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
71
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC71" class="line" lang="python"><span class="c1" style="color: #999988; font-style: italic;"># Mathematical operations</span></span>
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60
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<td class="new_line diff-line-num" data-linenumber="72" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
72
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC72" class="line" lang="python"><span class="c1" style="color: #999988; font-style: italic;">#########################</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="358" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="370" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -358,7 +370,7 @@ def int32_to_negative(int32):</td>
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358
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<td class="new_line diff-line-num" data-linenumber="370" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
370
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC370" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">int32</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">4294967295</span><span class="p">:</span> <span class="c1" style="color: #999988; font-style: italic;"># Special case in some structures (note, this is just a workaround)</span></span>
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<td class="old_line diff-line-num" data-linenumber="359" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
359
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<td class="new_line diff-line-num" data-linenumber="371" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
371
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC371" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1</span></span>
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360
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372
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC372" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nf" style="color: #990000; font-weight: 600;">range</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1000</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="361" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
361
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<td class="new_line diff-line-num old" data-linenumber="373" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC361" class="line" lang="python"> <span class="n" style="color: #333333;">dct</span><span class="p">[</span><span class="n" style="color: #333333;">np</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">uint32</span><span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">(</span></span><span class="n" style="color: #333333;"><span class="idiff right deletion" style="background-color: #fac5cd;">i</span></span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">i</span></span>
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<td class="old_line diff-line-num new" data-linenumber="362" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="373" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
373
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC373" class="line" lang="python"> <span class="n" style="color: #333333;">dct</span><span class="p">[</span><span class="nf" style="color: #990000; font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">int</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">np</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="nf" style="color: #990000; font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">array</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">i</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">).</span></span><span class="nf" style="color: #990000; font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">astype</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333333;">np</span><span class="p">.</span><span class="n" style="color: #333333;">uint32</span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">)</span>)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">i</span></span>
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<td class="old_line diff-line-num" data-linenumber="362" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
362
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<td class="new_line diff-line-num" data-linenumber="374" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
374
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC374" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">int32</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">dct</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="363" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
363
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<td class="new_line diff-line-num" data-linenumber="375" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
375
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC375" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">dct</span><span class="p">[</span><span class="n" style="color: #333333;">int32</span><span class="p">]</span></span>
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<td class="old_line diff-line-num" data-linenumber="364" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
364
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<td class="new_line diff-line-num" data-linenumber="376" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
376
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC376" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/plip/-/compare/9408f2de4e28772642baaea5c38da321a843cb5e...987142df85e4487ee8693e3417f93cd5d85a962c#7a4c9b79c2f1bb441895d677413efbc1cb536c35"><strong style="font-weight: 600;">plip/plipcmd.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
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<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -10,6 +10,7 @@ import logging</td>
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10
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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
10
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">multiprocessing</span></span>
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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
11
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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
11
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">os</span></span>
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12
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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
12
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">sys</span></span>
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<td class="old_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
13
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">ast</span></span>
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<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
13
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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333333;">argparse</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">ArgumentParser</span></span>
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14
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<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333333;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">namedtuple</span></span>
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15
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<td class="new_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
16
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC16" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="38" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="39" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -38,9 +39,19 @@ def threshold_limiter(aparser, arg):</td>
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<td class="new_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
39
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC39" class="line" lang="python"> <span class="n" style="color: #333333;">aparser</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">error</span><span class="p">(</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">All thresholds have to be values larger than zero.</span><span class="sh" style="color: #dd1144;">"</span><span class="p">)</span></span>
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39
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<td class="new_line diff-line-num" data-linenumber="40" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
40
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">arg</span></span>
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41
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC41" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
42
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC42" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #990000; font-weight: 600;">residue_list</span><span class="p">(</span><span class="n" style="color: #333333;">input_string</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
43
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC43" class="line" lang="python"> <span class="sh" style="color: #dd1144;">"""</span><span class="s" style="color: #dd1144;">Parse mix of residue numbers and ranges passed with the --residues flag into one list</span><span class="sh" style="color: #dd1144;">"""</span></span>
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<td class="new_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
44
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="45" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
45
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">part</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">input_string</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">split</span><span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">,</span><span class="sh" style="color: #dd1144;">'</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
46
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">-</span><span class="sh" style="color: #dd1144;">'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">part</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
47
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333333;">start</span><span class="p">,</span> <span class="n" style="color: #333333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333333;">part</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">split</span><span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">-</span><span class="sh" style="color: #dd1144;">'</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
48
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333333;">result</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">extend</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">range</span><span class="p">(</span><span class="n" style="color: #333333;">start</span><span class="p">,</span> <span class="n" style="color: #333333;">end</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #009999;">1</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
49
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
50
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333333;">result</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333333;">part</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="51" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
51
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">result</span></span>
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41
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<td class="new_line diff-line-num" data-linenumber="52" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
52
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC52" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="42" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
42
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<td class="new_line diff-line-num" data-linenumber="53" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
53
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC53" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #990000; font-weight: 600;">process_pdb</span><span class="p">(</span><span class="n" style="color: #333333;">pdbfile</span><span class="p">,</span> <span class="n" style="color: #333333;">outpath</span><span class="p">,</span> <span class="n" style="color: #333333;">as_string</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999999;">False</span><span class="p">,</span> <span class="n" style="color: #333333;">outputprefix</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">report</span><span class="sh" style="color: #dd1144;">'</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="43" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
43
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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC43" class="line" lang="python"> <span class="sh" style="color: #dd1144;">"""</span><span class="s" style="color: #dd1144;">Analysis of a single PDB file<span class="idiff left right deletion" style="background-color: #fac5cd;">. Can generate textual reports XML, PyMOL session files and images as output</span>.</span><span class="sh" style="color: #dd1144;">"""</span></span>
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<td class="old_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
54
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC54" class="line" lang="python"> <span class="sh" style="color: #dd1144;">"""</span><span class="s" style="color: #dd1144;">Analysis of a single PDB file<span class="idiff left right addition" style="background-color: #c7f0d2;"> with optional chain filtering</span>.</span><span class="sh" style="color: #dd1144;">"""</span></span>
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<td class="old_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
44
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<td class="new_line diff-line-num" data-linenumber="55" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
55
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333333;">as_string</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="56" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
56
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC56" class="line" lang="python"> <span class="n" style="color: #333333;">pdb_file_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">pdbfile</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">split</span><span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">/</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #009999;">1</span><span class="p">]</span></span>
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57
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC57" class="line" lang="python"> <span class="n" style="color: #333333;">startmessage</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">f</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">starting analysis of </span><span class="si" style="color: #dd1144;">{</span><span class="n" style="color: #333333;">pdb_file_name</span><span class="si" style="color: #dd1144;">}</span><span class="sh" style="color: #dd1144;">'</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="50" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="61" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -50,7 +61,6 @@ def process_pdb(pdbfile, outpath, as_string=False, outputprefix='report'):</td>
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<td class="old_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
50
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<td class="new_line diff-line-num" data-linenumber="61" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
61
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC61" class="line" lang="python"> <span class="n" style="color: #333333;">mol</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #445588; font-weight: 600;">PDBComplex</span><span class="p">()</span></span>
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<td class="old_line diff-line-num" data-linenumber="51" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
51
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<td class="new_line diff-line-num" data-linenumber="62" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
62
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC62" class="line" lang="python"> <span class="n" style="color: #333333;">mol</span><span class="p">.</span><span class="n" style="color: #333333;">output_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">outpath</span></span>
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<td class="old_line diff-line-num" data-linenumber="52" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
52
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<td class="new_line diff-line-num" data-linenumber="63" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
63
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC63" class="line" lang="python"> <span class="n" style="color: #333333;">mol</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">load_pdb</span><span class="p">(</span><span class="n" style="color: #333333;">pdbfile</span><span class="p">,</span> <span class="n" style="color: #333333;">as_string</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">as_string</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="53" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
53
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<td class="new_line diff-line-num old" data-linenumber="64" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC53" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># @todo Offers possibility for filter function from command line (by ligand chain, position, hetid)</span></span>
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<td class="old_line diff-line-num" data-linenumber="54" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
54
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<td class="new_line diff-line-num" data-linenumber="64" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
64
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">ligand</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">mol</span><span class="p">.</span><span class="n" style="color: #333333;">ligands</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="55" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
55
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<td class="new_line diff-line-num" data-linenumber="65" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
65
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC65" class="line" lang="python"> <span class="n" style="color: #333333;">mol</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">characterize_complex</span><span class="p">(</span><span class="n" style="color: #333333;">ligand</span><span class="p">)</span></span>
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56
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<td class="new_line diff-line-num" data-linenumber="66" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
66
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC66" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="116" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="126" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -116,7 +126,7 @@ def remove_duplicates(slist):</td>
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<td class="old_line diff-line-num" data-linenumber="116" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
116
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<td class="new_line diff-line-num" data-linenumber="126" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
126
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC126" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">unique</span></span>
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<td class="new_line diff-line-num" data-linenumber="127" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
127
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC127" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="118" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
118
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<td class="new_line diff-line-num" data-linenumber="128" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
128
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC128" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="119" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
119
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<td class="new_line diff-line-num old" data-linenumber="129" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC119" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #990000; font-weight: 600;">run_analysis</span><span class="p">(</span><span class="n" style="color: #333333;">inputstructs</span><span class="p">,</span> <span class="n" style="color: #333333;">inputpdbids</span><span class="p">):</span></span>
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<td class="old_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="129" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
129
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC129" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #990000; font-weight: 600;">run_analysis</span><span class="p">(</span><span class="n" style="color: #333333;">inputstructs</span><span class="p">,</span> <span class="n" style="color: #333333;">inputpdbids</span><span class="p"><span class="idiff left addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">chains</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="bp" style="color: #999999;"><span class="idiff right addition" style="background-color: #c7f0d2;">None</span></span><span class="p">):</span></span>
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<td class="old_line diff-line-num" data-linenumber="120" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
120
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<td class="new_line diff-line-num" data-linenumber="130" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
130
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC130" class="line" lang="python"> <span class="sh" style="color: #dd1144;">"""</span><span class="s" style="color: #dd1144;">Main function. Calls functions for processing, report generation and visualization.</span><span class="sh" style="color: #dd1144;">"""</span></span>
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<td class="old_line diff-line-num" data-linenumber="121" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
121
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<td class="new_line diff-line-num" data-linenumber="131" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
131
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC131" class="line" lang="python"> <span class="n" style="color: #333333;">pdbid</span><span class="p">,</span> <span class="n" style="color: #333333;">pdbpath</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999999;">None</span><span class="p">,</span> <span class="bp" style="color: #999999;">None</span></span>
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<td class="old_line diff-line-num" data-linenumber="122" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
122
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<td class="new_line diff-line-num" data-linenumber="132" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
132
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC132" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># @todo For multiprocessing, implement better stacktracing for errors</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="127" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="137" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -127,16 +137,16 @@ def run_analysis(inputstructs, inputpdbids):</td>
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127
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<td class="new_line diff-line-num" data-linenumber="137" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
137
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC137" class="line" lang="python"> <span class="n" style="color: #333333;">output_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">OUTPUTFILENAME</span></span>
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<td class="old_line diff-line-num" data-linenumber="128" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
128
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<td class="new_line diff-line-num" data-linenumber="138" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
138
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC138" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="129" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
129
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<td class="new_line diff-line-num" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
139
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">inputstructs</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999999;">None</span><span class="p">:</span> <span class="c1" style="color: #999988; font-style: italic;"># Process PDB file(s)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="130" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
130
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<td class="new_line diff-line-num old" data-linenumber="140" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC130" class="line" lang="python"> <span class="n" style="color: #333333;">num_structures</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333333;">inputstructs</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="131" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="140" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
140
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC140" class="line" lang="python"> <span class="n" style="color: #333333;">num_structures</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333333;">inputstructs</span><span class="p">)</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="c1" style="color: #999988; font-style: italic;"><span class="idiff right addition" style="background-color: #c7f0d2;"># @question: how can it become more than one file? The tilde_expansion function does not consider this case.</span></span></span>
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<td class="old_line diff-line-num" data-linenumber="131" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
131
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<td class="new_line diff-line-num" data-linenumber="141" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
141
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC141" class="line" lang="python"> <span class="n" style="color: #333333;">inputstructs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">remove_duplicates</span><span class="p">(</span><span class="n" style="color: #333333;">inputstructs</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="132" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
132
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<td class="new_line diff-line-num" data-linenumber="142" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
142
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC142" class="line" lang="python"> <span class="n" style="color: #333333;">read_from_stdin</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999999;">False</span></span>
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<td class="old_line diff-line-num" data-linenumber="133" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
133
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<td class="new_line diff-line-num" data-linenumber="143" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
143
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">inputstruct</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">inputstructs</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="134" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
134
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<td class="new_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">inputstruct</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">-</span><span class="sh" style="color: #dd1144;">'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="135" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
144
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">inputstruct</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">-</span><span class="sh" style="color: #dd1144;">'</span><span class="p">:</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="c1" style="color: #999988; font-style: italic;"><span class="idiff right addition" style="background-color: #c7f0d2;"># @expl: when user gives '-' as input, pdb file is read from stdin</span></span></span>
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<td class="old_line diff-line-num" data-linenumber="135" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
135
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<td class="new_line diff-line-num" data-linenumber="145" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
145
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC145" class="line" lang="python"> <span class="n" style="color: #333333;">inputstruct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">sys</span><span class="p">.</span><span class="n" style="color: #333333;">stdin</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">read</span><span class="p">()</span></span>
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<td class="old_line diff-line-num" data-linenumber="136" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
136
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<td class="new_line diff-line-num" data-linenumber="146" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
146
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC146" class="line" lang="python"> <span class="n" style="color: #333333;">read_from_stdin</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999999;">True</span></span>
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<td class="old_line diff-line-num" data-linenumber="137" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
137
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<td class="new_line diff-line-num" data-linenumber="147" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
147
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">RAWSTRING</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="138" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
138
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<td class="new_line diff-line-num" data-linenumber="148" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
148
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">sys</span><span class="p">.</span><span class="n" style="color: #333333;">version_info</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="mi" style="color: #009999;">3</span><span class="p">,):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="139" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
139
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<td class="new_line diff-line-num old" data-linenumber="149" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333333;">inputstruct</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">bytes</span><span class="p">(</span><span class="n" style="color: #333333;">inputstruct</span><span class="p">).</span><span class="nf" style="color: #990000; font-weight: 600;">decode</span><span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">unicode_escape</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="140" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
149
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333333;">inputstruct</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">bytes</span><span class="p">(</span><span class="n" style="color: #333333;">inputstruct</span><span class="p">).</span><span class="nf" style="color: #990000; font-weight: 600;">decode</span><span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">unicode_escape</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="c1" style="color: #999988; font-style: italic;"><span class="idiff right addition" style="background-color: #c7f0d2;"># @expl: in Python2, the bytes object is just a string.</span></span></span>
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140
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<td class="new_line diff-line-num" data-linenumber="150" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
150
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="141" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
141
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<td class="new_line diff-line-num" data-linenumber="151" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
151
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC151" class="line" lang="python"> <span class="n" style="color: #333333;">inputstruct</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">bytes</span><span class="p">(</span><span class="n" style="color: #333333;">inputstruct</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">utf8</span><span class="sh" style="color: #dd1144;">'</span><span class="p">).</span><span class="nf" style="color: #990000; font-weight: 600;">decode</span><span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">unicode_escape</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="142" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
142
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<td class="new_line diff-line-num" data-linenumber="152" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
152
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC152" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="218" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="228" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -218,6 +228,9 @@ def main():</td>
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<td class="old_line diff-line-num" data-linenumber="218" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
218
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<td class="new_line diff-line-num" data-linenumber="228" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
228
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC228" class="line" lang="python"> <span class="n" style="color: #333333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">Allows to define one or multiple chains as peptide ligands or to detect inter-chain contacts</span><span class="sh" style="color: #dd1144;">"</span><span class="p">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="219" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
219
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<td class="new_line diff-line-num" data-linenumber="229" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
229
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC229" class="line" lang="python"> <span class="n" style="color: #333333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">+</span><span class="sh" style="color: #dd1144;">"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="220" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
220
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<td class="new_line diff-line-num" data-linenumber="230" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
230
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC230" class="line" lang="python"> <span class="n" style="color: #333333;">ligandtype</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">add_argument</span><span class="p">(</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">--intra</span><span class="sh" style="color: #dd1144;">"</span><span class="p">,</span> <span class="n" style="color: #333333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">intra</span><span class="sh" style="color: #dd1144;">"</span><span class="p">,</span> <span class="n" style="color: #333333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">Allows to define one chain to analyze intra-chain contacts.</span><span class="sh" style="color: #dd1144;">"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="221" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="231" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
231
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC231" class="line" lang="python"> <span class="n" style="color: #333333;">parser</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">add_argument</span><span class="p">(</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">--residues</span><span class="sh" style="color: #dd1144;">"</span><span class="p">,</span> <span class="n" style="color: #333333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">residues</span><span class="sh" style="color: #dd1144;">"</span><span class="p">,</span> <span class="n" style="color: #333333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span> <span class="n" style="color: #333333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">+</span><span class="sh" style="color: #dd1144;">"</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="221" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="232" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
232
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC232" class="line" lang="python"> <span class="n" style="color: #333333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">"""</span><span class="s" style="color: #dd1144;">Allows to specify which residues of the chain(s) should be considered as peptide ligands.</span></span>
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<td class="old_line diff-line-num new" data-linenumber="221" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="233" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
233
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC233" class="line" lang="python"><span class="s" style="color: #dd1144;"> Give single residues (separated with comma) or ranges (with dash) or both, for several chains separate selections with one space</span><span class="sh" style="color: #dd1144;">"""</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="221" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
221
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<td class="new_line diff-line-num" data-linenumber="234" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
234
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC234" class="line" lang="python"> <span class="n" style="color: #333333;">parser</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">add_argument</span><span class="p">(</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">--keepmod</span><span class="sh" style="color: #dd1144;">"</span><span class="p">,</span> <span class="n" style="color: #333333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">keepmod</span><span class="sh" style="color: #dd1144;">"</span><span class="p">,</span> <span class="n" style="color: #333333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999999;">False</span><span class="p">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="222" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
222
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<td class="new_line diff-line-num" data-linenumber="235" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
235
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC235" class="line" lang="python"> <span class="n" style="color: #333333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">Keep modified residues as ligands</span><span class="sh" style="color: #dd1144;">"</span><span class="p">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="223" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
223
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<td class="new_line diff-line-num" data-linenumber="236" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
236
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC236" class="line" lang="python"> <span class="n" style="color: #333333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">store_true</span><span class="sh" style="color: #dd1144;">"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="241" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="254" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -241,7 +254,19 @@ def main():</td>
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<td class="old_line diff-line-num" data-linenumber="241" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
241
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<td class="new_line diff-line-num" data-linenumber="254" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
254
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC254" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">thresholds</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="242" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
242
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<td class="new_line diff-line-num" data-linenumber="255" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
255
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC255" class="line" lang="python"> <span class="n" style="color: #333333;">parser</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">add_argument</span><span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">--%s</span><span class="sh" style="color: #dd1144;">'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333333;">t</span><span class="p">.</span><span class="n" style="color: #333333;">name</span><span class="p">,</span> <span class="n" style="color: #333333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">t</span><span class="p">.</span><span class="n" style="color: #333333;">name</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333333;">val</span><span class="p">:</span> <span class="nf" style="color: #990000; font-weight: 600;">threshold_limiter</span><span class="p">(</span><span class="n" style="color: #333333;">parser</span><span class="p">,</span> <span class="n" style="color: #333333;">val</span><span class="p">),</span></span>
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<td class="old_line diff-line-num" data-linenumber="243" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
243
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<td class="new_line diff-line-num" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
256
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC256" class="line" lang="python"> <span class="n" style="color: #333333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">argparse</span><span class="p">.</span><span class="n" style="color: #333333;">SUPPRESS</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="257" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
257
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC257" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="258" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
258
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC258" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Add argument to define receptor and ligand chains</span></span>
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<td class="old_line diff-line-num new" data-linenumber="244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="259" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
259
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC259" class="line" lang="python"> <span class="n" style="color: #333333;">parser</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">add_argument</span><span class="p">(</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">--chains</span><span class="sh" style="color: #dd1144;">"</span><span class="p">,</span> <span class="n" style="color: #333333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">chains</span><span class="sh" style="color: #dd1144;">"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="260" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
260
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC260" class="line" lang="python"> <span class="n" style="color: #333333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">Specify chains as receptor/ligand groups, e.g., </span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">[[</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">A</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">], [</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">B</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">]]</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">. </span><span class="sh" style="color: #dd1144;">"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="261" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
261
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC261" class="line" lang="python"> <span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">Use format [[</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">A</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">], [</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">B</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">, </span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">C</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">]] to define A as receptor, and B, C as ligands.</span><span class="sh" style="color: #dd1144;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
262
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC262" class="line" lang="python"></span>
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<td class="old_line diff-line-num new" data-linenumber="244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="263" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
263
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC263" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
244
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<td class="new_line diff-line-num" data-linenumber="264" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
264
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC264" class="line" lang="python"> <span class="n" style="color: #333333;">arguments</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">parser</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">parse_args</span><span class="p">()</span></span>
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<td class="old_line diff-line-num new" data-linenumber="245" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="265" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
265
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC265" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># make sure, residues is only used together with --inter (could be expanded to --intra in the future)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="245" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="266" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
266
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC266" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">arguments</span><span class="p">.</span><span class="n" style="color: #333333;">residues</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="n" style="color: #333333;">arguments</span><span class="p">.</span><span class="n" style="color: #333333;">peptides</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333333;">arguments</span><span class="p">.</span><span class="n" style="color: #333333;">intra</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="267" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
267
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC267" class="line" lang="python"> <span class="n" style="color: #333333;">parser</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">error</span><span class="p">(</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">The --residues option requires specification of a chain with --inter or --peptide</span><span class="sh" style="color: #dd1144;">"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="245" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="268" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
268
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC268" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">arguments</span><span class="p">.</span><span class="n" style="color: #333333;">residues</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nf" style="color: #990000; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333333;">arguments</span><span class="p">.</span><span class="n" style="color: #333333;">residues</span><span class="p">)</span><span class="o" style="font-weight: 600;">!=</span><span class="nf" style="color: #990000; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333333;">arguments</span><span class="p">.</span><span class="n" style="color: #333333;">peptides</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="269" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
269
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC269" class="line" lang="python"> <span class="n" style="color: #333333;">parser</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">error</span><span class="p">(</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">Please provide residue numbers or ranges for each chain specified. Separate selections with a single space.</span><span class="sh" style="color: #dd1144;">"</span><span class="p">)</span></span>
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245
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<td class="new_line diff-line-num" data-linenumber="270" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
270
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC270" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># configure log levels</span></span>
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<td class="old_line diff-line-num" data-linenumber="246" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
246
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<td class="new_line diff-line-num" data-linenumber="271" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
271
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC271" class="line" lang="python"> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">VERBOSE</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999999;">True</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">arguments</span><span class="p">.</span><span class="n" style="color: #333333;">verbose</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999999;">False</span></span>
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247
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<td class="new_line diff-line-num" data-linenumber="272" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
272
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC272" class="line" lang="python"> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">QUIET</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999999;">True</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">arguments</span><span class="p">.</span><span class="n" style="color: #333333;">quiet</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999999;">False</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="268" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="293" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -268,15 +293,32 @@ def main():</td>
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<td class="old_line diff-line-num" data-linenumber="268" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
268
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<td class="new_line diff-line-num" data-linenumber="293" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
293
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC293" class="line" lang="python"> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">BREAKCOMPOSITE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">arguments</span><span class="p">.</span><span class="n" style="color: #333333;">breakcomposite</span></span>
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<td class="old_line diff-line-num" data-linenumber="269" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
269
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<td class="new_line diff-line-num" data-linenumber="294" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
294
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC294" class="line" lang="python"> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">ALTLOC</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">arguments</span><span class="p">.</span><span class="n" style="color: #333333;">altlocation</span></span>
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<td class="old_line diff-line-num" data-linenumber="270" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
270
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<td class="new_line diff-line-num" data-linenumber="295" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
295
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC295" class="line" lang="python"> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">PEPTIDES</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">arguments</span><span class="p">.</span><span class="n" style="color: #333333;">peptides</span></span>
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<td class="old_line diff-line-num new" data-linenumber="271" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="296" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
296
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC296" class="line" lang="python"> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">RESIDUES</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">dict</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">zip</span><span class="p">(</span><span class="n" style="color: #333333;">arguments</span><span class="p">.</span><span class="n" style="color: #333333;">peptides</span><span class="p">,</span> <span class="nf" style="color: #990000; font-weight: 600;">map</span><span class="p">(</span><span class="n" style="color: #333333;">residue_list</span><span class="p">,</span> <span class="n" style="color: #333333;">arguments</span><span class="p">.</span><span class="n" style="color: #333333;">residues</span><span class="p">)))</span></span>
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<td class="old_line diff-line-num" data-linenumber="271" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
271
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<td class="new_line diff-line-num" data-linenumber="297" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
297
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC297" class="line" lang="python"> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">INTRA</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">arguments</span><span class="p">.</span><span class="n" style="color: #333333;">intra</span></span>
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<td class="old_line diff-line-num" data-linenumber="272" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
272
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<td class="new_line diff-line-num" data-linenumber="298" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
298
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC298" class="line" lang="python"> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">NOFIX</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">arguments</span><span class="p">.</span><span class="n" style="color: #333333;">nofix</span></span>
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<td class="old_line diff-line-num" data-linenumber="273" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
273
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<td class="new_line diff-line-num" data-linenumber="299" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
299
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC299" class="line" lang="python"> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">NOFIXFILE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">arguments</span><span class="p">.</span><span class="n" style="color: #333333;">nofixfile</span></span>
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<td class="old_line diff-line-num old" data-linenumber="274" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
274
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<td class="new_line diff-line-num old" data-linenumber="300" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC274" class="line" lang="python"> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">NOPDBCANMAP</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">arguments</span><span class="p">.</span><span class="n" style="color: #333333;">nopdbcanmap</span></span>
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<td class="old_line diff-line-num new" data-linenumber="275" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="300" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
300
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC300" class="line" lang="python"> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">NOPDBCANMAP</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">bool</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333333;">arguments</span><span class="p">.</span><span class="n" style="color: #333333;">nopdbcanmap</span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="ow" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">or</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">config</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">INTRA</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="ow" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">or</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">config</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">PEPTIDES</span></span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">)</span></span></span>
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<td class="old_line diff-line-num" data-linenumber="275" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
275
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<td class="new_line diff-line-num" data-linenumber="301" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
301
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC301" class="line" lang="python"> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">KEEPMOD</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">arguments</span><span class="p">.</span><span class="n" style="color: #333333;">keepmod</span></span>
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<td class="old_line diff-line-num" data-linenumber="276" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
276
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<td class="new_line diff-line-num" data-linenumber="302" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
302
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC302" class="line" lang="python"> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">DNARECEPTOR</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">arguments</span><span class="p">.</span><span class="n" style="color: #333333;">dnareceptor</span></span>
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<td class="old_line diff-line-num" data-linenumber="277" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
277
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<td class="new_line diff-line-num" data-linenumber="303" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
303
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC303" class="line" lang="python"> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">OUTPUTFILENAME</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">arguments</span><span class="p">.</span><span class="n" style="color: #333333;">outputfilename</span></span>
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<td class="old_line diff-line-num" data-linenumber="278" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
278
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<td class="new_line diff-line-num" data-linenumber="304" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
304
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC304" class="line" lang="python"> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">NOHYDRO</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">arguments</span><span class="p">.</span><span class="n" style="color: #333333;">nohydro</span></span>
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<td class="old_line diff-line-num" data-linenumber="279" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
279
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<td class="new_line diff-line-num" data-linenumber="305" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
305
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC305" class="line" lang="python"> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">MODEL</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">arguments</span><span class="p">.</span><span class="n" style="color: #333333;">model</span></span>
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<td class="new_line diff-line-num new" data-linenumber="306" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
306
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC306" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="307" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
307
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC307" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="280" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="308" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
308
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC308" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># add inner quotes for python backend</span></span>
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<td class="new_line diff-line-num new" data-linenumber="309" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
309
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC309" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333333;">arguments</span><span class="p">.</span><span class="n" style="color: #333333;">chains</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="280" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="310" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
310
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC310" class="line" lang="python"> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">CHAINS</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999999;">None</span></span>
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<td class="new_line diff-line-num new" data-linenumber="311" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
311
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC311" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="312" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
312
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC312" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">re</span></span>
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<td class="new_line diff-line-num new" data-linenumber="313" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
313
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC313" class="line" lang="python"> <span class="n" style="color: #333333;">quoted_input</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">re</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">sub</span><span class="p">(</span><span class="sa">r</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">(?<![</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">\'])\b([a-zA-Z0-9_]+)\b(?![</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">\'])</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span> <span class="sa">r</span><span class="sh" style="color: #dd1144;">'"</span><span class="s" style="color: #dd1144;">\1</span><span class="sh" style="color: #dd1144;">"'</span><span class="p">,</span> <span class="n" style="color: #333333;">arguments</span><span class="p">.</span><span class="n" style="color: #333333;">chains</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="314" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
314
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC314" class="line" lang="python"> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">CHAINS</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">ast</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">literal_eval</span><span class="p">(</span><span class="n" style="color: #333333;">quoted_input</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="315" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
315
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC315" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">CHAINS</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="316" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
316
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC316" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">CHAINS</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nf" style="color: #990000; font-weight: 600;">all</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">isinstance</span><span class="p">(</span><span class="n" style="color: #333333;">c</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">CHAINS</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="317" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
317
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC317" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nc" style="color: #445588; font-weight: 600;">ValueError</span><span class="p">(</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">Chains should be specified as a list of lists, e.g., </span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">[[A], [B, C]]</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">.</span><span class="sh" style="color: #dd1144;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="318" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
318
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC318" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">except </span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">SyntaxError</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="319" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
319
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC319" class="line" lang="python"> <span class="n" style="color: #333333;">parser</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">error</span><span class="p">(</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">The --chains option must be in the format </span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">[[A], [B, C]]</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">.</span><span class="sh" style="color: #dd1144;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="320" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
320
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC320" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="321" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
321
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC321" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="280" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
280
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<td class="new_line diff-line-num" data-linenumber="322" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
322
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC322" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Make sure we have pymol with --pics and --pymol</span></span>
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<td class="old_line diff-line-num" data-linenumber="281" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
281
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<td class="new_line diff-line-num" data-linenumber="323" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
323
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC323" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">PICS</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">PYMOL</span><span class="p">:</span></span>
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282
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<td class="new_line diff-line-num" data-linenumber="324" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
324
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC324" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/plip/-/compare/9408f2de4e28772642baaea5c38da321a843cb5e...987142df85e4487ee8693e3417f93cd5d85a962c#27a6dfa55905f1bad1286d8de59653dccfc480fb"><strong style="font-weight: 600;">plip/structure/detection.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="291" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="291" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -291,7 +291,7 @@ def water_bridges(bs_hba, lig_hba, bs_hbd, lig_hbd, water):</td>
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<td class="old_line diff-line-num" data-linenumber="291" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
291
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<td class="new_line diff-line-num" data-linenumber="291" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
291
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC291" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333333;">wl</span><span class="p">.</span><span class="n" style="color: #333333;">oxy</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333333;">wd</span><span class="p">.</span><span class="n" style="color: #333333;">oxy</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="292" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
292
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<td class="new_line diff-line-num" data-linenumber="292" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
292
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC292" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="old_line diff-line-num" data-linenumber="293" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
293
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<td class="new_line diff-line-num" data-linenumber="293" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
293
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC293" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Same water molecule and angle within omega</span></span>
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<td class="old_line diff-line-num old" data-linenumber="294" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
294
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<td class="new_line diff-line-num old" data-linenumber="294" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC294" class="line" lang="python"> <span class="n" style="color: #333333;">w_angle</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">vecangle</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">vector</span><span class="p">(</span><span class="n" style="color: #333333;"><span class="idiff left deletion" style="background-color: #fac5cd;">acc</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">a</span></span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">,</span> <span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">wl</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="n" style="color: #333333;"><span class="idiff right deletion" style="background-color: #fac5cd;">oxy</span></span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">),</span> <span class="nf" style="color: #990000; font-weight: 600;">vector</span><span class="p">(</span><span class="n" style="color: #333333;">wl</span><span class="p">.</span><span class="n" style="color: #333333;">oxy</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">,</span> <span class="n" style="color: #333333;">don</span><span class="p">.</span><span class="n" style="color: #333333;">h</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="295" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="294" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
294
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC294" class="line" lang="python"> <span class="n" style="color: #333333;">w_angle</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">vecangle</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">vector</span><span class="p">(</span><span class="n" style="color: #333333;"><span class="idiff left addition" style="background-color: #c7f0d2;">wl</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">oxy</span></span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">,</span> <span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">acc</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">a</span></span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">),</span> <span class="nf" style="color: #990000; font-weight: 600;">vector</span><span class="p">(</span><span class="n" style="color: #333333;">wl</span><span class="p">.</span><span class="n" style="color: #333333;">oxy</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">,</span> <span class="n" style="color: #333333;">don</span><span class="p">.</span><span class="n" style="color: #333333;">h</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">))</span></span>
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<td class="old_line diff-line-num" data-linenumber="295" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
295
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<td class="new_line diff-line-num" data-linenumber="295" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
295
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC295" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">WATER_BRIDGE_OMEGA_MIN</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">w_angle</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">WATER_BRIDGE_OMEGA_MAX</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="296" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
296
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<td class="new_line diff-line-num" data-linenumber="296" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
296
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC296" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="old_line diff-line-num" data-linenumber="297" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
297
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<td class="new_line diff-line-num" data-linenumber="297" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
297
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC297" class="line" lang="python"> <span class="n" style="color: #333333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333333;">reschain</span><span class="p">,</span> <span class="n" style="color: #333333;">restype</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333333;">don</span><span class="p">.</span><span class="n" style="color: #333333;">d</span><span class="p">),</span> <span class="nf" style="color: #990000; font-weight: 600;">whichchain</span><span class="p">(</span><span class="n" style="color: #333333;">don</span><span class="p">.</span><span class="n" style="color: #333333;">d</span><span class="p">),</span> <span class="nf" style="color: #990000; font-weight: 600;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333333;">don</span><span class="p">.</span><span class="n" style="color: #333333;">d</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="309" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="309" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -309,7 +309,7 @@ def water_bridges(bs_hba, lig_hba, bs_hbd, lig_hbd, water):</td>
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<td class="old_line diff-line-num" data-linenumber="309" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
309
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<td class="new_line diff-line-num" data-linenumber="309" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
309
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC309" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333333;">wl</span><span class="p">.</span><span class="n" style="color: #333333;">oxy</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333333;">wd</span><span class="p">.</span><span class="n" style="color: #333333;">oxy</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="310" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
310
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<td class="new_line diff-line-num" data-linenumber="310" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
310
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC310" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="old_line diff-line-num" data-linenumber="311" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
311
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<td class="new_line diff-line-num" data-linenumber="311" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
311
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC311" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Same water molecule and angle within omega</span></span>
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<td class="old_line diff-line-num old" data-linenumber="312" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
312
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<td class="new_line diff-line-num old" data-linenumber="312" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC312" class="line" lang="python"> <span class="n" style="color: #333333;">w_angle</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">vecangle</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">vector</span><span class="p">(</span><span class="n" style="color: #333333;"><span class="idiff left deletion" style="background-color: #fac5cd;">acc</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">a</span></span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">,</span> <span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">wl</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="n" style="color: #333333;"><span class="idiff right deletion" style="background-color: #fac5cd;">oxy</span></span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">),</span> <span class="nf" style="color: #990000; font-weight: 600;">vector</span><span class="p">(</span><span class="n" style="color: #333333;">wl</span><span class="p">.</span><span class="n" style="color: #333333;">oxy</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">,</span> <span class="n" style="color: #333333;">don</span><span class="p">.</span><span class="n" style="color: #333333;">h</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="313" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="312" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
312
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC312" class="line" lang="python"> <span class="n" style="color: #333333;">w_angle</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">vecangle</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">vector</span><span class="p">(</span><span class="n" style="color: #333333;"><span class="idiff left addition" style="background-color: #c7f0d2;">wl</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">oxy</span></span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">,</span> <span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">acc</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">a</span></span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">),</span> <span class="nf" style="color: #990000; font-weight: 600;">vector</span><span class="p">(</span><span class="n" style="color: #333333;">wl</span><span class="p">.</span><span class="n" style="color: #333333;">oxy</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">,</span> <span class="n" style="color: #333333;">don</span><span class="p">.</span><span class="n" style="color: #333333;">h</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">))</span></span>
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<td class="old_line diff-line-num" data-linenumber="313" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
313
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<td class="new_line diff-line-num" data-linenumber="313" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
313
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC313" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">WATER_BRIDGE_OMEGA_MIN</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">w_angle</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">WATER_BRIDGE_OMEGA_MAX</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="314" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
314
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<td class="new_line diff-line-num" data-linenumber="314" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
314
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC314" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="old_line diff-line-num" data-linenumber="315" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
315
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<td class="new_line diff-line-num" data-linenumber="315" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
315
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC315" class="line" lang="python"> <span class="n" style="color: #333333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333333;">reschain</span><span class="p">,</span> <span class="n" style="color: #333333;">restype</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333333;">acc</span><span class="p">.</span><span class="n" style="color: #333333;">a</span><span class="p">),</span> <span class="nf" style="color: #990000; font-weight: 600;">whichchain</span><span class="p">(</span><span class="n" style="color: #333333;">acc</span><span class="p">.</span><span class="n" style="color: #333333;">a</span><span class="p">),</span> <span class="nf" style="color: #990000; font-weight: 600;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333333;">acc</span><span class="p">.</span><span class="n" style="color: #333333;">a</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/plip/-/compare/9408f2de4e28772642baaea5c38da321a843cb5e...987142df85e4487ee8693e3417f93cd5d85a962c#b72517a8cd7dbc6709d05fdad49ae468ebf79126"><strong style="font-weight: 600;">plip/structure/preparation.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -14,6 +14,7 @@ from plip.basic.supplemental import cluster_doubles, is_lig, normalize_vector, v</td>
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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14
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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
14
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333333;">plip.basic.supplemental</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">extract_pdbid</span><span class="p">,</span> <span class="n" style="color: #333333;">read_pdb</span><span class="p">,</span> <span class="n" style="color: #333333;">create_folder_if_not_exists</span><span class="p">,</span> <span class="n" style="color: #333333;">canonicalize</span></span>
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<td class="old_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15
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<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
15
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333333;">plip.basic.supplemental</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">read</span><span class="p">,</span> <span class="n" style="color: #333333;">nucleotide_linkage</span><span class="p">,</span> <span class="n" style="color: #333333;">sort_members_by_importance</span></span>
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<td class="old_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
16
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<td class="new_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
16
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333333;">plip.basic.supplemental</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">whichchain</span><span class="p">,</span> <span class="n" style="color: #333333;">whichrestype</span><span class="p">,</span> <span class="n" style="color: #333333;">whichresnumber</span><span class="p">,</span> <span class="n" style="color: #333333;">euclidean3d</span><span class="p">,</span> <span class="n" style="color: #333333;">int32_to_negative</span></span>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
17
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333333;">plip.basic.supplemental</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">residue_belongs_to_receptor</span></span>
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<td class="old_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
17
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<td class="new_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
18
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333333;">plip.structure.detection</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">halogen</span><span class="p">,</span> <span class="n" style="color: #333333;">pication</span><span class="p">,</span> <span class="n" style="color: #333333;">water_bridges</span><span class="p">,</span> <span class="n" style="color: #333333;">metal_complexation</span></span>
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<td class="old_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
18
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<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
19
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333333;">plip.structure.detection</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">hydrophobic_interactions</span><span class="p">,</span> <span class="n" style="color: #333333;">pistacking</span><span class="p">,</span> <span class="n" style="color: #333333;">hbonds</span><span class="p">,</span> <span class="n" style="color: #333333;">saltbridge</span></span>
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19
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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
20
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC20" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -243,7 +244,7 @@ class LigandFinder:</td>
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243
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<td class="new_line diff-line-num" data-linenumber="244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
244
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC244" class="line" lang="python"><span class="s" style="color: #dd1144;"> given chain without water</span></span>
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<td class="old_line diff-line-num" data-linenumber="244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
244
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<td class="new_line diff-line-num" data-linenumber="245" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
245
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC245" class="line" lang="python"><span class="s" style="color: #dd1144;"> </span><span class="sh" style="color: #dd1144;">"""</span></span>
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<td class="old_line diff-line-num" data-linenumber="245" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
245
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<td class="new_line diff-line-num" data-linenumber="246" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
246
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC246" class="line" lang="python"> <span class="n" style="color: #333333;">all_from_chain</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">o</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">o</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBResidueIter</span><span class="p">(</span></span>
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<td class="old_line diff-line-num old" data-linenumber="246" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
246
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<td class="new_line diff-line-num old" data-linenumber="247" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC246" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">proteincomplex</span><span class="p">.</span><span class="n" style="color: #333333;">OBMol</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">o</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetChain</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333333;">chain</span><span class="p">]</span> <span class="c1" style="color: #999988; font-style: italic;"># All residues from chain</span></span>
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<td class="new_line diff-line-num new" data-linenumber="247" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
247
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC247" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">proteincomplex</span><span class="p">.</span><span class="n" style="color: #333333;">OBMol</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">o</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetChain</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333333;">chain</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="ow" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">and</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="ow" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">not</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">self</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="nf" style="color: #990000; font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">is_het_residue</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">o</span></span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">)</span>]</span> <span class="c1" style="color: #999988; font-style: italic;"># All residues from chain</span></span>
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<td class="old_line diff-line-num" data-linenumber="247" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
247
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<td class="new_line diff-line-num" data-linenumber="248" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
248
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC248" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #990000; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333333;">all_from_chain</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">0</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="248" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
248
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<td class="new_line diff-line-num" data-linenumber="249" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
249
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC249" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999999;">None</span></span>
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249
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<td class="new_line diff-line-num" data-linenumber="250" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
250
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC250" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="257" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -256,7 +257,7 @@ class LigandFinder:</td>
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<td class="old_line diff-line-num" data-linenumber="256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
256
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<td class="new_line diff-line-num" data-linenumber="257" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
257
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC257" class="line" lang="python"><span class="s" style="color: #dd1144;"> Returns all non-empty ligands.</span></span>
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<td class="old_line diff-line-num" data-linenumber="257" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
257
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<td class="new_line diff-line-num" data-linenumber="258" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
258
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC258" class="line" lang="python"><span class="s" style="color: #dd1144;"> </span><span class="sh" style="color: #dd1144;">"""</span></span>
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258
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<td class="new_line diff-line-num" data-linenumber="259" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
259
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC259" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="259" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
259
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<td class="new_line diff-line-num old" data-linenumber="260" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC259" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">PEPTIDES</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">INTRA</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999999;">None</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="260" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="260" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
260
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC260" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">PEPTIDES</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">INTRA</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999999;"><span class="idiff left addition" style="background-color: #c7f0d2;">None</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="ow" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">and</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">config</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">CHAINS</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="ow" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">is</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="bp" style="color: #999999;">None</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="260" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="261" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
261
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC261" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Extract small molecule ligands (default)</span></span>
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262
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="285" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -284,8 +285,16 @@ class LigandFinder:</td>
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284
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<td class="new_line diff-line-num" data-linenumber="285" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
285
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC285" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="285" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
285
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<td class="new_line diff-line-num" data-linenumber="286" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
286
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC286" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Extract peptides from given chains</span></span>
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<td class="old_line diff-line-num" data-linenumber="286" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
286
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<td class="new_line diff-line-num" data-linenumber="287" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
287
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC287" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">water</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">o</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">o</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBResidueIter</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">proteincomplex</span><span class="p">.</span><span class="n" style="color: #333333;">OBMol</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">o</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetResidueProperty</span><span class="p">(</span><span class="mi" style="color: #009999;">9</span><span class="p">)]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="287" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
287
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<td class="new_line diff-line-num old" data-linenumber="288" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC287" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">PEPTIDES</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="288" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="288" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
288
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC288" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">PEPTIDES</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="ow" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">and</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="ow" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">not</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">config</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">CHAINS</span></span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="288" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
288
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<td class="new_line diff-line-num" data-linenumber="289" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
289
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC289" class="line" lang="python"> <span class="n" style="color: #333333;">peptide_ligands</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">getpeptides</span><span class="p">(</span><span class="n" style="color: #333333;">chain</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">chain</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">PEPTIDES</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="290" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
290
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC290" class="line" lang="python"></span>
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<td class="old_line diff-line-num new" data-linenumber="289" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="291" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
291
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC291" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;">#Todo: Validate change here... Do we want to combine multiple chains to a single ligand?</span></span>
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<td class="old_line diff-line-num new" data-linenumber="289" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="292" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
292
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC292" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># if yes can be easily added to the getpeptides function by flatten the resulting list - Philipp</span></span>
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<td class="old_line diff-line-num new" data-linenumber="289" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="293" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
293
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC293" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">CHAINS</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="289" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="294" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
294
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC294" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># chains is defined as list of list e.g. [['A'], ['B', 'C']] in which second list contains the</span></span>
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<td class="new_line diff-line-num new" data-linenumber="295" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
295
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC295" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># ligand chains and the first one should be the receptor</span></span>
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<td class="new_line diff-line-num new" data-linenumber="296" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
296
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC296" class="line" lang="python"> <span class="n" style="color: #333333;">peptide_ligands</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">getpeptides</span><span class="p">(</span><span class="n" style="color: #333333;">chain</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">chain</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">CHAINS</span><span class="p">[</span><span class="mi" style="color: #009999;">1</span><span class="p">]]</span></span>
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297
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC297" class="line" lang="python"></span>
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298
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC298" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">INTRA</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999999;">None</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="290" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
290
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<td class="new_line diff-line-num" data-linenumber="299" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
299
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC299" class="line" lang="python"> <span class="n" style="color: #333333;">peptide_ligands</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">getpeptides</span><span class="p">(</span><span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">INTRA</span><span class="p">),</span> <span class="p">]</span></span>
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<td class="old_line diff-line-num" data-linenumber="291" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
291
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<td class="new_line diff-line-num" data-linenumber="300" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
300
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC300" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="304" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="313" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -304,7 +313,7 @@ class LigandFinder:</td>
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<td class="old_line diff-line-num" data-linenumber="304" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
304
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<td class="new_line diff-line-num" data-linenumber="313" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
313
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC313" class="line" lang="python"> <span class="n" style="color: #333333;">names</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">x</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">members</span><span class="p">]</span></span>
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<td class="old_line diff-line-num" data-linenumber="305" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
305
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<td class="new_line diff-line-num" data-linenumber="314" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
314
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC314" class="line" lang="python"> <span class="n" style="color: #333333;">longname</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">-</span><span class="sh" style="color: #dd1144;">'</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">join</span><span class="p">([</span><span class="n" style="color: #333333;">x</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">members</span><span class="p">])</span></span>
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<td class="old_line diff-line-num" data-linenumber="306" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
306
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<td class="new_line diff-line-num" data-linenumber="315" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
315
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC315" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="307" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
307
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<td class="new_line diff-line-num old" data-linenumber="316" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC307" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">PEPTIDES</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="308" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="316" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
316
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC316" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">PEPTIDES</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="ow" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">or</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">config</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">CHAINS</span></span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="308" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
308
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<td class="new_line diff-line-num" data-linenumber="317" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
317
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC317" class="line" lang="python"> <span class="n" style="color: #333333;">ligtype</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">PEPTIDE</span><span class="sh" style="color: #dd1144;">'</span></span>
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<td class="old_line diff-line-num" data-linenumber="309" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
309
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<td class="new_line diff-line-num" data-linenumber="318" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
318
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC318" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">INTRA</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999999;">None</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="310" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
310
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<td class="new_line diff-line-num" data-linenumber="319" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
319
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC319" class="line" lang="python"> <span class="n" style="color: #333333;">ligtype</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">INTRA</span><span class="sh" style="color: #dd1144;">'</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="328" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="337" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -328,26 +337,20 @@ class LigandFinder:</td>
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<td class="old_line diff-line-num" data-linenumber="328" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
328
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<td class="new_line diff-line-num" data-linenumber="337" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
337
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC337" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="329" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
329
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<td class="new_line diff-line-num" data-linenumber="338" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
338
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC338" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># create a new ligand molecule representing any k-mer linked structures</span></span>
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<td class="old_line diff-line-num" data-linenumber="330" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
330
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<td class="new_line diff-line-num" data-linenumber="339" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
339
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC339" class="line" lang="python"> <span class="n" style="color: #333333;">lig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBMol</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="331" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
331
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<td class="new_line diff-line-num old" data-linenumber="340" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC331" class="line" lang="python"> <span class="n" style="color: #333333;">neighbours</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">dict</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="332" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
332
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<td class="new_line diff-line-num old" data-linenumber="340" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC332" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">obatom</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">hetatoms</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">values</span><span class="p">():</span> <span class="c1" style="color: #999988; font-style: italic;"># iterate over atom objects</span></span>
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333
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<td class="new_line diff-line-num old" data-linenumber="340" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC333" class="line" lang="python"> <span class="n" style="color: #333333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">obatom</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetIdx</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="334" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
334
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<td class="new_line diff-line-num old" data-linenumber="340" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC334" class="line" lang="python"> <span class="n" style="color: #333333;">lig</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">AddAtom</span><span class="p">(</span><span class="n" style="color: #333333;">obatom</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="335" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
335
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<td class="new_line diff-line-num old" data-linenumber="340" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC335" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># ids of all neighbours of obatom</span></span>
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336
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<td class="new_line diff-line-num old" data-linenumber="340" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC336" class="line" lang="python"> <span class="n" style="color: #333333;">neighbours</span><span class="p">[</span><span class="n" style="color: #333333;">idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">set</span><span class="p">([</span><span class="n" style="color: #333333;">neighbour_atom</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetIdx</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">neighbour_atom</span></span>
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<td class="old_line diff-line-num old" data-linenumber="337" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
337
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<td class="new_line diff-line-num old" data-linenumber="340" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC337" class="line" lang="python"> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBAtomAtomIter</span><span class="p">(</span><span class="n" style="color: #333333;">obatom</span><span class="p">)])</span> <span class="o" style="font-weight: 600;">&</span> <span class="nf" style="color: #990000; font-weight: 600;">set</span><span class="p">(</span><span class="n" style="color: #333333;">hetatoms</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">keys</span><span class="p">())</span></span>
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338
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<td class="new_line diff-line-num old" data-linenumber="340" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC338" class="line" lang="python"> <span class="n" style="color: #333333;">logger</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">debug</span><span class="p">(</span><span class="sa">f</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">atom neighbours mapped</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="340" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
340
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC340" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># create bit vector with 1 for all ligand atoms and 0 for all others</span></span>
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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="341" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
341
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC341" class="line" lang="python"> <span class="n" style="color: #333333;">atomsBitVec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBBitVec</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">proteincomplex</span><span class="p">.</span><span class="n" style="color: #333333;">OBMol</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">NumAtoms</span><span class="p">())</span></span>
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<td class="new_line diff-line-num new" data-linenumber="342" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
342
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC342" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">atomidx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">hetatoms</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">keys</span><span class="p">():</span></span>
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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="343" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
343
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC343" class="line" lang="python"> <span class="n" style="color: #333333;">atomsBitVec</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">SetBitOn</span><span class="p">(</span><span class="n" style="color: #333333;">atomidx</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="344" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
344
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC344" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># safe substructure defined by those atoms to previously empty lig</span></span>
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<td class="new_line diff-line-num new" data-linenumber="345" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
345
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC345" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">proteincomplex</span><span class="p">.</span><span class="n" style="color: #333333;">OBMol</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">CopySubstructure</span><span class="p">(</span><span class="n" style="color: #333333;">lig</span><span class="p">,</span> <span class="n" style="color: #333333;">atomsBitVec</span><span class="p">,</span> <span class="bp" style="color: #999999;">None</span><span class="p">,</span> <span class="mi" style="color: #009999;">0</span><span class="p">)</span></span>
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339
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<td class="new_line diff-line-num" data-linenumber="346" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
346
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC346" class="line" lang="python"></span>
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340
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<td class="new_line diff-line-num" data-linenumber="347" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
347
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC347" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;">##############################################################</span></span>
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<td class="old_line diff-line-num" data-linenumber="341" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
341
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<td class="new_line diff-line-num" data-linenumber="348" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
348
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC348" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># map the old atom idx of OBMol to the new idx of the ligand #</span></span>
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342
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<td class="new_line diff-line-num" data-linenumber="349" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
349
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC349" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;">##############################################################</span></span>
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343
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350
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC350" class="line" lang="python"></span>
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<td class="new_line diff-line-num old" data-linenumber="351" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC344" class="line" lang="python"> <span class="n" style="color: #333333;">newidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">dict</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">zip</span><span class="p">(</span><span class="n" style="color: #333333;">hetatoms</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">keys</span><span class="p">(),</span> <span class="p">[</span><span class="n" style="color: #333333;">obatom</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetIdx</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">obatom</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBMolAtomIter</span><span class="p">(</span><span class="n" style="color: #333333;">lig</span><span class="p">)]))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="351" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
351
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC351" class="line" lang="python"> <span class="n" style="color: #333333;">newidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">dict</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">zip</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">sorted</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333333;">hetatoms</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">keys</span><span class="p">()<span class="idiff right addition" style="background-color: #c7f0d2;">)</span>,</span> <span class="p">[</span><span class="n" style="color: #333333;">obatom</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetIdx</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">obatom</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBMolAtomIter</span><span class="p">(</span><span class="n" style="color: #333333;">lig</span><span class="p">)]))</span></span>
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<td class="old_line diff-line-num" data-linenumber="345" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
345
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<td class="new_line diff-line-num" data-linenumber="352" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
352
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC352" class="line" lang="python"> <span class="n" style="color: #333333;">mapold</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">dict</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">zip</span><span class="p">(</span><span class="n" style="color: #333333;">newidx</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">values</span><span class="p">(),</span> <span class="n" style="color: #333333;">newidx</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="346" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
346
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<td class="new_line diff-line-num old" data-linenumber="353" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC346" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># copy the bonds</span></span>
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<td class="old_line diff-line-num old" data-linenumber="347" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
347
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<td class="new_line diff-line-num old" data-linenumber="353" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC347" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">obatom</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">hetatoms</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="348" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
348
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<td class="new_line diff-line-num old" data-linenumber="353" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC348" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">neighbour_atom</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">neighbours</span><span class="p">[</span><span class="n" style="color: #333333;">obatom</span><span class="p">]:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="349" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
349
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<td class="new_line diff-line-num old" data-linenumber="353" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC349" class="line" lang="python"> <span class="n" style="color: #333333;">bond</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">hetatoms</span><span class="p">[</span><span class="n" style="color: #333333;">obatom</span><span class="p">].</span><span class="nc" style="color: #445588; font-weight: 600;">GetBond</span><span class="p">(</span><span class="n" style="color: #333333;">hetatoms</span><span class="p">[</span><span class="n" style="color: #333333;">neighbour_atom</span><span class="p">])</span></span>
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<td class="old_line diff-line-num old" data-linenumber="350" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
350
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<td class="new_line diff-line-num old" data-linenumber="353" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC350" class="line" lang="python"> <span class="n" style="color: #333333;">lig</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">AddBond</span><span class="p">(</span><span class="n" style="color: #333333;">newidx</span><span class="p">[</span><span class="n" style="color: #333333;">obatom</span><span class="p">],</span> <span class="n" style="color: #333333;">newidx</span><span class="p">[</span><span class="n" style="color: #333333;">neighbour_atom</span><span class="p">],</span> <span class="n" style="color: #333333;">bond</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetBondOrder</span><span class="p">())</span></span>
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<td class="old_line diff-line-num new" data-linenumber="351" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="353" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
353
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC353" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="351" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
351
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<td class="new_line diff-line-num" data-linenumber="354" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
354
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC354" class="line" lang="python"> <span class="n" style="color: #333333;">lig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">Molecule</span><span class="p">(</span><span class="n" style="color: #333333;">lig</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="352" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
352
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<td class="new_line diff-line-num" data-linenumber="355" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
355
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC355" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="353" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
353
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<td class="new_line diff-line-num" data-linenumber="356" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
356
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC356" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># For kmers, the representative ids are chosen (first residue of kmer)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="515" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="518" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -515,11 +518,12 @@ class Mol:</td>
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<td class="old_line diff-line-num" data-linenumber="515" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
515
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<td class="new_line diff-line-num" data-linenumber="518" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
518
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC518" class="line" lang="python"> <span class="sh" style="color: #dd1144;">"""</span><span class="s" style="color: #dd1144;">Find all possible hydrogen bond acceptors</span><span class="sh" style="color: #dd1144;">"""</span></span>
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<td class="old_line diff-line-num" data-linenumber="516" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
516
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<td class="new_line diff-line-num" data-linenumber="519" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
519
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC519" class="line" lang="python"> <span class="n" style="color: #333333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">namedtuple</span><span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">hbondacceptor</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">a a_orig_atom a_orig_idx type</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)</span></span>
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517
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<td class="new_line diff-line-num" data-linenumber="520" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
520
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC520" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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518
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<td class="new_line diff-line-num old" data-linenumber="521" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC518" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">atom</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nf" style="color: #990000; font-weight: 600;"><span class="idiff left deletion" style="background-color: #fac5cd;">filter</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">lambda</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">at</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">:</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">at</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">OBAtom</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="nc" style="color: #445588; font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">IsHbondAcceptor</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">(),</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;">all_atoms</span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">)</span>:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="521" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
521
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC521" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">atom</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">all_atoms</span><span class="p">:</span></span>
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519
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<td class="new_line diff-line-num" data-linenumber="522" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
522
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC522" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">atom</span><span class="p">.</span><span class="n" style="color: #333333;">atomicnum</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="mi" style="color: #009999;">9</span><span class="p">,</span> <span class="mi" style="color: #009999;">17</span><span class="p">,</span> <span class="mi" style="color: #009999;">35</span><span class="p">,</span> <span class="mi" style="color: #009999;">53</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333333;">atom</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">altconf</span><span class="p">:</span> <span class="c1" style="color: #999988; font-style: italic;"># Exclude halogen atoms</span></span>
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<td class="old_line diff-line-num" data-linenumber="520" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
520
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<td class="new_line diff-line-num" data-linenumber="523" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
523
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC523" class="line" lang="python"> <span class="n" style="color: #333333;">a_orig_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">mapid</span><span class="p">(</span><span class="n" style="color: #333333;">atom</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">mtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">mtype</span><span class="p">,</span> <span class="n" style="color: #333333;">bsid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bsid</span><span class="p">)</span></span>
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521
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<td class="new_line diff-line-num" data-linenumber="524" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
524
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC524" class="line" lang="python"> <span class="n" style="color: #333333;">a_orig_atom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">id_to_atom</span><span class="p">(</span><span class="n" style="color: #333333;">a_orig_idx</span><span class="p">)</span></span>
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522
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<td class="new_line diff-line-num old" data-linenumber="525" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC522" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">data</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">atom</span><span class="p">,</span> <span class="n" style="color: #333333;">a_orig_atom</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_orig_atom</span><span class="p">,</span> <span class="n" style="color: #333333;">a_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_orig_idx</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">regular</span><span class="sh" style="color: #dd1144;">'</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="525" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
525
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC525" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">a_orig_atom</span><span class="p">.</span><span class="n" style="color: #333333;">OBAtom</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">IsHbondAcceptor</span><span class="p">():</span></span>
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<td class="new_line diff-line-num new" data-linenumber="526" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
526
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC526" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">data</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">atom</span><span class="p">,</span> <span class="n" style="color: #333333;">a_orig_atom</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_orig_atom</span><span class="p">,</span> <span class="n" style="color: #333333;">a_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_orig_idx</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">regular</span><span class="sh" style="color: #dd1144;">'</span><span class="p">))</span></span>
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523
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<td class="new_line diff-line-num" data-linenumber="527" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
527
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC527" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">sorted</span><span class="p">(</span><span class="n" style="color: #333333;">a_set</span><span class="p">,</span> <span class="n" style="color: #333333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333333;">x</span><span class="p">:</span> <span class="n" style="color: #333333;">x</span><span class="p">.</span><span class="n" style="color: #333333;">a_orig_idx</span><span class="p">)</span></span>
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524
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<td class="new_line diff-line-num" data-linenumber="528" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
528
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC528" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">a_set</span></span>
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529
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC529" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="528" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="532" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -528,13 +532,11 @@ class Mol:</td>
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<td class="new_line diff-line-num" data-linenumber="532" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
532
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC532" class="line" lang="python"> <span class="n" style="color: #333333;">donor_pairs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="new_line diff-line-num" data-linenumber="533" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
533
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC533" class="line" lang="python"> <span class="n" style="color: #333333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">namedtuple</span><span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">hbonddonor</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">d d_orig_atom d_orig_idx h type</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="530" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
530
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<td class="new_line diff-line-num" data-linenumber="534" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
534
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC534" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">donor</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333333;">a</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">all_atoms</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">OBAtom</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">IsHbondDonor</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">altconf</span><span class="p">]:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="531" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
531
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<td class="new_line diff-line-num old" data-linenumber="535" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC531" class="line" lang="python"> <span class="n" style="color: #333333;">in_ring</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999999;">False</span></span>
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<td class="old_line diff-line-num old" data-linenumber="532" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
532
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<td class="new_line diff-line-num old" data-linenumber="535" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC532" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333333;">in_ring</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="533" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
533
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<td class="new_line diff-line-num old" data-linenumber="535" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC533" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">adj_atom</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333333;">a</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBAtomAtomIter</span><span class="p">(</span><span class="n" style="color: #333333;">donor</span><span class="p">.</span><span class="n" style="color: #333333;">OBAtom</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">IsHbondDonorH</span><span class="p">()]:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="534" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
534
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<td class="new_line diff-line-num old" data-linenumber="535" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC534" class="line" lang="python"> <span class="n" style="color: #333333;">d_orig_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">mapid</span><span class="p">(</span><span class="n" style="color: #333333;">donor</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">mtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">mtype</span><span class="p">,</span> <span class="n" style="color: #333333;">bsid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bsid</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="535" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
535
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<td class="new_line diff-line-num old" data-linenumber="535" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC535" class="line" lang="python"> <span class="n" style="color: #333333;">d_orig_atom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">id_to_atom</span><span class="p">(</span><span class="n" style="color: #333333;">d_orig_idx</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="536" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
536
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<td class="new_line diff-line-num old" data-linenumber="535" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC536" class="line" lang="python"> <span class="n" style="color: #333333;">donor_pairs</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">data</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">donor</span><span class="p">,</span> <span class="n" style="color: #333333;">d_orig_atom</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">d_orig_atom</span><span class="p">,</span> <span class="n" style="color: #333333;">d_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">d_orig_idx</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="537" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
537
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<td class="new_line diff-line-num old" data-linenumber="535" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC537" class="line" lang="python"> <span class="n" style="color: #333333;">h</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">Atom</span><span class="p">(</span><span class="n" style="color: #333333;">adj_atom</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">regular</span><span class="sh" style="color: #dd1144;">'</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="538" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="535" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
535
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC535" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">adj_atom</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333333;">a</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBAtomAtomIter</span><span class="p">(</span><span class="n" style="color: #333333;">donor</span><span class="p">.</span><span class="n" style="color: #333333;">OBAtom</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">IsHbondDonorH</span><span class="p">()]:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="538" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="536" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
536
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC536" class="line" lang="python"> <span class="n" style="color: #333333;">d_orig_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">mapid</span><span class="p">(</span><span class="n" style="color: #333333;">donor</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">mtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">mtype</span><span class="p">,</span> <span class="n" style="color: #333333;">bsid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bsid</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="537" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
537
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC537" class="line" lang="python"> <span class="n" style="color: #333333;">d_orig_atom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">id_to_atom</span><span class="p">(</span><span class="n" style="color: #333333;">d_orig_idx</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="538" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="538" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
538
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC538" class="line" lang="python"> <span class="n" style="color: #333333;">donor_pairs</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">data</span><span class="p">(</span><span class="n" style="color: #333333;">d</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">donor</span><span class="p">,</span> <span class="n" style="color: #333333;">d_orig_atom</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">d_orig_atom</span><span class="p">,</span> <span class="n" style="color: #333333;">d_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">d_orig_idx</span><span class="p">,</span></span>
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539
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC539" class="line" lang="python"> <span class="n" style="color: #333333;">h</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">Atom</span><span class="p">(</span><span class="n" style="color: #333333;">adj_atom</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">regular</span><span class="sh" style="color: #dd1144;">'</span><span class="p">))</span></span>
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<td class="old_line diff-line-num" data-linenumber="538" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
538
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<td class="new_line diff-line-num" data-linenumber="540" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
540
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC540" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">carbon</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">hydroph_atoms</span><span class="p">:</span></span>
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539
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<td class="new_line diff-line-num" data-linenumber="541" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
541
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC541" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">adj_atom</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333333;">a</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBAtomAtomIter</span><span class="p">(</span><span class="n" style="color: #333333;">carbon</span><span class="p">.</span><span class="n" style="color: #333333;">atom</span><span class="p">.</span><span class="n" style="color: #333333;">OBAtom</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetAtomicNum</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">1</span><span class="p">]:</span></span>
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540
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<td class="new_line diff-line-num" data-linenumber="542" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
542
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC542" class="line" lang="python"> <span class="n" style="color: #333333;">d_orig_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">mapid</span><span class="p">(</span><span class="n" style="color: #333333;">carbon</span><span class="p">.</span><span class="n" style="color: #333333;">atom</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">mtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">mtype</span><span class="p">,</span> <span class="n" style="color: #333333;">bsid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bsid</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="631" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="633" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -631,10 +633,11 @@ class PLInteraction:</td>
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631
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<td class="new_line diff-line-num" data-linenumber="633" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
633
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC633" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="632" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
632
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<td class="new_line diff-line-num" data-linenumber="634" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
634
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC634" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">pistacking</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">pistacking</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bindingsite</span><span class="p">.</span><span class="n" style="color: #333333;">rings</span><span class="p">,</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">ligand</span><span class="p">.</span><span class="n" style="color: #333333;">rings</span><span class="p">)</span></span>
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633
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<td class="new_line diff-line-num" data-linenumber="635" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
635
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC635" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="634" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
634
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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC634" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">all_pi<span class="idiff left right deletion" style="background-color: #fac5cd;">_</span>cation_laro</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">pication</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">ligand</span><span class="p">.</span><span class="n" style="color: #333333;">rings</span><span class="p">,</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bindingsite</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">get_pos_charged</span><span class="p">(),</span> <span class="bp" style="color: #999999;">True</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="635" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
635
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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC635" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">pication_paro</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">pication</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bindingsite</span><span class="p">.</span><span class="n" style="color: #333333;">rings</span><span class="p">,</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">ligand</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">get_pos_charged</span><span class="p">(),</span> <span class="bp" style="color: #999999;">False</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="636" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="636" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
636
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC636" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">all_pication_laro</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">pication</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">ligand</span><span class="p">.</span><span class="n" style="color: #333333;">rings</span><span class="p">,</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bindingsite</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">get_pos_charged</span><span class="p">(),</span> <span class="bp" style="color: #999999;">True</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="637" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
637
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC637" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;"><span class="idiff left right addition" style="background-color: #c7f0d2;">all_</span>pication_paro</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">pication</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bindingsite</span><span class="p">.</span><span class="n" style="color: #333333;">rings</span><span class="p">,</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">ligand</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">get_pos_charged</span><span class="p">(),</span> <span class="bp" style="color: #999999;">False</span><span class="p">)</span></span>
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636
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<td class="new_line diff-line-num" data-linenumber="638" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
638
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC638" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="637" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
637
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<td class="new_line diff-line-num old" data-linenumber="639" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC637" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">pication_laro</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">refine_pi_cation_laro</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">all_pi_cation_laro</span><span class="p">,</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">pistacking</span><span class="p">)</span></span>
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639
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC639" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">pication_laro</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">refine_pication</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">all_pication_laro</span><span class="p">,</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">pistacking</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="638" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="640" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
640
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC640" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">pication_paro</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">refine_pication</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">all_pication_paro</span><span class="p">,</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">pistacking</span><span class="p">)</span></span>
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638
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<td class="new_line diff-line-num" data-linenumber="641" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
641
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC641" class="line" lang="python"></span>
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639
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<td class="new_line diff-line-num" data-linenumber="642" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
642
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC642" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">all_hydrophobic_contacts</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">hydrophobic_interactions</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bindingsite</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">get_hydrophobic_atoms</span><span class="p">(),</span></span>
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640
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<td class="new_line diff-line-num" data-linenumber="643" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
643
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC643" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">ligand</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">get_hydrophobic_atoms</span><span class="p">())</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="748" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="751" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -748,47 +751,59 @@ class PLInteraction:</td>
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<td class="old_line diff-line-num" data-linenumber="748" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
748
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<td class="new_line diff-line-num" data-linenumber="751" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
751
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC751" class="line" lang="python"> <span class="n" style="color: #333333;">sel2</span><span class="p">[(</span><span class="n" style="color: #333333;">h</span><span class="p">.</span><span class="n" style="color: #333333;">ligatom</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">h</span><span class="p">.</span><span class="n" style="color: #333333;">resnr</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">h</span></span>
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<td class="old_line diff-line-num" data-linenumber="749" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
749
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<td class="new_line diff-line-num" data-linenumber="752" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
752
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC752" class="line" lang="python"> <span class="n" style="color: #333333;">hydroph</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">h</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">h</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">sel2</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">values</span><span class="p">()]</span></span>
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<td class="old_line diff-line-num" data-linenumber="750" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
750
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<td class="new_line diff-line-num" data-linenumber="753" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
753
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC753" class="line" lang="python"> <span class="n" style="color: #333333;">hydroph_final</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="751" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
751
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<td class="new_line diff-line-num old" data-linenumber="754" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC751" class="line" lang="python"> <span class="n" style="color: #333333;">bsclust</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="old_line diff-line-num" data-linenumber="752" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
752
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<td class="new_line diff-line-num" data-linenumber="754" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
754
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC754" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># 3. If a protein atom interacts with several neighboring ligand atoms, just keep the one with the closest dist</span></span>
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<td class="old_line diff-line-num old" data-linenumber="753" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
753
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC753" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">h</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">hydroph</span><span class="p">:</span></span>
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754
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC754" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">h</span><span class="p">.</span><span class="n" style="color: #333333;">bsatom</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">bsclust</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
755
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC755" class="line" lang="python"> <span class="n" style="color: #333333;">bsclust</span><span class="p">[</span><span class="n" style="color: #333333;">h</span><span class="p">.</span><span class="n" style="color: #333333;">bsatom</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">h</span><span class="p">,</span> <span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="756" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
756
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC756" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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757
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC757" class="line" lang="python"> <span class="n" style="color: #333333;">bsclust</span><span class="p">[</span><span class="n" style="color: #333333;">h</span><span class="p">.</span><span class="n" style="color: #333333;">bsatom</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">].</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333333;">h</span><span class="p">)</span></span>
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758
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC758" class="line" lang="python"></span>
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759
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC759" class="line" lang="python"> <span class="n" style="color: #333333;">idx_to_h</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="760" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
760
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC760" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">bs</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333333;">a</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">bsclust</span> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #990000; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333333;">bsclust</span><span class="p">[</span><span class="n" style="color: #333333;">a</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">1</span><span class="p">]:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="761" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
761
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC761" class="line" lang="python"> <span class="n" style="color: #333333;">hydroph_final</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333333;">bsclust</span><span class="p">[</span><span class="n" style="color: #333333;">bs</span><span class="p">][</span><span class="mi" style="color: #009999;">0</span><span class="p">])</span></span>
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<td class="old_line diff-line-num old" data-linenumber="762" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
762
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC762" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="763" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
763
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC763" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># A list of tuples with the idx of an atom and one of its neighbours is created</span></span>
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<td class="old_line diff-line-num old" data-linenumber="764" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
764
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC764" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">bs</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333333;">a</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">bsclust</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nf" style="color: #990000; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333333;">bsclust</span><span class="p">[</span><span class="n" style="color: #333333;">a</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">1</span><span class="p">]:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="765" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
765
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC765" class="line" lang="python"> <span class="n" style="color: #333333;">tuples</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="766" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
766
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC766" class="line" lang="python"> <span class="n" style="color: #333333;">all_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">i</span><span class="p">.</span><span class="n" style="color: #333333;">ligatom</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">bsclust</span><span class="p">[</span><span class="n" style="color: #333333;">bs</span><span class="p">]]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="767" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
767
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC767" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">b</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">bsclust</span><span class="p">[</span><span class="n" style="color: #333333;">bs</span><span class="p">]:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="768" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
768
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC768" class="line" lang="python"> <span class="n" style="color: #333333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">b</span><span class="p">.</span><span class="n" style="color: #333333;">ligatom</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span></span>
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<td class="old_line diff-line-num old" data-linenumber="769" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
769
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC769" class="line" lang="python"> <span class="n" style="color: #333333;">neigh</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">na</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">na</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBAtomAtomIter</span><span class="p">(</span><span class="n" style="color: #333333;">b</span><span class="p">.</span><span class="n" style="color: #333333;">ligatom</span><span class="p">.</span><span class="n" style="color: #333333;">OBAtom</span><span class="p">)]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="770" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
770
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC770" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">n</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">neigh</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="771" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
771
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC771" class="line" lang="python"> <span class="n" style="color: #333333;">n_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">n</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetIdx</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="772" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
772
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC772" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">n_idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">all_idx</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="773" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
773
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC773" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">n_idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">idx</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="774" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
774
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC774" class="line" lang="python"> <span class="n" style="color: #333333;">tuples</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">((</span><span class="n" style="color: #333333;">n_idx</span><span class="p">,</span> <span class="n" style="color: #333333;">idx</span><span class="p">))</span></span>
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775
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC775" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="776" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
776
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC776" class="line" lang="python"> <span class="n" style="color: #333333;">tuples</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">((</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">n_idx</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="777" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
777
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC777" class="line" lang="python"> <span class="n" style="color: #333333;">idx_to_h</span><span class="p">[</span><span class="n" style="color: #333333;">idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">b</span></span>
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<td class="old_line diff-line-num old" data-linenumber="778" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
778
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC778" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="779" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
779
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC779" class="line" lang="python"> <span class="n" style="color: #333333;">tuples</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">list</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">set</span><span class="p">(</span><span class="n" style="color: #333333;">tuples</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="780" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
780
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC780" class="line" lang="python"> <span class="n" style="color: #333333;">tuples</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">sorted</span><span class="p">(</span><span class="n" style="color: #333333;">tuples</span><span class="p">,</span> <span class="n" style="color: #333333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #990000; font-weight: 600;">itemgetter</span><span class="p">(</span><span class="mi" style="color: #009999;">1</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="781" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
781
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC781" class="line" lang="python"> <span class="n" style="color: #333333;">clusters</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">cluster_doubles</span><span class="p">(</span><span class="n" style="color: #333333;">tuples</span><span class="p">)</span> <span class="c1" style="color: #999988; font-style: italic;"># Cluster connected atoms (i.e. find hydrophobic patches)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="782" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
782
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC782" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="783" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
783
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC783" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">cluster</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">clusters</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="784" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
784
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC784" class="line" lang="python"> <span class="n" style="color: #333333;">min_dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">float</span><span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">inf</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="785" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
785
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC785" class="line" lang="python"> <span class="n" style="color: #333333;">min_h</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999999;">None</span></span>
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<td class="old_line diff-line-num old" data-linenumber="786" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
786
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC786" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">atm_idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">cluster</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="787" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
787
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC787" class="line" lang="python"> <span class="n" style="color: #333333;">h</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">idx_to_h</span><span class="p">[</span><span class="n" style="color: #333333;">atm_idx</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="788" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
788
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC788" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">h</span><span class="p">.</span><span class="n" style="color: #333333;">distance</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">min_dist</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="789" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
789
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC789" class="line" lang="python"> <span class="n" style="color: #333333;">min_dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">h</span><span class="p">.</span><span class="n" style="color: #333333;">distance</span></span>
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<td class="old_line diff-line-num old" data-linenumber="790" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
790
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC790" class="line" lang="python"> <span class="n" style="color: #333333;">min_h</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">h</span></span>
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<td class="old_line diff-line-num old" data-linenumber="791" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
791
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<td class="new_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC791" class="line" lang="python"> <span class="n" style="color: #333333;">hydroph_final</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333333;">min_h</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
755
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC755" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">PEPTIDES</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">INTRA</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">CHAINS</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="756" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
756
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC756" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># the ligand also consists of amino acid residues, repeat step 2 just the other way around</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="757" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
757
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC757" class="line" lang="python"> <span class="n" style="color: #333333;">sel3</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="758" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
758
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC758" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">h</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">hydroph</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="759" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
759
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC759" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="n" style="color: #333333;">h</span><span class="p">.</span><span class="n" style="color: #333333;">bsatom</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">h</span><span class="p">.</span><span class="n" style="color: #333333;">resnr_l</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">sel3</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="760" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
760
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC760" class="line" lang="python"> <span class="n" style="color: #333333;">sel3</span><span class="p">[(</span><span class="n" style="color: #333333;">h</span><span class="p">.</span><span class="n" style="color: #333333;">bsatom</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">h</span><span class="p">.</span><span class="n" style="color: #333333;">resnr_l</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">h</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="761" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
761
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC761" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="762" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
762
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC762" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">sel3</span><span class="p">[(</span><span class="n" style="color: #333333;">h</span><span class="p">.</span><span class="n" style="color: #333333;">bsatom</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">h</span><span class="p">.</span><span class="n" style="color: #333333;">resnr_l</span><span class="p">)].</span><span class="n" style="color: #333333;">distance</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333333;">h</span><span class="p">.</span><span class="n" style="color: #333333;">distance</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="763" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
763
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC763" class="line" lang="python"> <span class="n" style="color: #333333;">sel3</span><span class="p">[(</span><span class="n" style="color: #333333;">h</span><span class="p">.</span><span class="n" style="color: #333333;">bsatom</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">h</span><span class="p">.</span><span class="n" style="color: #333333;">resnr_l</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">h</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="764" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
764
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC764" class="line" lang="python"> <span class="n" style="color: #333333;">hydroph_final</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">h</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">h</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">sel3</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">values</span><span class="p">()]</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="765" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
765
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC765" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="766" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
766
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC766" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># for other ligands find hydrophobic patches for which only the shortest interactions is reported</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="767" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
767
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC767" class="line" lang="python"> <span class="n" style="color: #333333;">bsclust</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="768" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
768
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC768" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">h</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">hydroph</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="769" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
769
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC769" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">h</span><span class="p">.</span><span class="n" style="color: #333333;">bsatom</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">bsclust</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="770" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
770
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC770" class="line" lang="python"> <span class="n" style="color: #333333;">bsclust</span><span class="p">[</span><span class="n" style="color: #333333;">h</span><span class="p">.</span><span class="n" style="color: #333333;">bsatom</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">h</span><span class="p">,</span> <span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="771" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
771
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC771" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="772" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
772
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC772" class="line" lang="python"> <span class="n" style="color: #333333;">bsclust</span><span class="p">[</span><span class="n" style="color: #333333;">h</span><span class="p">.</span><span class="n" style="color: #333333;">bsatom</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">].</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333333;">h</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="773" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
773
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC773" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="774" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
774
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC774" class="line" lang="python"> <span class="n" style="color: #333333;">idx_to_h</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="775" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
775
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC775" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">bs</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333333;">a</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">bsclust</span> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #990000; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333333;">bsclust</span><span class="p">[</span><span class="n" style="color: #333333;">a</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">1</span><span class="p">]:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="776" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
776
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC776" class="line" lang="python"> <span class="n" style="color: #333333;">hydroph_final</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333333;">bsclust</span><span class="p">[</span><span class="n" style="color: #333333;">bs</span><span class="p">][</span><span class="mi" style="color: #009999;">0</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="777" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
777
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC777" class="line" lang="python"></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="778" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
778
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC778" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># A list of tuples with the idx of an atom and one of its neighbours is created</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="779" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
779
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC779" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">bs</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333333;">a</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">bsclust</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nf" style="color: #990000; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333333;">bsclust</span><span class="p">[</span><span class="n" style="color: #333333;">a</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">1</span><span class="p">]:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="780" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
780
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC780" class="line" lang="python"> <span class="n" style="color: #333333;">tuples</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="781" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
781
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC781" class="line" lang="python"> <span class="n" style="color: #333333;">all_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">i</span><span class="p">.</span><span class="n" style="color: #333333;">ligatom</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">bsclust</span><span class="p">[</span><span class="n" style="color: #333333;">bs</span><span class="p">]]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="782" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
782
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC782" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">b</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">bsclust</span><span class="p">[</span><span class="n" style="color: #333333;">bs</span><span class="p">]:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="783" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
783
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC783" class="line" lang="python"> <span class="n" style="color: #333333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">b</span><span class="p">.</span><span class="n" style="color: #333333;">ligatom</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span></span>
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<td class="new_line diff-line-num new" data-linenumber="784" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
784
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC784" class="line" lang="python"> <span class="n" style="color: #333333;">neigh</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">na</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">na</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBAtomAtomIter</span><span class="p">(</span><span class="n" style="color: #333333;">b</span><span class="p">.</span><span class="n" style="color: #333333;">ligatom</span><span class="p">.</span><span class="n" style="color: #333333;">OBAtom</span><span class="p">)]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="785" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
785
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC785" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">n</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">neigh</span><span class="p">:</span></span>
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786
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC786" class="line" lang="python"> <span class="n" style="color: #333333;">n_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">n</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetIdx</span><span class="p">()</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="787" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
787
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC787" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">n_idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">all_idx</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="788" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
788
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC788" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">n_idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">idx</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="789" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
789
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC789" class="line" lang="python"> <span class="n" style="color: #333333;">tuples</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">((</span><span class="n" style="color: #333333;">n_idx</span><span class="p">,</span> <span class="n" style="color: #333333;">idx</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="790" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
790
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC790" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="791" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
791
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC791" class="line" lang="python"> <span class="n" style="color: #333333;">tuples</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">((</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">n_idx</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
792
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC792" class="line" lang="python"> <span class="n" style="color: #333333;">idx_to_h</span><span class="p">[</span><span class="n" style="color: #333333;">idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">b</span></span>
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<td class="new_line diff-line-num new" data-linenumber="793" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
793
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC793" class="line" lang="python"></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="794" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
794
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC794" class="line" lang="python"> <span class="n" style="color: #333333;">tuples</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">list</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">set</span><span class="p">(</span><span class="n" style="color: #333333;">tuples</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="795" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
795
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC795" class="line" lang="python"> <span class="n" style="color: #333333;">tuples</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">sorted</span><span class="p">(</span><span class="n" style="color: #333333;">tuples</span><span class="p">,</span> <span class="n" style="color: #333333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #990000; font-weight: 600;">itemgetter</span><span class="p">(</span><span class="mi" style="color: #009999;">1</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="796" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
796
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC796" class="line" lang="python"> <span class="n" style="color: #333333;">clusters</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">cluster_doubles</span><span class="p">(</span><span class="n" style="color: #333333;">tuples</span><span class="p">)</span> <span class="c1" style="color: #999988; font-style: italic;"># Cluster connected atoms (i.e. find hydrophobic patches)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="797" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
797
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC797" class="line" lang="python"></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="798" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
798
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC798" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">cluster</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">clusters</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="799" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
799
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC799" class="line" lang="python"> <span class="n" style="color: #333333;">min_dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">float</span><span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">inf</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
800
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC800" class="line" lang="python"> <span class="n" style="color: #333333;">min_h</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999999;">None</span></span>
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<td class="new_line diff-line-num new" data-linenumber="801" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
801
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC801" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">atm_idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">cluster</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="802" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
802
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC802" class="line" lang="python"> <span class="n" style="color: #333333;">h</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">idx_to_h</span><span class="p">[</span><span class="n" style="color: #333333;">atm_idx</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="803" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
803
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC803" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">h</span><span class="p">.</span><span class="n" style="color: #333333;">distance</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">min_dist</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="804" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
804
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC804" class="line" lang="python"> <span class="n" style="color: #333333;">min_dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">h</span><span class="p">.</span><span class="n" style="color: #333333;">distance</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="805" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
805
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC805" class="line" lang="python"> <span class="n" style="color: #333333;">min_h</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">h</span></span>
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<td class="old_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="806" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
806
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC806" class="line" lang="python"> <span class="n" style="color: #333333;">hydroph_final</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333333;">min_h</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="792" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
792
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<td class="new_line diff-line-num" data-linenumber="807" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
807
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC807" class="line" lang="python"> <span class="n" style="color: #333333;">before</span><span class="p">,</span> <span class="n" style="color: #333333;">reduced</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333333;">all_h</span><span class="p">),</span> <span class="nf" style="color: #990000; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333333;">hydroph_final</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="793" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
793
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<td class="new_line diff-line-num" data-linenumber="808" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
808
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC808" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333333;">before</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333333;">before</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333333;">reduced</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="794" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
794
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<td class="new_line diff-line-num" data-linenumber="809" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
809
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC809" class="line" lang="python"> <span class="n" style="color: #333333;">logger</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">info</span><span class="p">(</span><span class="sa">f</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">reduced number of hydrophobic contacts from </span><span class="si" style="color: #dd1144;">{</span><span class="n" style="color: #333333;">before</span><span class="si" style="color: #dd1144;">}</span><span class="s" style="color: #dd1144;"> to </span><span class="si" style="color: #dd1144;">{</span><span class="n" style="color: #333333;">reduced</span><span class="si" style="color: #dd1144;">}</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="849" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="864" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -849,7 +864,7 @@ class PLInteraction:</td>
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<td class="old_line diff-line-num" data-linenumber="849" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
849
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<td class="new_line diff-line-num" data-linenumber="864" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
864
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC864" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333333;">hb</span><span class="p">[</span><span class="mi" style="color: #009999;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">hb</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">second_set</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">values</span><span class="p">()]</span></span>
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<td class="old_line diff-line-num" data-linenumber="850" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
850
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<td class="new_line diff-line-num" data-linenumber="865" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
865
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC865" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="851" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
851
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<td class="new_line diff-line-num" data-linenumber="866" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
866
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC866" class="line" lang="python"> <span class="nd">@staticmethod</span></span>
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<td class="old_line diff-line-num old" data-linenumber="852" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
852
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<td class="new_line diff-line-num old" data-linenumber="867" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC852" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #990000; font-weight: 600;">refine_pi<span class="idiff left deletion" style="background-color: #fac5cd;">_</span>cation<span class="idiff right deletion" style="background-color: #fac5cd;">_laro</span></span><span class="p">(</span><span class="n" style="color: #333333;">all_picat</span><span class="p">,</span> <span class="n" style="color: #333333;">stacks</span><span class="p">):</span></span>
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<td class="old_line diff-line-num new" data-linenumber="853" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="867" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
867
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC867" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #990000; font-weight: 600;">refine_pication</span><span class="p">(</span><span class="n" style="color: #333333;">all_picat</span><span class="p">,</span> <span class="n" style="color: #333333;">stacks</span><span class="p">):</span></span>
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<td class="old_line diff-line-num" data-linenumber="853" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
853
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<td class="new_line diff-line-num" data-linenumber="868" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
868
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC868" class="line" lang="python"> <span class="sh" style="color: #dd1144;">"""</span><span class="s" style="color: #dd1144;">Just important for constellations with histidine involved. If the histidine ring is positioned in stacking</span></span>
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<td class="old_line diff-line-num" data-linenumber="854" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
854
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<td class="new_line diff-line-num" data-linenumber="869" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
869
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC869" class="line" lang="python"><span class="s" style="color: #dd1144;"> position to an aromatic ring in the ligand, there is in most cases stacking and pi-cation interaction reported</span></span>
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<td class="old_line diff-line-num" data-linenumber="855" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
855
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<td class="new_line diff-line-num" data-linenumber="870" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
870
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC870" class="line" lang="python"><span class="s" style="color: #dd1144;"> as histidine also carries a positive charge in the ring. For such cases, only report stacking.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="857" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="872" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -857,9 +872,15 @@ class PLInteraction:</td>
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<td class="old_line diff-line-num" data-linenumber="857" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
857
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<td class="new_line diff-line-num" data-linenumber="872" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
872
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC872" class="line" lang="python"> <span class="n" style="color: #333333;">i_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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858
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<td class="new_line diff-line-num" data-linenumber="873" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
873
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC873" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">picat</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">all_picat</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="859" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
859
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<td class="new_line diff-line-num" data-linenumber="874" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
874
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC874" class="line" lang="python"> <span class="n" style="color: #333333;">exclude</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999999;">False</span></span>
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<td class="old_line diff-line-num old" data-linenumber="860" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
860
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<td class="new_line diff-line-num old" data-linenumber="875" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC860" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">stack</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">stacks</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="861" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
861
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<td class="new_line diff-line-num old" data-linenumber="875" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC861" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #990000; font-weight: 600;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333333;">stack</span><span class="p">.</span><span class="n" style="color: #333333;">proteinring</span><span class="p">.</span><span class="n" style="color: #333333;">atoms</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">HIS</span><span class="sh" style="color: #dd1144;">'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333333;">picat</span><span class="p">.</span><span class="n" style="color: #333333;">ring</span><span class="p">.</span><span class="n" style="color: #333333;">obj</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333333;">stack</span><span class="p">.</span><span class="n" style="color: #333333;">ligandring</span><span class="p">.</span><span class="n" style="color: #333333;">obj</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="862" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
862
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<td class="new_line diff-line-num old" data-linenumber="875" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC862" class="line" lang="python"> <span class="n" style="color: #333333;">exclude</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999999;">True</span></span>
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<td class="old_line diff-line-num new" data-linenumber="863" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="875" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
875
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC875" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">picat</span><span class="p">.</span><span class="n" style="color: #333333;">restype</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">HIS</span><span class="sh" style="color: #dd1144;">'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="863" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="876" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
876
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC876" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">stack</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">stacks</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="863" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="877" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
877
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC877" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #990000; font-weight: 600;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333333;">stack</span><span class="p">.</span><span class="n" style="color: #333333;">proteinring</span><span class="p">.</span><span class="n" style="color: #333333;">atoms</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333333;">picat</span><span class="p">.</span><span class="n" style="color: #333333;">resnr</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333333;">picat</span><span class="p">.</span><span class="n" style="color: #333333;">ring</span><span class="p">.</span><span class="n" style="color: #333333;">obj</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333333;">stack</span><span class="p">.</span><span class="n" style="color: #333333;">ligandring</span><span class="p">.</span><span class="n" style="color: #333333;">obj</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="863" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="878" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
878
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC878" class="line" lang="python"> <span class="n" style="color: #333333;">exclude</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999999;">True</span></span>
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<td class="old_line diff-line-num new" data-linenumber="863" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
879
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC879" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># HIS could also be on ligand side for protein-protein interactions</span></span>
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<td class="old_line diff-line-num new" data-linenumber="863" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="880" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
880
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC880" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">picat</span><span class="p">.</span><span class="n" style="color: #333333;">restype_l</span> <span class="o" style="font-weight: 600;">==</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">HIS</span><span class="sh" style="color: #dd1144;">'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="863" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="881" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
881
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC881" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">stack</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">stacks</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="863" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="882" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
882
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC882" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #990000; font-weight: 600;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333333;">stack</span><span class="p">.</span><span class="n" style="color: #333333;">ligandring</span><span class="p">.</span><span class="n" style="color: #333333;">atoms</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333333;">picat</span><span class="p">.</span><span class="n" style="color: #333333;">resnr_l</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333333;">picat</span><span class="p">.</span><span class="n" style="color: #333333;">ring</span><span class="p">.</span><span class="n" style="color: #333333;">obj</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333333;">stack</span><span class="p">.</span><span class="n" style="color: #333333;">proteinring</span><span class="p">.</span><span class="n" style="color: #333333;">obj</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="863" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="883" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
883
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC883" class="line" lang="python"> <span class="n" style="color: #333333;">exclude</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999999;">True</span></span>
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<td class="old_line diff-line-num" data-linenumber="863" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
863
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<td class="new_line diff-line-num" data-linenumber="884" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
884
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC884" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333333;">exclude</span><span class="p">:</span></span>
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864
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<td class="new_line diff-line-num" data-linenumber="885" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
885
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC885" class="line" lang="python"> <span class="n" style="color: #333333;">i_set</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333333;">picat</span><span class="p">)</span></span>
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865
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886
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC886" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">i_set</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="868" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="889" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -868,18 +889,24 @@ class PLInteraction:</td>
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<td class="old_line diff-line-num" data-linenumber="868" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
868
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<td class="new_line diff-line-num" data-linenumber="889" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
889
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC889" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #990000; font-weight: 600;">refine_water_bridges</span><span class="p">(</span><span class="n" style="color: #333333;">wbridges</span><span class="p">,</span> <span class="n" style="color: #333333;">hbonds_ldon</span><span class="p">,</span> <span class="n" style="color: #333333;">hbonds_pdon</span><span class="p">):</span></span>
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<td class="old_line diff-line-num" data-linenumber="869" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
869
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<td class="new_line diff-line-num" data-linenumber="890" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
890
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC890" class="line" lang="python"> <span class="sh" style="color: #dd1144;">"""</span><span class="s" style="color: #dd1144;">A donor atom already forming a hydrogen bond is not allowed to form a water bridge. Each water molecule</span></span>
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<td class="old_line diff-line-num" data-linenumber="870" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
870
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<td class="new_line diff-line-num" data-linenumber="891" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
891
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC891" class="line" lang="python"><span class="s" style="color: #dd1144;"> can only be donor for two water bridges, selecting the constellation with the omega angle closest to 110 deg.</span><span class="sh" style="color: #dd1144;">"""</span></span>
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<td class="old_line diff-line-num old" data-linenumber="871" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
871
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<td class="new_line diff-line-num old" data-linenumber="892" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC871" class="line" lang="python"> <span class="n" style="color: #333333;">donor_atoms_hbonds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">hb</span><span class="p">.</span><span class="n" style="color: #333333;">d</span><span class="p"><span class="idiff left right deletion" style="background-color: #fac5cd;">.</span></span><span class="n" style="color: #333333;">idx</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">hb</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">hbonds_ldon</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333333;">hbonds_pdon</span><span class="p">]</span></span>
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<td class="old_line diff-line-num new" data-linenumber="872" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="892" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
892
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC892" class="line" lang="python"> <span class="n" style="color: #333333;">donor_atoms_hbonds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">hb</span><span class="p">.</span><span class="n" style="color: #333333;">d<span class="idiff left right addition" style="background-color: #c7f0d2;">_orig_</span>idx</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">hb</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">hbonds_ldon</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333333;">hbonds_pdon</span><span class="p">]</span></span>
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872
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<td class="new_line diff-line-num" data-linenumber="893" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
893
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC893" class="line" lang="python"> <span class="n" style="color: #333333;">wb_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="old_line diff-line-num" data-linenumber="873" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
873
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<td class="new_line diff-line-num" data-linenumber="894" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
894
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC894" class="line" lang="python"> <span class="n" style="color: #333333;">wb_dict2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="old_line diff-line-num" data-linenumber="874" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
874
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<td class="new_line diff-line-num" data-linenumber="895" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
895
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC895" class="line" lang="python"> <span class="n" style="color: #333333;">omega</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #009999;">110.0</span></span>
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875
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<td class="new_line diff-line-num" data-linenumber="896" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
896
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC896" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="876" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
876
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<td class="new_line diff-line-num" data-linenumber="897" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
897
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC897" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Just one hydrogen bond per donor atom</span></span>
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<td class="old_line diff-line-num old" data-linenumber="877" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
877
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<td class="new_line diff-line-num old" data-linenumber="898" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC877" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">wbridge</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333333;">wb</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">wb</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">wbridges</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">wb</span><span class="p">.</span><span class="n" style="color: #333333;">d</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">donor_atoms_hbonds</span><span class="p">]:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="878" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
878
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<td class="new_line diff-line-num old" data-linenumber="898" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC878" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">if </span><span class="p">(</span><span class="n" style="color: #333333;">wbridge</span><span class="p">.</span><span class="n" style="color: #333333;">water</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">wbridge</span><span class="p">.</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">wb_dict</span><span class="p">:</span></span>
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879
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<td class="new_line diff-line-num old" data-linenumber="898" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC879" class="line" lang="python"> <span class="n" style="color: #333333;">wb_dict</span><span class="p">[(</span><span class="n" style="color: #333333;">wbridge</span><span class="p">.</span><span class="n" style="color: #333333;">water</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">wbridge</span><span class="p">.</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">wbridge</span></span>
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<td class="old_line diff-line-num new" data-linenumber="880" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="898" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
898
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC898" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># (TODO: looks wrong, what about donor atoms with multiple H? Does PLIP cover that somehow?</span></span>
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<td class="old_line diff-line-num new" data-linenumber="880" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="899" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
899
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC899" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># and only one donor per water-acceptor combination</span></span>
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<td class="old_line diff-line-num new" data-linenumber="880" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="900" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
900
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC900" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># (each water-acceptor combo only kept once after this loop,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="880" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="901" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
901
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC901" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># the one with angle at water closest to omega)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="880" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="902" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
902
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC902" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">wbridge</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333333;">wb</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">wb</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">wbridges</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">wb</span><span class="p">.</span><span class="n" style="color: #333333;">d_orig_idx</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">donor_atoms_hbonds</span><span class="p">]:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="880" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="903" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
903
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC903" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">if </span><span class="p">(</span><span class="n" style="color: #333333;">wbridge</span><span class="p">.</span><span class="n" style="color: #333333;">water_orig_idx</span><span class="p">,</span> <span class="n" style="color: #333333;">wbridge</span><span class="p">.</span><span class="n" style="color: #333333;">a_orig_idx</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">wb_dict</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="880" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="904" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
904
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC904" class="line" lang="python"> <span class="n" style="color: #333333;">wb_dict</span><span class="p">[(</span><span class="n" style="color: #333333;">wbridge</span><span class="p">.</span><span class="n" style="color: #333333;">water_orig_idx</span><span class="p">,</span> <span class="n" style="color: #333333;">wbridge</span><span class="p">.</span><span class="n" style="color: #333333;">a_orig_idx</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">wbridge</span></span>
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<td class="old_line diff-line-num" data-linenumber="880" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
880
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<td class="new_line diff-line-num" data-linenumber="905" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
905
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC905" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="881" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
881
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<td class="new_line diff-line-num old" data-linenumber="906" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC881" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #990000; font-weight: 600;">abs</span><span class="p">(</span><span class="n" style="color: #333333;">omega</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333333;">wb_dict</span><span class="p">[(</span><span class="n" style="color: #333333;">wbridge</span><span class="p">.</span><span class="n" style="color: #333333;">water</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">wbridge</span><span class="p">.</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">)].</span><span class="n" style="color: #333333;">w_angle</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="nf" style="color: #990000; font-weight: 600;">abs</span><span class="p">(</span><span class="n" style="color: #333333;">omega</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333333;">wbridge</span><span class="p">.</span><span class="n" style="color: #333333;">w_angle</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="882" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
882
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<td class="new_line diff-line-num old" data-linenumber="906" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC882" class="line" lang="python"> <span class="n" style="color: #333333;">wb_dict</span><span class="p">[(</span><span class="n" style="color: #333333;">wbridge</span><span class="p">.</span><span class="n" style="color: #333333;">water</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">wbridge</span><span class="p">.</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">wbridge</span></span>
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<td class="old_line diff-line-num new" data-linenumber="883" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="906" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
906
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC906" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #990000; font-weight: 600;">abs</span><span class="p">(</span><span class="n" style="color: #333333;">omega</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333333;">wb_dict</span><span class="p">[(</span><span class="n" style="color: #333333;">wbridge</span><span class="p">.</span><span class="n" style="color: #333333;">water_orig_idx</span><span class="p">,</span> <span class="n" style="color: #333333;">wbridge</span><span class="p">.</span><span class="n" style="color: #333333;">a_orig_idx</span><span class="p">)].</span><span class="n" style="color: #333333;">w_angle</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="nf" style="color: #990000; font-weight: 600;">abs</span><span class="p">(</span><span class="n" style="color: #333333;">omega</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333333;">wbridge</span><span class="p">.</span><span class="n" style="color: #333333;">w_angle</span><span class="p">):</span></span>
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<td class="old_line diff-line-num new" data-linenumber="883" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="907" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
907
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC907" class="line" lang="python"> <span class="n" style="color: #333333;">wb_dict</span><span class="p">[(</span><span class="n" style="color: #333333;">wbridge</span><span class="p">.</span><span class="n" style="color: #333333;">water_orig_idx</span><span class="p">,</span> <span class="n" style="color: #333333;">wbridge</span><span class="p">.</span><span class="n" style="color: #333333;">a_orig_idx</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">wbridge</span></span>
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<td class="old_line diff-line-num new" data-linenumber="883" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="908" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
908
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC908" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Just two hydrogen bonds per water molecule</span></span>
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<td class="old_line diff-line-num new" data-linenumber="883" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="909" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
909
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC909" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># only the two water-acceptor combos with angle closest to omega are kept</span></span>
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<td class="old_line diff-line-num" data-linenumber="883" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
883
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<td class="new_line diff-line-num" data-linenumber="910" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
910
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC910" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">wb_tuple</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">wb_dict</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="884" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
884
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<td class="new_line diff-line-num" data-linenumber="911" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
911
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC911" class="line" lang="python"> <span class="n" style="color: #333333;">water</span><span class="p">,</span> <span class="n" style="color: #333333;">acceptor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">wb_tuple</span></span>
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<td class="old_line diff-line-num" data-linenumber="885" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
885
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<td class="new_line diff-line-num" data-linenumber="912" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
912
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC912" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">water</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">wb_dict2</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="888" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="915" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -888,7 +915,7 @@ class PLInteraction:</td>
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<td class="old_line diff-line-num" data-linenumber="888" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
888
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<td class="new_line diff-line-num" data-linenumber="915" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
915
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC915" class="line" lang="python"> <span class="n" style="color: #333333;">wb_dict2</span><span class="p">[</span><span class="n" style="color: #333333;">water</span><span class="p">].</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">((</span><span class="nf" style="color: #990000; font-weight: 600;">abs</span><span class="p">(</span><span class="n" style="color: #333333;">omega</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333333;">wb_dict</span><span class="p">[</span><span class="n" style="color: #333333;">wb_tuple</span><span class="p">].</span><span class="n" style="color: #333333;">w_angle</span><span class="p">),</span> <span class="n" style="color: #333333;">wb_dict</span><span class="p">[</span><span class="n" style="color: #333333;">wb_tuple</span><span class="p">]))</span></span>
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<td class="old_line diff-line-num" data-linenumber="889" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
889
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<td class="new_line diff-line-num" data-linenumber="916" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
916
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC916" class="line" lang="python"> <span class="n" style="color: #333333;">wb_dict2</span><span class="p">[</span><span class="n" style="color: #333333;">water</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">sorted</span><span class="p">(</span><span class="n" style="color: #333333;">wb_dict2</span><span class="p">[</span><span class="n" style="color: #333333;">water</span><span class="p">],</span> <span class="n" style="color: #333333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333333;">x</span><span class="p">:</span> <span class="n" style="color: #333333;">x</span><span class="p">[</span><span class="mi" style="color: #009999;">0</span><span class="p">])</span></span>
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<td class="old_line diff-line-num" data-linenumber="890" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
890
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<td class="new_line diff-line-num" data-linenumber="917" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
917
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC917" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="891" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
891
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<td class="new_line diff-line-num old" data-linenumber="918" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC891" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">wb_dict2</span><span class="p">[</span><span class="n" style="color: #333333;">water</span><span class="p">][</span><span class="mi" style="color: #009999;">1</span><span class="p">][</span><span class="mi" style="color: #009999;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><span class="idiff left right deletion" style="background-color: #fac5cd;"><</span></span> <span class="nf" style="color: #990000; font-weight: 600;">abs</span><span class="p">(</span><span class="n" style="color: #333333;">omega</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333333;">wb_dict</span><span class="p">[</span><span class="n" style="color: #333333;">wb_tuple</span><span class="p">].</span><span class="n" style="color: #333333;">w_angle</span><span class="p">):</span></span>
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<td class="old_line diff-line-num new" data-linenumber="892" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="918" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
918
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC918" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">wb_dict2</span><span class="p">[</span><span class="n" style="color: #333333;">water</span><span class="p">][</span><span class="mi" style="color: #009999;">1</span><span class="p">][</span><span class="mi" style="color: #009999;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><span class="idiff left right addition" style="background-color: #c7f0d2;">></span></span> <span class="nf" style="color: #990000; font-weight: 600;">abs</span><span class="p">(</span><span class="n" style="color: #333333;">omega</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333333;">wb_dict</span><span class="p">[</span><span class="n" style="color: #333333;">wb_tuple</span><span class="p">].</span><span class="n" style="color: #333333;">w_angle</span><span class="p">):</span></span>
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<td class="old_line diff-line-num" data-linenumber="892" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
892
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<td class="new_line diff-line-num" data-linenumber="919" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
919
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC919" class="line" lang="python"> <span class="n" style="color: #333333;">wb_dict2</span><span class="p">[</span><span class="n" style="color: #333333;">water</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">wb_dict2</span><span class="p">[</span><span class="n" style="color: #333333;">water</span><span class="p">][</span><span class="mi" style="color: #009999;">0</span><span class="p">],</span> <span class="p">(</span><span class="n" style="color: #333333;">wb_dict</span><span class="p">[</span><span class="n" style="color: #333333;">wb_tuple</span><span class="p">].</span><span class="n" style="color: #333333;">w_angle</span><span class="p">,</span> <span class="n" style="color: #333333;">wb_dict</span><span class="p">[</span><span class="n" style="color: #333333;">wb_tuple</span><span class="p">])]</span></span>
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<td class="old_line diff-line-num" data-linenumber="893" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
893
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<td class="new_line diff-line-num" data-linenumber="920" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
920
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC920" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="894" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
894
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<td class="new_line diff-line-num" data-linenumber="921" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
921
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC921" class="line" lang="python"> <span class="n" style="color: #333333;">filtered_wb</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="933" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -933,7 +960,7 @@ class BindingSite(Mol):</td>
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<td class="old_line diff-line-num" data-linenumber="933" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
933
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<td class="new_line diff-line-num" data-linenumber="960" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
960
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC960" class="line" lang="python"> <span class="n" style="color: #333333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">namedtuple</span><span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">pcharge</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">atoms atoms_orig_idx type center restype resnr reschain</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="934" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
934
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<td class="new_line diff-line-num" data-linenumber="961" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
961
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC961" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="old_line diff-line-num" data-linenumber="935" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
935
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<td class="new_line diff-line-num" data-linenumber="962" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
962
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC962" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Iterate through all residue, exclude those in chains defined as peptides</span></span>
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<td class="old_line diff-line-num old" data-linenumber="936" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
936
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<td class="new_line diff-line-num old" data-linenumber="963" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC936" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">res</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333333;">r</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBResidueIter</span><span class="p">(</span><span class="n" style="color: #333333;">mol</span><span class="p">.</span><span class="n" style="color: #333333;">OBMol</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;"><span class="idiff left deletion" style="background-color: #fac5cd;">not</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">r</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="nc" style="color: #445588; font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">GetChain</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">()</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="ow" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">in</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">config</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="n" style="color: #333333;"><span class="idiff right deletion" style="background-color: #fac5cd;">PEPTIDES</span></span><span class="p">]:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="937" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="963" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
963
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC963" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">res</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333333;">r</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBResidueIter</span><span class="p">(</span><span class="n" style="color: #333333;">mol</span><span class="p">.</span><span class="n" style="color: #333333;">OBMol</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #990000; font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">residue_belongs_to_receptor</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">r</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">config</span></span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">)</span>]:</span></span>
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<td class="old_line diff-line-num" data-linenumber="937" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
937
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<td class="new_line diff-line-num" data-linenumber="964" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
964
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC964" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">INTRA</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999999;">None</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="938" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
938
</td>
<td class="new_line diff-line-num" data-linenumber="965" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
965
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC965" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">res</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetChain</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">INTRA</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="939" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
939
</td>
<td class="new_line diff-line-num" data-linenumber="966" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
966
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC966" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="974" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1001" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -974,7 +1001,7 @@ class BindingSite(Mol):</td>
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<td class="old_line diff-line-num" data-linenumber="974" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
974
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<td class="new_line diff-line-num" data-linenumber="1001" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1001
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1001" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">Atom</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">))</span></span>
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<td class="old_line diff-line-num" data-linenumber="975" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
975
</td>
<td class="new_line diff-line-num" data-linenumber="1002" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1002
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1002" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">mapid</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetIdx</span><span class="p">(),</span> <span class="n" style="color: #333333;">mtype</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">protein</span><span class="sh" style="color: #dd1144;">'</span><span class="p">))</span></span>
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<td class="old_line diff-line-num" data-linenumber="976" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
976
</td>
<td class="new_line diff-line-num" data-linenumber="1003" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1003
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1003" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nf" style="color: #990000; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333333;">a_contributing</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">0</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="977" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
977
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<td class="new_line diff-line-num old" data-linenumber="1004" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC977" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">data</span><span class="p">(</span><span class="n" style="color: #333333;">atoms</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing</span><span class="p">,</span><span class="n" style="color: #333333;">atoms_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">negative</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span><span class="idiff left right deletion" style="background-color: #fac5cd;"> </span></span>
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<td class="old_line diff-line-num new" data-linenumber="978" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1004" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1004
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1004" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">data</span><span class="p">(</span><span class="n" style="color: #333333;">atoms</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing</span><span class="p">,</span><span class="n" style="color: #333333;">atoms_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">negative</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="978" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
978
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<td class="new_line diff-line-num" data-linenumber="1005" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1005
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1005" class="line" lang="python"> <span class="n" style="color: #333333;">center</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #990000; font-weight: 600;">centroid</span><span class="p">([</span><span class="n" style="color: #333333;">ac</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">ac</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing</span><span class="p">]),</span> <span class="n" style="color: #333333;">restype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">res</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetName</span><span class="p">(),</span></span>
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<td class="old_line diff-line-num" data-linenumber="979" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
979
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<td class="new_line diff-line-num" data-linenumber="1006" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1006
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1006" class="line" lang="python"> <span class="n" style="color: #333333;">resnr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">res</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetNum</span><span class="p">(),</span></span>
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<td class="old_line diff-line-num" data-linenumber="980" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
980
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<td class="new_line diff-line-num" data-linenumber="1007" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1007
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1007" class="line" lang="python"> <span class="n" style="color: #333333;">reschain</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">res</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetChain</span><span class="p">()))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1032" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1059" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1032,7 +1059,8 @@ class Ligand(Mol):</td>
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<td class="old_line diff-line-num" data-linenumber="1032" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1032
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<td class="new_line diff-line-num" data-linenumber="1059" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1059
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1059" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">ligand</span><span class="p">.</span><span class="nb" style="color: #0086b3;">type</span></span>
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<td class="old_line diff-line-num" data-linenumber="1033" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1033
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<td class="new_line diff-line-num" data-linenumber="1060" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1060
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1060" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">complex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">cclass</span></span>
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<td class="old_line diff-line-num" data-linenumber="1034" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1034
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<td class="new_line diff-line-num" data-linenumber="1061" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1061
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1061" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">molecule</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">ligand</span><span class="p">.</span><span class="n" style="color: #333333;">mol</span> <span class="c1" style="color: #999988; font-style: italic;"># Pybel Molecule</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1035" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1035
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<td class="new_line diff-line-num old" data-linenumber="1062" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1035" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">smiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">molecule</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">write</span><span class="p">(</span><span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">can</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)</span> <span class="c1" style="color: #999988; font-style: italic;"># SMILES String</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1036" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1062" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1062
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1062" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># get canonical SMILES String, but not for peptide ligand (tend to be too long -> openBabel crashes)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1036" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1063" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1063
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1063" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">smiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #dd1144;">""</span> <span class="nf" style="color: #990000; font-weight: 600;">if </span><span class="p">(</span><span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">INTRA</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">PEPTIDES</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">CHAINS</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">molecule</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">write</span><span class="p">(</span><span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">can</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="1036" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1036
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<td class="new_line diff-line-num" data-linenumber="1064" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1064
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1064" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">inchikey</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">molecule</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">write</span><span class="p">(</span><span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">inchikey</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="1037" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1037
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<td class="new_line diff-line-num" data-linenumber="1065" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1065
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1065" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">can_to_pdb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">ligand</span><span class="p">.</span><span class="n" style="color: #333333;">can_to_pdb</span></span>
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<td class="old_line diff-line-num" data-linenumber="1038" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1038
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<td class="new_line diff-line-num" data-linenumber="1066" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1066
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1066" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nf" style="color: #990000; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">smiles</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">0</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1173" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1201" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1173,74 +1201,110 @@ class Ligand(Mol):</td>
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<td class="old_line diff-line-num" data-linenumber="1173" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1173
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<td class="new_line diff-line-num" data-linenumber="1201" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1201
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1201" class="line" lang="python"><span class="s" style="color: #dd1144;"> </span><span class="sh" style="color: #dd1144;">"""</span></span>
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<td class="old_line diff-line-num" data-linenumber="1174" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1174
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<td class="new_line diff-line-num" data-linenumber="1202" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1202
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1202" class="line" lang="python"> <span class="n" style="color: #333333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">namedtuple</span><span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">lcharge</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">atoms orig_atoms atoms_orig_idx type center fgroup</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="1175" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1175
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<td class="new_line diff-line-num" data-linenumber="1203" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1203
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1203" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1176" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1176
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1176" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">all_atoms</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1177" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1177
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1177" class="line" lang="python"> <span class="n" style="color: #333333;">a_orig_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">mapid</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">mtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">mtype</span><span class="p">,</span> <span class="n" style="color: #333333;">bsid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bsid</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1178" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1178
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1178" class="line" lang="python"> <span class="n" style="color: #333333;">a_orig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">id_to_atom</span><span class="p">(</span><span class="n" style="color: #333333;">a_orig_idx</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1179" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1179
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1179" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">is_functional_group</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">quartamine</span><span class="sh" style="color: #dd1144;">'</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1180" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1180
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1180" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">data</span><span class="p">(</span><span class="n" style="color: #333333;">atoms</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="p">],</span> <span class="n" style="color: #333333;">orig_atoms</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333333;">a_orig</span><span class="p">,</span> <span class="p">],</span> <span class="n" style="color: #333333;">atoms_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333333;">a_orig_idx</span><span class="p">,</span> <span class="p">],</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">positive</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1181" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1181
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1181" class="line" lang="python"> <span class="n" style="color: #333333;">center</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #990000; font-weight: 600;">list</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">),</span> <span class="n" style="color: #333333;">fgroup</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">quartamine</span><span class="sh" style="color: #dd1144;">'</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1182" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1182
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1182" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">is_functional_group</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">tertamine</span><span class="sh" style="color: #dd1144;">'</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1183" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1183
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1183" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">data</span><span class="p">(</span><span class="n" style="color: #333333;">atoms</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="p">],</span> <span class="n" style="color: #333333;">orig_atoms</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333333;">a_orig</span><span class="p">,</span> <span class="p">],</span> <span class="n" style="color: #333333;">atoms_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333333;">a_orig_idx</span><span class="p">,</span> <span class="p">],</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">positive</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1184" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1184
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1184" class="line" lang="python"> <span class="n" style="color: #333333;">center</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #990000; font-weight: 600;">list</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">),</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1185" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1185
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1185" class="line" lang="python"> <span class="n" style="color: #333333;">fgroup</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">tertamine</span><span class="sh" style="color: #dd1144;">'</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1186" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1186
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1186" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">is_functional_group</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">sulfonium</span><span class="sh" style="color: #dd1144;">'</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1187" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1187
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1187" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">data</span><span class="p">(</span><span class="n" style="color: #333333;">atoms</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="p">],</span> <span class="n" style="color: #333333;">orig_atoms</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333333;">a_orig</span><span class="p">,</span> <span class="p">],</span> <span class="n" style="color: #333333;">atoms_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333333;">a_orig_idx</span><span class="p">,</span> <span class="p">],</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">positive</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1188" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1188
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1188" class="line" lang="python"> <span class="n" style="color: #333333;">center</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #990000; font-weight: 600;">list</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">),</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1189" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1189
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1189" class="line" lang="python"> <span class="n" style="color: #333333;">fgroup</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">sulfonium</span><span class="sh" style="color: #dd1144;">'</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1190" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1190
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1190" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">is_functional_group</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">phosphate</span><span class="sh" style="color: #dd1144;">'</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1191" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1191
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1191" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1192" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1192
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1192" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing_orig_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">a_orig_idx</span><span class="p">,</span> <span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1193" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1193
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1193" class="line" lang="python"> <span class="p">[</span><span class="n" style="color: #333333;">a_contributing</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">Atom</span><span class="p">(</span><span class="n" style="color: #333333;">neighbor</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">neighbor</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBAtomAtomIter</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">OBAtom</span><span class="p">)]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1194" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1194
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1194" class="line" lang="python"> <span class="p">[</span><span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">mapid</span><span class="p">(</span><span class="n" style="color: #333333;">neighbor</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">mtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">mtype</span><span class="p">,</span> <span class="n" style="color: #333333;">bsid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bsid</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1195" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1195
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1195" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">neighbor</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1196" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1196
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1196" class="line" lang="python"> <span class="n" style="color: #333333;">orig_contributing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">id_to_atom</span><span class="p">(</span><span class="n" style="color: #333333;">idx</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1197" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1197
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1197" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1198" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1198
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1198" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">data</span><span class="p">(</span><span class="n" style="color: #333333;">atoms</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing</span><span class="p">,</span> <span class="n" style="color: #333333;">orig_atoms</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">orig_contributing</span><span class="p">,</span> <span class="n" style="color: #333333;">atoms_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1199" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1199
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1199" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">negative</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1200" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1200
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1200" class="line" lang="python"> <span class="n" style="color: #333333;">center</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">,</span> <span class="n" style="color: #333333;">fgroup</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">phosphate</span><span class="sh" style="color: #dd1144;">'</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1201" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1201
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1201" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">is_functional_group</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">sulfonicacid</span><span class="sh" style="color: #dd1144;">'</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1202" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1202
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1202" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1203" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1203
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1203" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing_orig_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">a_orig_idx</span><span class="p">,</span> <span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1204
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1204" class="line" lang="python"> <span class="p">[</span><span class="n" style="color: #333333;">a_contributing</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">Atom</span><span class="p">(</span><span class="n" style="color: #333333;">neighbor</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">neighbor</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBAtomAtomIter</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">OBAtom</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1205" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1205
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1205" class="line" lang="python"> <span class="n" style="color: #333333;">neighbor</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetAtomicNum</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">8</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1206" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1206
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1206" class="line" lang="python"> <span class="p">[</span><span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">mapid</span><span class="p">(</span><span class="n" style="color: #333333;">neighbor</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">mtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">mtype</span><span class="p">,</span> <span class="n" style="color: #333333;">bsid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bsid</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1207" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1207
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1207" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">neighbor</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1208" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1208
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1208" class="line" lang="python"> <span class="n" style="color: #333333;">orig_contributing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">id_to_atom</span><span class="p">(</span><span class="n" style="color: #333333;">idx</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1209" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1209
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1209" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1210" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1210
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1210" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">data</span><span class="p">(</span><span class="n" style="color: #333333;">atoms</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing</span><span class="p">,</span> <span class="n" style="color: #333333;">orig_atoms</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">orig_contributing</span><span class="p">,</span> <span class="n" style="color: #333333;">atoms_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1211" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1211
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1211" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">negative</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1212" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1212
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1212" class="line" lang="python"> <span class="n" style="color: #333333;">center</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">,</span> <span class="n" style="color: #333333;">fgroup</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">sulfonicacid</span><span class="sh" style="color: #dd1144;">'</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1213" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1213
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1213" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">is_functional_group</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">sulfate</span><span class="sh" style="color: #dd1144;">'</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1214" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1214
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1214" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1215" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1215
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1215" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing_orig_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">a_orig_idx</span><span class="p">,</span> <span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1216" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1216
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1216" class="line" lang="python"> <span class="p">[</span><span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">mapid</span><span class="p">(</span><span class="n" style="color: #333333;">neighbor</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">mtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">mtype</span><span class="p">,</span> <span class="n" style="color: #333333;">bsid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bsid</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1217" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1217
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1217" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">neighbor</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1218" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1218
</td>
<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1218" class="line" lang="python"> <span class="p">[</span><span class="n" style="color: #333333;">a_contributing</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">Atom</span><span class="p">(</span><span class="n" style="color: #333333;">neighbor</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">neighbor</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBAtomAtomIter</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">OBAtom</span><span class="p">)]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1219" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1219
</td>
<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1219" class="line" lang="python"> <span class="n" style="color: #333333;">orig_contributing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">id_to_atom</span><span class="p">(</span><span class="n" style="color: #333333;">idx</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1220" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1220
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1220" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1221" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1221
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1221" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">data</span><span class="p">(</span><span class="n" style="color: #333333;">atoms</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing</span><span class="p">,</span> <span class="n" style="color: #333333;">orig_atoms</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">orig_contributing</span><span class="p">,</span> <span class="n" style="color: #333333;">atoms_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1222" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1222
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1222" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">negative</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1223" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1223
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1223" class="line" lang="python"> <span class="n" style="color: #333333;">center</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">,</span> <span class="n" style="color: #333333;">fgroup</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">sulfate</span><span class="sh" style="color: #dd1144;">'</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1224" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1224
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1224" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">is_functional_group</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">carboxylate</span><span class="sh" style="color: #dd1144;">'</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1225" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1225
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1225" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">Atom</span><span class="p">(</span><span class="n" style="color: #333333;">neighbor</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">neighbor</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBAtomAtomIter</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">OBAtom</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1226" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1226
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1226" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">neighbor</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetAtomicNum</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">8</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1227" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1227
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1227" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing_orig_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">mapid</span><span class="p">(</span><span class="n" style="color: #333333;">neighbor</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">mtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">mtype</span><span class="p">,</span> <span class="n" style="color: #333333;">bsid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bsid</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1228" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1228
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1228" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">neighbor</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1229" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1229
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1229" class="line" lang="python"> <span class="n" style="color: #333333;">orig_contributing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">id_to_atom</span><span class="p">(</span><span class="n" style="color: #333333;">idx</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1230" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1230
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1230" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1231" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1231
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1231" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">data</span><span class="p">(</span><span class="n" style="color: #333333;">atoms</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing</span><span class="p">,</span> <span class="n" style="color: #333333;">orig_atoms</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">orig_contributing</span><span class="p">,</span> <span class="n" style="color: #333333;">atoms_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1232" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1232
</td>
<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1232" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">negative</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1233" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1233
</td>
<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1233" class="line" lang="python"> <span class="n" style="color: #333333;">center</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #990000; font-weight: 600;">centroid</span><span class="p">([</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing</span><span class="p">]),</span> <span class="n" style="color: #333333;">fgroup</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">carboxylate</span><span class="sh" style="color: #dd1144;">'</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1234" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1234
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1234" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">is_functional_group</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">guanidine</span><span class="sh" style="color: #dd1144;">'</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1235" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1235
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1235" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">Atom</span><span class="p">(</span><span class="n" style="color: #333333;">neighbor</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">neighbor</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBAtomAtomIter</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">OBAtom</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1236" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1236
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1236" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">neighbor</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetAtomicNum</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">7</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1237" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1237
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1237" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing_orig_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">mapid</span><span class="p">(</span><span class="n" style="color: #333333;">neighbor</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">mtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">mtype</span><span class="p">,</span> <span class="n" style="color: #333333;">bsid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bsid</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1238" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1238
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1238" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">neighbor</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1239" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1239
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1239" class="line" lang="python"> <span class="n" style="color: #333333;">orig_contributing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">id_to_atom</span><span class="p">(</span><span class="n" style="color: #333333;">idx</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1240" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1240
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1240" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1241" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1241
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1241" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">data</span><span class="p">(</span><span class="n" style="color: #333333;">atoms</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing</span><span class="p">,</span> <span class="n" style="color: #333333;">orig_atoms</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">orig_contributing</span><span class="p">,</span> <span class="n" style="color: #333333;">atoms_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1242" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1242
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1242" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">positive</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1243" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1243
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<td class="new_line diff-line-num old" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1243" class="line" lang="python"> <span class="n" style="color: #333333;">center</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">,</span> <span class="n" style="color: #333333;">fgroup</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">guanidine</span><span class="sh" style="color: #dd1144;">'</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1204" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1204
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1204" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">INTRA</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">PEPTIDES</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">CHAINS</span><span class="p">):</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1205" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1205
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1205" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">all_atoms</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1206" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1206
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1206" class="line" lang="python"> <span class="n" style="color: #333333;">a_orig_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">mapid</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">mtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">mtype</span><span class="p">,</span> <span class="n" style="color: #333333;">bsid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bsid</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1207" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1207
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1207" class="line" lang="python"> <span class="n" style="color: #333333;">a_orig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">id_to_atom</span><span class="p">(</span><span class="n" style="color: #333333;">a_orig_idx</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1208" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1208
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1208" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">is_functional_group</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">quartamine</span><span class="sh" style="color: #dd1144;">'</span><span class="p">):</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1209" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1209
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1209" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">data</span><span class="p">(</span><span class="n" style="color: #333333;">atoms</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="p">],</span> <span class="n" style="color: #333333;">orig_atoms</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333333;">a_orig</span><span class="p">,</span> <span class="p">],</span> <span class="n" style="color: #333333;">atoms_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333333;">a_orig_idx</span><span class="p">,</span> <span class="p">],</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">positive</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1210" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1210
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1210" class="line" lang="python"> <span class="n" style="color: #333333;">center</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #990000; font-weight: 600;">list</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">),</span> <span class="n" style="color: #333333;">fgroup</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">quartamine</span><span class="sh" style="color: #dd1144;">'</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1211" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1211
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1211" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">is_functional_group</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">tertamine</span><span class="sh" style="color: #dd1144;">'</span><span class="p">):</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1212" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1212
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1212" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">data</span><span class="p">(</span><span class="n" style="color: #333333;">atoms</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="p">],</span> <span class="n" style="color: #333333;">orig_atoms</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333333;">a_orig</span><span class="p">,</span> <span class="p">],</span> <span class="n" style="color: #333333;">atoms_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333333;">a_orig_idx</span><span class="p">,</span> <span class="p">],</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">positive</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1213" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1213
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1213" class="line" lang="python"> <span class="n" style="color: #333333;">center</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #990000; font-weight: 600;">list</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">),</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1214" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1214
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1214" class="line" lang="python"> <span class="n" style="color: #333333;">fgroup</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">tertamine</span><span class="sh" style="color: #dd1144;">'</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1215" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1215
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1215" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">is_functional_group</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">sulfonium</span><span class="sh" style="color: #dd1144;">'</span><span class="p">):</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1216" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1216
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1216" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">data</span><span class="p">(</span><span class="n" style="color: #333333;">atoms</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="p">],</span> <span class="n" style="color: #333333;">orig_atoms</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333333;">a_orig</span><span class="p">,</span> <span class="p">],</span> <span class="n" style="color: #333333;">atoms_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333333;">a_orig_idx</span><span class="p">,</span> <span class="p">],</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">positive</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1217" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1217
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1217" class="line" lang="python"> <span class="n" style="color: #333333;">center</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #990000; font-weight: 600;">list</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">),</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1218" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1218
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1218" class="line" lang="python"> <span class="n" style="color: #333333;">fgroup</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">sulfonium</span><span class="sh" style="color: #dd1144;">'</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1219" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1219
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1219" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">is_functional_group</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">phosphate</span><span class="sh" style="color: #dd1144;">'</span><span class="p">):</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1220" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1220
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1220" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1221" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1221
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1221" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing_orig_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">a_orig_idx</span><span class="p">,</span> <span class="p">]</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1222" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1222
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1222" class="line" lang="python"> <span class="p">[</span><span class="n" style="color: #333333;">a_contributing</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">Atom</span><span class="p">(</span><span class="n" style="color: #333333;">neighbor</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">neighbor</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBAtomAtomIter</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">OBAtom</span><span class="p">)]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1223" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1223
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1223" class="line" lang="python"> <span class="p">[</span><span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">mapid</span><span class="p">(</span><span class="n" style="color: #333333;">neighbor</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">mtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">mtype</span><span class="p">,</span> <span class="n" style="color: #333333;">bsid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bsid</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1224" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1224
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1224" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">neighbor</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing</span><span class="p">]</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1225" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1225
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1225" class="line" lang="python"> <span class="n" style="color: #333333;">orig_contributing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">id_to_atom</span><span class="p">(</span><span class="n" style="color: #333333;">idx</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1226" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1226
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1226" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1227" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1227
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1227" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">data</span><span class="p">(</span><span class="n" style="color: #333333;">atoms</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing</span><span class="p">,</span> <span class="n" style="color: #333333;">orig_atoms</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">orig_contributing</span><span class="p">,</span> <span class="n" style="color: #333333;">atoms_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1228" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1228
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1228" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">negative</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1229" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1229
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1229" class="line" lang="python"> <span class="n" style="color: #333333;">center</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">,</span> <span class="n" style="color: #333333;">fgroup</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">phosphate</span><span class="sh" style="color: #dd1144;">'</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1230" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1230
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1230" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">is_functional_group</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">sulfonicacid</span><span class="sh" style="color: #dd1144;">'</span><span class="p">):</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1231" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1231
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1231" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="p">]</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1232" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1232
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1232" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing_orig_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">a_orig_idx</span><span class="p">,</span> <span class="p">]</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1233" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1233
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1233" class="line" lang="python"> <span class="p">[</span><span class="n" style="color: #333333;">a_contributing</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">Atom</span><span class="p">(</span><span class="n" style="color: #333333;">neighbor</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">neighbor</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBAtomAtomIter</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">OBAtom</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1234" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1234
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1234" class="line" lang="python"> <span class="n" style="color: #333333;">neighbor</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetAtomicNum</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">8</span><span class="p">]</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1235" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1235
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1235" class="line" lang="python"> <span class="p">[</span><span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">mapid</span><span class="p">(</span><span class="n" style="color: #333333;">neighbor</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">mtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">mtype</span><span class="p">,</span> <span class="n" style="color: #333333;">bsid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bsid</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1236" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1236
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1236" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">neighbor</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1237
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1237" class="line" lang="python"> <span class="n" style="color: #333333;">orig_contributing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">id_to_atom</span><span class="p">(</span><span class="n" style="color: #333333;">idx</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1238" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1238
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1238" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1239" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1239
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1239" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">data</span><span class="p">(</span><span class="n" style="color: #333333;">atoms</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing</span><span class="p">,</span> <span class="n" style="color: #333333;">orig_atoms</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">orig_contributing</span><span class="p">,</span> <span class="n" style="color: #333333;">atoms_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1240" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1240
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1240" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">negative</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1241" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1241
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1241" class="line" lang="python"> <span class="n" style="color: #333333;">center</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">,</span> <span class="n" style="color: #333333;">fgroup</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">sulfonicacid</span><span class="sh" style="color: #dd1144;">'</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1242" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1242
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1242" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">is_functional_group</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">sulfate</span><span class="sh" style="color: #dd1144;">'</span><span class="p">):</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1243" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1243
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1243" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="p">]</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1244
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1244" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing_orig_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">a_orig_idx</span><span class="p">,</span> <span class="p">]</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1245" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1245
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1245" class="line" lang="python"> <span class="p">[</span><span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">mapid</span><span class="p">(</span><span class="n" style="color: #333333;">neighbor</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">mtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">mtype</span><span class="p">,</span> <span class="n" style="color: #333333;">bsid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bsid</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1246" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1246
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1246" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">neighbor</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1247" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1247
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1247" class="line" lang="python"> <span class="p">[</span><span class="n" style="color: #333333;">a_contributing</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">Atom</span><span class="p">(</span><span class="n" style="color: #333333;">neighbor</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">neighbor</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBAtomAtomIter</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">OBAtom</span><span class="p">)]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1248" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1248
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1248" class="line" lang="python"> <span class="n" style="color: #333333;">orig_contributing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">id_to_atom</span><span class="p">(</span><span class="n" style="color: #333333;">idx</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">]</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1249" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1249
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1249" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1250" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1250
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1250" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">data</span><span class="p">(</span><span class="n" style="color: #333333;">atoms</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing</span><span class="p">,</span> <span class="n" style="color: #333333;">orig_atoms</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">orig_contributing</span><span class="p">,</span> <span class="n" style="color: #333333;">atoms_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1251" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1251
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1251" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">negative</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1252" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1252
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1252" class="line" lang="python"> <span class="n" style="color: #333333;">center</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">,</span> <span class="n" style="color: #333333;">fgroup</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">sulfate</span><span class="sh" style="color: #dd1144;">'</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1253" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1253
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1253" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">is_functional_group</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">carboxylate</span><span class="sh" style="color: #dd1144;">'</span><span class="p">):</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1254" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1254
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1254" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">Atom</span><span class="p">(</span><span class="n" style="color: #333333;">neighbor</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">neighbor</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBAtomAtomIter</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">OBAtom</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1255" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1255
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1255" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">neighbor</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetAtomicNum</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">8</span><span class="p">]</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1256" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1256
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1256" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing_orig_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">mapid</span><span class="p">(</span><span class="n" style="color: #333333;">neighbor</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">mtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">mtype</span><span class="p">,</span> <span class="n" style="color: #333333;">bsid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bsid</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1257" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1257
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1257" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">neighbor</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing</span><span class="p">]</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1258" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1258
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1258" class="line" lang="python"> <span class="n" style="color: #333333;">orig_contributing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">id_to_atom</span><span class="p">(</span><span class="n" style="color: #333333;">idx</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">]</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1259" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1259
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1259" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1260" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1260
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1260" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">data</span><span class="p">(</span><span class="n" style="color: #333333;">atoms</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing</span><span class="p">,</span> <span class="n" style="color: #333333;">orig_atoms</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">orig_contributing</span><span class="p">,</span> <span class="n" style="color: #333333;">atoms_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1261" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1261
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1261" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">negative</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1262" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1262
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1262" class="line" lang="python"> <span class="n" style="color: #333333;">center</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #990000; font-weight: 600;">centroid</span><span class="p">([</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing</span><span class="p">]),</span> <span class="n" style="color: #333333;">fgroup</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">carboxylate</span><span class="sh" style="color: #dd1144;">'</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1263" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1263
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1263" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">is_functional_group</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">guanidine</span><span class="sh" style="color: #dd1144;">'</span><span class="p">):</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1264" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1264
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1264" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">Atom</span><span class="p">(</span><span class="n" style="color: #333333;">neighbor</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">neighbor</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBAtomAtomIter</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">OBAtom</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1265" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1265
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1265" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">neighbor</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetAtomicNum</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">7</span><span class="p">]</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1266" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1266
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1266" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing_orig_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">mapid</span><span class="p">(</span><span class="n" style="color: #333333;">neighbor</span><span class="p">.</span><span class="n" style="color: #333333;">idx</span><span class="p">,</span> <span class="n" style="color: #333333;">mtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">mtype</span><span class="p">,</span> <span class="n" style="color: #333333;">bsid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bsid</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1267" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1267
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1267" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">neighbor</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing</span><span class="p">]</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1268" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1268
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1268" class="line" lang="python"> <span class="n" style="color: #333333;">orig_contributing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">id_to_atom</span><span class="p">(</span><span class="n" style="color: #333333;">idx</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1269" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1269
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1269" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1270" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1270
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1270" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">data</span><span class="p">(</span><span class="n" style="color: #333333;">atoms</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing</span><span class="p">,</span> <span class="n" style="color: #333333;">orig_atoms</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">orig_contributing</span><span class="p">,</span> <span class="n" style="color: #333333;">atoms_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1271" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1271
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1271" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">positive</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1272" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1272
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1272" class="line" lang="python"> <span class="n" style="color: #333333;">center</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span><span class="p">,</span> <span class="n" style="color: #333333;">fgroup</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">guanidine</span><span class="sh" style="color: #dd1144;">'</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1273" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1273
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1273" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1274" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1274
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1274" class="line" lang="python"> <span class="sh" style="color: #dd1144;">"""</span><span class="s" style="color: #dd1144;">We have peptide/protein chain as ligand</span><span class="sh" style="color: #dd1144;">"""</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1275" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1275
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1275" class="line" lang="python"> <span class="sh" style="color: #dd1144;">"""</span><span class="s" style="color: #dd1144;">Looks for positive charges in arginine, histidine or lysine, for negative in aspartic and glutamic acid.</span><span class="sh" style="color: #dd1144;">"""</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1276" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1276
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1276" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">res</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBResidueIter</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">molecule</span><span class="p">.</span><span class="n" style="color: #333333;">OBMol</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1277" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1277
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1277" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">INTRA</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999999;">None</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1278" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1278
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1278" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">res</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetChain</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">INTRA</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1279" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1279
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1279" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1280" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1280
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1280" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1281" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1281
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1281" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing_orig_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1282" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1282
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1282" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">res</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetName</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">ARG</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">HIS</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">LYS</span><span class="sh" style="color: #dd1144;">'</span><span class="p">):</span> <span class="c1" style="color: #999988; font-style: italic;"># Arginine, Histidine or Lysine have charged sidechains</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1283" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1283
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1283" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBResidueAtomIter</span><span class="p">(</span><span class="n" style="color: #333333;">res</span><span class="p">):</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1284" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1284
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1284" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetType</span><span class="p">().</span><span class="nf" style="color: #990000; font-weight: 600;">startswith</span><span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">N</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333333;">res</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetAtomProperty</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="mi" style="color: #009999;">8</span><span class="p">)</span> \</span>
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<td class="new_line diff-line-num new" data-linenumber="1285" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1285
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1285" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">mapid</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetIdx</span><span class="p">(),</span> <span class="n" style="color: #333333;">mtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">mtype</span><span class="p">,</span> <span class="n" style="color: #333333;">bsid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bsid</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">altconf</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1286" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1286
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1286" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">Atom</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1287" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1287
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1287" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">mapid</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetIdx</span><span class="p">(),</span> <span class="n" style="color: #333333;">mtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">mtype</span><span class="p">,</span> <span class="n" style="color: #333333;">bsid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bsid</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1288" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1288
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1288" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nf" style="color: #990000; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333333;">a_contributing</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">0</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1289" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1289
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1289" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">data</span><span class="p">(</span><span class="n" style="color: #333333;">atoms</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1290" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1290
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1290" class="line" lang="python"> <span class="n" style="color: #333333;">orig_atoms</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">id_to_atom</span><span class="p">(</span><span class="n" style="color: #333333;">idx</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">],</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1291" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1291
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1291" class="line" lang="python"> <span class="n" style="color: #333333;">atoms_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1292" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1292
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1292" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">positive</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1293" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1293
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1293" class="line" lang="python"> <span class="n" style="color: #333333;">center</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #990000; font-weight: 600;">centroid</span><span class="p">([</span><span class="n" style="color: #333333;">ac</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">ac</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing</span><span class="p">]),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1294" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1294
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1294" class="line" lang="python"> <span class="n" style="color: #333333;">fgroup</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">res</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetName</span><span class="p">()</span><span class="o" style="font-weight: 600;">+</span><span class="nf" style="color: #990000; font-weight: 600;">str</span><span class="p">(</span><span class="n" style="color: #333333;">res</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetNum</span><span class="p">())</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">res</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetChain</span><span class="p">()))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1295" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1295
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1295" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">res</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetName</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">GLU</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">ASP</span><span class="sh" style="color: #dd1144;">'</span><span class="p">):</span> <span class="c1" style="color: #999988; font-style: italic;"># Aspartic or Glutamic Acid</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1296" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1296
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1296" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBResidueAtomIter</span><span class="p">(</span><span class="n" style="color: #333333;">res</span><span class="p">):</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1297" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1297
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1297" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetType</span><span class="p">().</span><span class="nf" style="color: #990000; font-weight: 600;">startswith</span><span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">O</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333333;">res</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetAtomProperty</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">,</span> <span class="mi" style="color: #009999;">8</span><span class="p">)</span> \</span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1298" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1298
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1298" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">mapid</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetIdx</span><span class="p">(),</span> <span class="n" style="color: #333333;">mtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">mtype</span><span class="p">,</span> <span class="n" style="color: #333333;">bsid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bsid</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">altconf</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1299" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1299
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1299" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">Atom</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1300" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1300
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1300" class="line" lang="python"> <span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">mapid</span><span class="p">(</span><span class="n" style="color: #333333;">a</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetIdx</span><span class="p">(),</span> <span class="n" style="color: #333333;">mtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">mtype</span><span class="p">,</span> <span class="n" style="color: #333333;">bsid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">bsid</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1301" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1301
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1301" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nf" style="color: #990000; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333333;">a_contributing</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #009999;">0</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1302" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1302
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1302" class="line" lang="python"> <span class="n" style="color: #333333;">a_set</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">append</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">data</span><span class="p">(</span><span class="n" style="color: #333333;">atoms</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1303" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1303
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1303" class="line" lang="python"> <span class="n" style="color: #333333;">orig_atoms</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">Mapper</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">id_to_atom</span><span class="p">(</span><span class="n" style="color: #333333;">idx</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">],</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1304" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1304
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1304" class="line" lang="python"> <span class="n" style="color: #333333;">atoms_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">a_contributing_orig_idx</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1305" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1305
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1305" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">negative</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1306" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1306
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1306" class="line" lang="python"> <span class="n" style="color: #333333;">center</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #990000; font-weight: 600;">centroid</span><span class="p">([</span><span class="n" style="color: #333333;">ac</span><span class="p">.</span><span class="n" style="color: #333333;">coords</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">ac</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">a_contributing</span><span class="p">]),</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1307" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1307
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1307" class="line" lang="python"> <span class="n" style="color: #333333;">fgroup</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">res</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetName</span><span class="p">()</span><span class="o" style="font-weight: 600;">+</span><span class="nf" style="color: #990000; font-weight: 600;">str</span><span class="p">(</span><span class="n" style="color: #333333;">res</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetNum</span><span class="p">())</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">res</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">GetChain</span><span class="p">()))</span></span>
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<td class="old_line diff-line-num" data-linenumber="1244" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1244
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<td class="new_line diff-line-num" data-linenumber="1308" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1308
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1308" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">a_set</span></span>
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<td class="old_line diff-line-num" data-linenumber="1245" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1245
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<td class="new_line diff-line-num" data-linenumber="1309" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1309
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1309" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="1246" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1246
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<td class="new_line diff-line-num" data-linenumber="1310" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1310
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1310" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #990000; font-weight: 600;">find_metal_binding</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">,</span> <span class="n" style="color: #333333;">lig_atoms</span><span class="p">,</span> <span class="n" style="color: #333333;">water_oxygens</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1512" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1576" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1512,9 +1576,9 @@ class PDBComplex:</td>
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<td class="old_line diff-line-num" data-linenumber="1512" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1512
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<td class="new_line diff-line-num" data-linenumber="1576" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1576
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1576" class="line" lang="python"> <span class="n" style="color: #333333;">rescentroid</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">centroid</span><span class="p">([(</span><span class="n" style="color: #333333;">atm</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">x</span><span class="p">(),</span> <span class="n" style="color: #333333;">atm</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">y</span><span class="p">(),</span> <span class="n" style="color: #333333;">atm</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">z</span><span class="p">())</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">atm</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">pybel</span><span class="p">.</span><span class="n" style="color: #333333;">ob</span><span class="p">.</span><span class="nc" style="color: #445588; font-weight: 600;">OBResidueAtomIter</span><span class="p">(</span><span class="n" style="color: #333333;">res</span><span class="p">)])</span></span>
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<td class="old_line diff-line-num" data-linenumber="1513" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1513
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<td class="new_line diff-line-num" data-linenumber="1577" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1577
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1577" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Check geometry</span></span>
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<td class="old_line diff-line-num" data-linenumber="1514" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1514
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<td class="new_line diff-line-num" data-linenumber="1578" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1578
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1578" class="line" lang="python"> <span class="n" style="color: #333333;">near_enough</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999999;">True</span> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #990000; font-weight: 600;">euclidean3d</span><span class="p">(</span><span class="n" style="color: #333333;">rescentroid</span><span class="p">,</span> <span class="n" style="color: #333333;">ligcentroid</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333333;">cutoff</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999999;">False</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1515" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1515
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<td class="new_line diff-line-num old" data-linenumber="1579" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1515" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;">#<span class="idiff left right deletion" style="background-color: #fac5cd;"> Check chain membership</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="1516" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1516
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<td class="new_line diff-line-num old" data-linenumber="1579" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1516" class="line" lang="python"> <span class="n" style="color: #333333;">restrict<span class="idiff left deletion" style="background-color: #fac5cd;">ed_chain</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">=</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="bp" style="color: #999999;"><span class="idiff deletion" style="background-color: #fac5cd;">True</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="k" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">if</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">res</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="nc" style="color: #445588; font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">GetChain</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">()</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="ow" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">in</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">config</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">PEPTIDES</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="k" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">else</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="bp" style="color: #999999;"><span class="idiff right deletion" style="background-color: #fac5cd;">False</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="1517" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1517
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<td class="new_line diff-line-num old" data-linenumber="1579" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1517" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">return </span><span class="p"><span class="idiff left deletion" style="background-color: #fac5cd;">(</span></span><span class="n" style="color: #333333;">near_enough</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">not</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;"><span class="idiff right deletion" style="background-color: #fac5cd;">restricted_chain</span></span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1518" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1579" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1579
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1579" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;">#<span class="idiff left right addition" style="background-color: #c7f0d2;">Todo: Test if properly working</span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="1580" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1580
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1580" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"><span class="idiff left addition" style="background-color: #c7f0d2;"># Add </span>restrict<span class="idiff right addition" style="background-color: #c7f0d2;">ion via chains flag</span></span></span>
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<td class="old_line diff-line-num new" data-linenumber="1518" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1581" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1581
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1581" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">near_enough</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nf" style="color: #990000; font-weight: 600;"><span class="idiff left addition" style="background-color: #c7f0d2;">residue_belongs_to_receptor</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">(</span></span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">res</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">config</span></span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="1518" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1518
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<td class="new_line diff-line-num" data-linenumber="1582" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1582
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1582" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="1519" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1519
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<td class="new_line diff-line-num" data-linenumber="1583" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1583
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1583" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #990000; font-weight: 600;">get_atom</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">,</span> <span class="n" style="color: #333333;">idx</span><span class="p">):</span></span>
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<td class="old_line diff-line-num" data-linenumber="1520" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1520
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<td class="new_line diff-line-num" data-linenumber="1584" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1584
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1584" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">atoms</span><span class="p">[</span><span class="n" style="color: #333333;">idx</span><span class="p">]</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1525" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1589" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -1525,4 +1589,4 @@ class PDBComplex:</td>
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<td class="old_line diff-line-num" data-linenumber="1525" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1525
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<td class="new_line diff-line-num" data-linenumber="1589" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1589
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1589" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="1526" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1526
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<td class="new_line diff-line-num" data-linenumber="1590" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1590
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1590" class="line" lang="python"> <span class="nd">@output_path.setter</span></span>
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<td class="old_line diff-line-num" data-linenumber="1527" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1527
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<td class="new_line diff-line-num" data-linenumber="1591" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1591
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1591" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #990000; font-weight: 600;">output_path</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">,</span> <span class="n" style="color: #333333;">path</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1528" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1528
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<td class="new_line diff-line-num old" data-linenumber="1592" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1528" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">_output_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">tilde_expansion</span><span class="p">(</span><span class="n" style="color: #333333;">path</span><span class="p">)</span></span></pre></td>
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<td class="old_line diff-line-num new" data-linenumber="1529" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1592" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1592
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1592" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="n" style="color: #333333;">_output_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #990000; font-weight: 600;">tilde_expansion</span><span class="p">(</span><span class="n" style="color: #333333;">path</span><span class="p">)</span></span></pre></td>
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<td class="new_line diff-line-num" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd"></td>
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<a href="https://salsa.debian.org/med-team/plip/-/compare/9408f2de4e28772642baaea5c38da321a843cb5e...987142df85e4487ee8693e3417f93cd5d85a962c#2525073c8fbdbd4c496cc540b74b251789f6c700"><strong style="font-weight: 600;">plip/test/test_literature_validated.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="232" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="232" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -232,6 +232,9 @@ class LiteratureValidatedTest(unittest.TestCase):</td>
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<td class="old_line diff-line-num" data-linenumber="232" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
232
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<td class="new_line diff-line-num" data-linenumber="232" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
232
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC232" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Water bridges to Lys307, Arg309 and 111 from phosphate groups</span></span>
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<td class="old_line diff-line-num" data-linenumber="233" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
233
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<td class="new_line diff-line-num" data-linenumber="233" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
233
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC233" class="line" lang="python"> <span class="n" style="color: #333333;">waterbridges</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333333;">wb</span><span class="p">.</span><span class="n" style="color: #333333;">resnr</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">wb</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">s</span><span class="p">.</span><span class="n" style="color: #333333;">water_bridges</span><span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="234" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
234
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<td class="new_line diff-line-num" data-linenumber="234" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
234
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC234" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Water bridge to 60 not found due to prioritization</span></span>
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<td class="old_line diff-line-num new" data-linenumber="235" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="235" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
235
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC235" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Philipp: No interaction to 111 due to prioritization/omega angle compute correction</span></span>
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<td class="old_line diff-line-num new" data-linenumber="235" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="236" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
236
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC236" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># --> Now two interactions with ASN92 which were before only one that is not checked here</span></span>
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237
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC237" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># self.assertTrue({307, 309}.issubset(waterbridges))</span></span>
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<td class="old_line diff-line-num" data-linenumber="235" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
235
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<td class="new_line diff-line-num" data-linenumber="238" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
238
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC238" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">assertTrue</span><span class="p">({</span><span class="mi" style="color: #009999;">307</span><span class="p">,</span> <span class="mi" style="color: #009999;">309</span><span class="p">,</span> <span class="mi" style="color: #009999;">111</span><span class="p">}.</span><span class="nf" style="color: #990000; font-weight: 600;">issubset</span><span class="p">(</span><span class="n" style="color: #333333;">waterbridges</span><span class="p">))</span></span>
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<td class="old_line diff-line-num" data-linenumber="236" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
236
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<td class="new_line diff-line-num" data-linenumber="239" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
239
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC239" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># pi-stacking interaction with Phe209</span></span>
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<td class="old_line diff-line-num" data-linenumber="237" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
237
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<td class="new_line diff-line-num" data-linenumber="240" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
240
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC240" class="line" lang="python"> <span class="n" style="color: #333333;">pistackres</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333333;">pistack</span><span class="p">.</span><span class="n" style="color: #333333;">resnr</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">pistack</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">s</span><span class="p">.</span><span class="n" style="color: #333333;">pistacking</span><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="312" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="315" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -312,6 +315,8 @@ class LiteratureValidatedTest(unittest.TestCase):</td>
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<td class="old_line diff-line-num" data-linenumber="312" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
312
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<td class="new_line diff-line-num" data-linenumber="315" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
315
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC315" class="line" lang="python"> <span class="n" style="color: #333333;">tmpmol</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">characterize_complex</span><span class="p">(</span><span class="n" style="color: #333333;">ligand</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="313" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
313
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<td class="new_line diff-line-num" data-linenumber="316" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
316
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC316" class="line" lang="python"> <span class="n" style="color: #333333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">tmpmol</span><span class="p">.</span><span class="n" style="color: #333333;">interaction_sets</span><span class="p">[</span><span class="n" style="color: #333333;">bsid</span><span class="p">]</span></span>
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<td class="old_line diff-line-num" data-linenumber="314" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
314
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<td class="new_line diff-line-num" data-linenumber="317" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
317
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC317" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Hydrogen bonds to Ala609</span></span>
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<td class="old_line diff-line-num new" data-linenumber="315" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="318" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
318
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC318" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Philipp: In this case the protein is the acceptor</span></span>
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<td class="old_line diff-line-num new" data-linenumber="315" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="319" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
319
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC319" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># hbonds = {hbond.resnr for hbond in s.hbonds_pdon + s.hbonds_ldon}</span></span>
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<td class="old_line diff-line-num" data-linenumber="315" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
315
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<td class="new_line diff-line-num" data-linenumber="320" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
320
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC320" class="line" lang="python"> <span class="n" style="color: #333333;">hbonds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333333;">hbond</span><span class="p">.</span><span class="n" style="color: #333333;">resnr</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">hbond</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">s</span><span class="p">.</span><span class="n" style="color: #333333;">hbonds_pdon</span><span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="316" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
316
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<td class="new_line diff-line-num" data-linenumber="321" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
321
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC321" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">assertTrue</span><span class="p">({</span><span class="mi" style="color: #009999;">609</span><span class="p">}.</span><span class="nf" style="color: #990000; font-weight: 600;">issubset</span><span class="p">(</span><span class="n" style="color: #333333;">hbonds</span><span class="p">))</span></span>
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<td class="old_line diff-line-num" data-linenumber="317" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
317
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<td class="new_line diff-line-num" data-linenumber="322" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
322
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC322" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Saltbridge to Asp513</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="515" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="520" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -515,12 +520,16 @@ class LiteratureValidatedTest(unittest.TestCase):</td>
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<td class="old_line diff-line-num" data-linenumber="515" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
515
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<td class="new_line diff-line-num" data-linenumber="520" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
520
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC520" class="line" lang="python"> <span class="n" style="color: #333333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">tmpmol</span><span class="p">.</span><span class="n" style="color: #333333;">interaction_sets</span><span class="p">[</span><span class="n" style="color: #333333;">bsid</span><span class="p">]</span></span>
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<td class="old_line diff-line-num" data-linenumber="516" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
516
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<td class="new_line diff-line-num" data-linenumber="521" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
521
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC521" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;">#@todo Publication show hydrogen bond interactions for Gly219</span></span>
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<td class="old_line diff-line-num" data-linenumber="517" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
517
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<td class="new_line diff-line-num" data-linenumber="522" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
522
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC522" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Hydrogen bonds to Ser190, Ser195, Gly219 and Asp189</span></span>
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<td class="old_line diff-line-num new" data-linenumber="518" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="523" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
523
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC523" class="line" lang="python"></span>
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<td class="old_line diff-line-num new" data-linenumber="518" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="524" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
524
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC524" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;">#Philipp: Only Hbont to 189 + 195 are possible. Else, donors would be included in multiple interactions</span></span>
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<td class="old_line diff-line-num" data-linenumber="518" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
518
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<td class="new_line diff-line-num" data-linenumber="525" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
525
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC525" class="line" lang="python"> <span class="n" style="color: #333333;">hbonds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333333;">hbond</span><span class="p">.</span><span class="n" style="color: #333333;">resnr</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">hbond</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">s</span><span class="p">.</span><span class="n" style="color: #333333;">hbonds_pdon</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">s</span><span class="p">.</span><span class="n" style="color: #333333;">hbonds_ldon</span><span class="p">}</span></span>
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519
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<td class="new_line diff-line-num old" data-linenumber="526" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC519" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">assertTrue</span><span class="p">({</span><span class="mi" style="color: #009999;">189</span><span class="p">,</span> <span class="mi" style="color: #009999;">190</span><span class="p">,</span> <span class="mi" style="color: #009999;">195</span><span class="p">}.</span><span class="nf" style="color: #990000; font-weight: 600;">issubset</span><span class="p">(</span><span class="n" style="color: #333333;">hbonds</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="520" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="526" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
526
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC526" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;">#self.assertTrue({189, 190, 195}.issubset(hbonds))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="527" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
527
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC527" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">assertTrue</span><span class="p">({</span><span class="mi" style="color: #009999;">189</span><span class="p">,</span> <span class="mi" style="color: #009999;">195</span><span class="p">}.</span><span class="nf" style="color: #990000; font-weight: 600;">issubset</span><span class="p">(</span><span class="n" style="color: #333333;">hbonds</span><span class="p">))</span></span>
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<td class="old_line diff-line-num" data-linenumber="520" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
520
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<td class="new_line diff-line-num" data-linenumber="528" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
528
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC528" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Water bridges to Ser190 and Val227</span></span>
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<td class="old_line diff-line-num" data-linenumber="521" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
521
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<td class="new_line diff-line-num" data-linenumber="529" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
529
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC529" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Water bridge to 190 not detected due to prioritization</span></span>
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<td class="old_line diff-line-num new" data-linenumber="522" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="530" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
530
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC530" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Philipp: Listen to the comment above</span></span>
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522
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<td class="new_line diff-line-num" data-linenumber="531" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
531
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC531" class="line" lang="python"> <span class="n" style="color: #333333;">waterbridges</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333333;">wb</span><span class="p">.</span><span class="n" style="color: #333333;">resnr</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">wb</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">s</span><span class="p">.</span><span class="n" style="color: #333333;">water_bridges</span><span class="p">}</span></span>
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523
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<td class="new_line diff-line-num old" data-linenumber="532" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC523" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">assertTrue</span><span class="p">({</span><span class="mi" style="color: #009999;">227</span><span class="p">}.</span><span class="nf" style="color: #990000; font-weight: 600;">issubset</span><span class="p">(</span><span class="n" style="color: #333333;">waterbridges</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="524" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="532" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
532
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC532" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"><span class="idiff left right addition" style="background-color: #c7f0d2;">#</span>self.assertTrue({227}.issubset(waterbridges))</span></span>
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<td class="old_line diff-line-num" data-linenumber="524" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
524
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<td class="new_line diff-line-num" data-linenumber="533" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
533
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC533" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># hydrophobic interaction of Leu99</span></span>
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525
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<td class="new_line diff-line-num" data-linenumber="534" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
534
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC534" class="line" lang="python"> <span class="n" style="color: #333333;">hydrophobics</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333333;">hydrophobic</span><span class="p">.</span><span class="n" style="color: #333333;">resnr</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">hydrophobic</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">s</span><span class="p">.</span><span class="n" style="color: #333333;">all_hydrophobic_contacts</span><span class="p">}</span></span>
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526
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<td class="new_line diff-line-num" data-linenumber="535" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
535
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC535" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">assertTrue</span><span class="p">({</span><span class="mi" style="color: #009999;">99</span><span class="p">}.</span><span class="nf" style="color: #990000; font-weight: 600;">issubset</span><span class="p">(</span><span class="n" style="color: #333333;">hydrophobics</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="587" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="596" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -587,6 +596,8 @@ class LiteratureValidatedTest(unittest.TestCase):</td>
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<td class="old_line diff-line-num" data-linenumber="587" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
587
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<td class="new_line diff-line-num" data-linenumber="596" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
596
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC596" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Water bridges to Trp137</span></span>
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<td class="old_line diff-line-num" data-linenumber="588" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
588
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<td class="new_line diff-line-num" data-linenumber="597" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
597
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC597" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># res nr 52 mentioned in alternative conformation not considered</span></span>
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589
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598
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC598" class="line" lang="python"> <span class="n" style="color: #333333;">waterbridges</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333333;">wb</span><span class="p">.</span><span class="n" style="color: #333333;">resnr</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">wb</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">s</span><span class="p">.</span><span class="n" style="color: #333333;">water_bridges</span><span class="p">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="590" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="599" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
599
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC599" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Philipp: Now detects two wbridges with ARG57 because the omega angles are better</span></span>
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<td class="old_line diff-line-num new" data-linenumber="590" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="600" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
600
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC600" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;">#self.assertTrue({57}.issubset(waterbridges))</span></span>
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<td class="old_line diff-line-num" data-linenumber="590" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
590
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<td class="new_line diff-line-num" data-linenumber="601" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
601
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC601" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">assertTrue</span><span class="p">({</span><span class="mi" style="color: #009999;">322</span><span class="p">}.</span><span class="nf" style="color: #990000; font-weight: 600;">issubset</span><span class="p">(</span><span class="n" style="color: #333333;">waterbridges</span><span class="p">))</span></span>
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<td class="old_line diff-line-num" data-linenumber="591" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
591
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<td class="new_line diff-line-num" data-linenumber="602" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
602
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC602" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># pi-stacking interaction with Trp384, Trp137 and Trp52</span></span>
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<td class="old_line diff-line-num" data-linenumber="592" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
592
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<td class="new_line diff-line-num" data-linenumber="603" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
603
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC603" class="line" lang="python"> <span class="n" style="color: #333333;">pistackres</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333333;">pistack</span><span class="p">.</span><span class="n" style="color: #333333;">resnr</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">pistack</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">s</span><span class="p">.</span><span class="n" style="color: #333333;">pistacking</span><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="701" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="712" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -701,6 +712,8 @@ class LiteratureValidatedTest(unittest.TestCase):</td>
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<td class="old_line diff-line-num" data-linenumber="701" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
701
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<td class="new_line diff-line-num" data-linenumber="712" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
712
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC712" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Water bridges</span></span>
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<td class="old_line diff-line-num" data-linenumber="702" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
702
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<td class="new_line diff-line-num" data-linenumber="713" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
713
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC713" class="line" lang="python"> <span class="n" style="color: #333333;">waterbridges</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="nf" style="color: #990000; font-weight: 600;">str</span><span class="p">(</span><span class="n" style="color: #333333;">wb</span><span class="p">.</span><span class="n" style="color: #333333;">resnr</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">wb</span><span class="p">.</span><span class="n" style="color: #333333;">reschain</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">wb</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">s</span><span class="p">.</span><span class="n" style="color: #333333;">water_bridges</span><span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="703" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
703
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<td class="new_line diff-line-num" data-linenumber="714" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
714
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC714" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># #@todo Water bridge with 50B not detected</span></span>
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<td class="old_line diff-line-num new" data-linenumber="704" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="715" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
715
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC715" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Philipp: Water bridge with 50A not detected -> Angle prio leads to two wbridges with 50B</span></span>
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<td class="old_line diff-line-num new" data-linenumber="704" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="716" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
716
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC716" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># self.assertTrue({'50B'}.issubset(waterbridges))</span></span>
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<td class="old_line diff-line-num" data-linenumber="704" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
704
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<td class="new_line diff-line-num" data-linenumber="717" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
717
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC717" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">assertTrue</span><span class="p">({</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">50A</span><span class="sh" style="color: #dd1144;">'</span><span class="p">}.</span><span class="nf" style="color: #990000; font-weight: 600;">issubset</span><span class="p">(</span><span class="n" style="color: #333333;">waterbridges</span><span class="p">))</span> <span class="c1" style="color: #999988; font-style: italic;"># Bridging Ile-B50 and Ile-A50 with ligand</span></span>
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<td class="old_line diff-line-num" data-linenumber="705" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
705
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<td class="new_line diff-line-num" data-linenumber="718" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
718
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC718" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># pi-cation Interactions</span></span>
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<td class="old_line diff-line-num" data-linenumber="706" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
706
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<td class="new_line diff-line-num" data-linenumber="719" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
719
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC719" class="line" lang="python"> <span class="n" style="color: #333333;">picat</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333333;">pication</span><span class="p">.</span><span class="n" style="color: #333333;">resnr</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">pication</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">s</span><span class="p">.</span><span class="n" style="color: #333333;">pication_laro</span><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="752" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="765" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -752,4 +765,6 @@ class LiteratureValidatedTest(unittest.TestCase):</td>
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<td class="old_line diff-line-num" data-linenumber="752" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
752
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<td class="new_line diff-line-num" data-linenumber="765" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
765
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC765" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Water bridges</span></span>
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753
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766
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC766" class="line" lang="python"> <span class="n" style="color: #333333;">waterbridges</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="nf" style="color: #990000; font-weight: 600;">str</span><span class="p">(</span><span class="n" style="color: #333333;">wb</span><span class="p">.</span><span class="n" style="color: #333333;">resnr</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333333;">wb</span><span class="p">.</span><span class="n" style="color: #333333;">reschain</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">wb</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">s</span><span class="p">.</span><span class="n" style="color: #333333;">water_bridges</span><span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="754" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
754
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<td class="new_line diff-line-num" data-linenumber="767" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
767
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC767" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Waterbridge with Gly27 is detected instead of Ala28/Asp29</span></span>
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<td class="old_line diff-line-num new" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="768" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
768
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC768" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># Philipp: Waterbridge with 50B not detected rather two towards 50A</span></span>
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<td class="old_line diff-line-num new" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="769" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
769
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC769" class="line" lang="python"> <span class="c1" style="color: #999988; font-style: italic;"># self.assertTrue({'50B', '29A'}.issubset(waterbridges))</span></span>
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<td class="old_line diff-line-num" data-linenumber="755" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
755
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<td class="new_line diff-line-num" data-linenumber="770" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
770
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC770" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">assertTrue</span><span class="p">({</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">50A</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">50B</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">29A</span><span class="sh" style="color: #dd1144;">'</span><span class="p">}.</span><span class="nf" style="color: #990000; font-weight: 600;">issubset</span><span class="p">(</span><span class="n" style="color: #333333;">waterbridges</span><span class="p">))</span></span></pre></td>
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<li id="814e5fbe237dcc3e3aabaee96b3a65b231d08b1c">
<a href="https://salsa.debian.org/med-team/plip/-/compare/9408f2de4e28772642baaea5c38da321a843cb5e...987142df85e4487ee8693e3417f93cd5d85a962c#814e5fbe237dcc3e3aabaee96b3a65b231d08b1c"><strong style="font-weight: 600;">plip/visualization/visualize.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -19,7 +19,7 @@ def visualize_in_pymol(plcomplex):</td>
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<td class="old_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
19
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<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
19
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC19" class="line" lang="python"> <span class="n" style="color: #333333;">pdbid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">plcomplex</span><span class="p">.</span><span class="n" style="color: #333333;">pdbid</span></span>
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<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
20
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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
20
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC20" class="line" lang="python"> <span class="n" style="color: #333333;">lig_members</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">plcomplex</span><span class="p">.</span><span class="n" style="color: #333333;">lig_members</span></span>
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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
21
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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
21
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC21" class="line" lang="python"> <span class="n" style="color: #333333;">chain</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">plcomplex</span><span class="p">.</span><span class="n" style="color: #333333;">chain</span></span>
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<td class="old_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
22
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<td class="new_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">PEPTIDES</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
22
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">PEPTIDES</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="ow" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">or</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">config</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">CHAINS</span></span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
23
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<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
23
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC23" class="line" lang="python"> <span class="n" style="color: #333333;">vis</span><span class="p">.</span><span class="n" style="color: #333333;">ligname</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">PeptideChain%s</span><span class="sh" style="color: #dd1144;">'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333333;">plcomplex</span><span class="p">.</span><span class="n" style="color: #333333;">chain</span></span>
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<td class="old_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
24
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<td class="new_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
24
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">INTRA</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999999;">None</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
25
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<td class="new_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
25
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC25" class="line" lang="python"> <span class="n" style="color: #333333;">vis</span><span class="p">.</span><span class="n" style="color: #333333;">ligname</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">Intra%s</span><span class="sh" style="color: #dd1144;">'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333333;">plcomplex</span><span class="p">.</span><span class="n" style="color: #333333;">chain</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="45" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="45" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -45,7 +45,10 @@ def visualize_in_pymol(plcomplex):</td>
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45
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<td class="new_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
45
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC45" class="line" lang="python"> <span class="n" style="color: #333333;">cmd</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">set_name</span><span class="p">(</span><span class="n" style="color: #333333;">current_name</span><span class="p">,</span> <span class="n" style="color: #333333;">pdbid</span><span class="p">)</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC46" class="line" lang="python"> <span class="n" style="color: #333333;">cmd</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">hide</span><span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">everything</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">all</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
47
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<td class="new_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
47
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">PEPTIDES</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="48" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
48
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<td class="new_line diff-line-num old" data-linenumber="48" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333333;">cmd</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">select</span><span class="p">(</span><span class="n" style="color: #333333;">ligname</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">chain %s and not resn HOH</span><span class="sh" style="color: #dd1144;">'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333333;">plcomplex</span><span class="p">.</span><span class="n" style="color: #333333;">chain</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
48
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">plcomplex</span><span class="p">.</span><span class="n" style="color: #333333;">chain</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">RESIDUES</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">keys</span><span class="p">():</span></span>
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<td class="old_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
49
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333333;">cmd</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">select</span><span class="p">(</span><span class="n" style="color: #333333;">ligname</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">chain %s and not resn HOH and resi %s</span><span class="sh" style="color: #dd1144;">'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333333;">plcomplex</span><span class="p">.</span><span class="n" style="color: #333333;">chain</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">+</span><span class="sh" style="color: #dd1144;">"</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">join</span><span class="p">(</span><span class="nf" style="color: #990000; font-weight: 600;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">RESIDUES</span><span class="p">[</span><span class="n" style="color: #333333;">plcomplex</span><span class="p">.</span><span class="n" style="color: #333333;">chain</span><span class="p">]))))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
50
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="51" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
51
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333333;">cmd</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">select</span><span class="p">(</span><span class="n" style="color: #333333;">ligname</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">chain %s and not resn HOH</span><span class="sh" style="color: #dd1144;">'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333333;">plcomplex</span><span class="p">.</span><span class="n" style="color: #333333;">chain</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
49
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<td class="new_line diff-line-num" data-linenumber="52" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
52
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
50
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<td class="new_line diff-line-num" data-linenumber="53" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
53
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC53" class="line" lang="python"> <span class="n" style="color: #333333;">cmd</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">select</span><span class="p">(</span><span class="n" style="color: #333333;">ligname</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">resn %s and chain %s and resi %s*</span><span class="sh" style="color: #dd1144;">'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333333;">hetid</span><span class="p">,</span> <span class="n" style="color: #333333;">chain</span><span class="p">,</span> <span class="n" style="color: #333333;">plcomplex</span><span class="p">.</span><span class="n" style="color: #333333;">position</span><span class="p">))</span></span>
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51
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<td class="new_line diff-line-num" data-linenumber="54" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
54
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC54" class="line" lang="python"> <span class="n" style="color: #333333;">logger</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">debug</span><span class="p">(</span><span class="sa">f</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">selecting ligand for PDBID </span><span class="si" style="color: #dd1144;">{</span><span class="n" style="color: #333333;">pdbid</span><span class="si" style="color: #dd1144;">}</span><span class="s" style="color: #dd1144;"> and ligand name </span><span class="si" style="color: #dd1144;">{</span><span class="n" style="color: #333333;">ligname</span><span class="si" style="color: #dd1144;">}</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="97" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="100" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -97,7 +100,7 @@ def visualize_in_pymol(plcomplex):</td>
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<td class="old_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
97
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<td class="new_line diff-line-num" data-linenumber="100" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
100
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC100" class="line" lang="python"> <span class="n" style="color: #333333;">cmd</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">hide</span><span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">cartoon</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">%sLines</span><span class="sh" style="color: #dd1144;">'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333333;">plcomplex</span><span class="p">.</span><span class="n" style="color: #333333;">pdbid</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="98" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
98
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<td class="new_line diff-line-num" data-linenumber="101" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
101
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC101" class="line" lang="python"> <span class="n" style="color: #333333;">cmd</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">show</span><span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">lines</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">%sLines</span><span class="sh" style="color: #dd1144;">'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333333;">plcomplex</span><span class="p">.</span><span class="n" style="color: #333333;">pdbid</span><span class="p">)</span></span>
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99
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<td class="new_line diff-line-num" data-linenumber="102" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
102
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC102" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
100
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<td class="new_line diff-line-num old" data-linenumber="103" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">PEPTIDES</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="103" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
103
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">PEPTIDES</span><span class="idiff left addition" style="background-color: #c7f0d2;"> </span><span class="ow" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">or</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">config</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">.</span></span><span class="n" style="color: #333333;"><span class="idiff right addition" style="background-color: #c7f0d2;">CHAINS</span></span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="101" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
101
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<td class="new_line diff-line-num" data-linenumber="104" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
104
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC104" class="line" lang="python"> <span class="n" style="color: #333333;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">%s_PeptideChain%s</span><span class="sh" style="color: #dd1144;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333333;">pdbid</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">upper</span><span class="p">(),</span> <span class="n" style="color: #333333;">plcomplex</span><span class="p">.</span><span class="n" style="color: #333333;">chain</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="102" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
102
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<td class="new_line diff-line-num" data-linenumber="105" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
105
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">PYMOL</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="103" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
103
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<td class="new_line diff-line-num" data-linenumber="106" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
106
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC106" class="line" lang="python"> <span class="n" style="color: #333333;">vis</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">save_session</span><span class="p">(</span><span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">OUTPATH</span><span class="p">,</span> <span class="n" style="color: #333333;">override</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">filename</span><span class="p">)</span></span>
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<li id="8e2edce0d507e1297474f25c00cae94258db38d8">
<a href="https://salsa.debian.org/med-team/plip/-/compare/9408f2de4e28772642baaea5c38da321a843cb5e...987142df85e4487ee8693e3417f93cd5d85a962c#8e2edce0d507e1297474f25c00cae94258db38d8"><strong style="font-weight: 600;">setup.py</strong></a>
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1
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<td class="new_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
1
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333333;">setuptools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">setup</span><span class="p">,</span> <span class="n" style="color: #333333;">find_packages</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333333;">setuptools.command.build_ext</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">build_ext</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333333;">setuptools.command.install</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">install</span></span>
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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
4
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333333;">distutils.command.build</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">build</span></span>
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2
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
5
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5" class="line" lang="python"></span>
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3
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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
6
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333333;">plip.basic</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">config</span></span>
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4
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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
8
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC8" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #990000; font-weight: 600;">install_pkg_via_pip</span><span class="p">(</span><span class="n" style="color: #333333;">package</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
9
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC9" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">sys</span></span>
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10
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">subprocess</span></span>
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<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
11
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC11" class="line" lang="python"> <span class="n" style="color: #333333;">subprocess</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">check_call</span><span class="p">([</span><span class="n" style="color: #333333;">sys</span><span class="p">.</span><span class="n" style="color: #333333;">executable</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">-m</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">pip</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">install</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span> <span class="n" style="color: #333333;">package</span><span class="p">])</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC12" class="line" lang="python"></span>
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13
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC13" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #990000; font-weight: 600;">build_ob_py_bindings</span><span class="p">():</span></span>
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<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
14
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC14" class="line" lang="python"> <span class="sh" style="color: #dd1144;">"""</span><span class="s" style="color: #dd1144;"> Fix openbabel issue (https://github.com/openbabel/openbabel/issues/2408) manually</span></span>
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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
15
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC15" class="line" lang="python"><span class="s" style="color: #dd1144;"> - Download openbabel bindings from pypi</span></span>
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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
16
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC16" class="line" lang="python"><span class="s" style="color: #dd1144;"> - extract to a tmpdir</span></span>
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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
17
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC17" class="line" lang="python"><span class="s" style="color: #dd1144;"> - fix version in $tmpdir/openbabel-3.1.1.1/openbabel/__init__.py to have 2 dot version only</span></span>
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<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
18
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC18" class="line" lang="python"><span class="s" style="color: #dd1144;"> - install the fixed version with setuptools/pip</span></span>
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<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
19
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC19" class="line" lang="python"><span class="s" style="color: #dd1144;"> - cleanup the tmpdir</span></span>
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<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
20
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC20" class="line" lang="python"><span class="s" style="color: #dd1144;"> </span><span class="sh" style="color: #dd1144;">"""</span></span>
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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
21
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC21" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">requests</span></span>
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<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
22
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC22" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">tarfile</span></span>
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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
23
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC23" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">tempfile</span></span>
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24
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC24" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">shutil</span></span>
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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
25
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC25" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">fileinput</span></span>
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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
26
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC26" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">subprocess</span></span>
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<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
27
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC27" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">sys</span></span>
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<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
28
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC28" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
29
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333333;">openbabel_pypi_url</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">https://files.pythonhosted.org/packages/9d/3f/f08f5d1422d74ed0e1e612870b343bfcc26313bdf9efec9165c3ea4b3ae2/openbabel-3.1.1.1.tar.gz</span><span class="sh" style="color: #dd1144;">'</span></span>
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30
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC30" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
31
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC31" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">print </span><span class="p">(</span><span class="sa">f</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">Downloading openbabel package from : </span><span class="si" style="color: #dd1144;">{</span><span class="n" style="color: #333333;">openbabel_pypi_url</span><span class="si" style="color: #dd1144;">}</span><span class="sh" style="color: #dd1144;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
32
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333333;">obtar</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">requests</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">get</span><span class="p">(</span><span class="n" style="color: #333333;">openbabel_pypi_url</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
33
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333333;">obtmpdir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">tempfile</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">mkdtemp</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
34
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333333;">obtmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">obtmpdir</span><span class="o" style="font-weight: 600;">+</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">/openbabel-3.1.1.1.tar</span><span class="sh" style="color: #dd1144;">'</span></span>
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<td class="new_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
35
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC35" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333333;">obtmp</span><span class="p">,</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">wb</span><span class="sh" style="color: #dd1144;">'</span><span class="p">).</span><span class="nf" style="color: #990000; font-weight: 600;">write</span><span class="p">(</span><span class="n" style="color: #333333;">obtar</span><span class="p">.</span><span class="n" style="color: #333333;">content</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
36
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC36" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">print</span><span class="p">(</span><span class="sa">f</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">Saving openbabel tar.gz to </span><span class="si" style="color: #dd1144;">{</span><span class="n" style="color: #333333;">obtmpdir</span><span class="si" style="color: #dd1144;">}</span><span class="sh" style="color: #dd1144;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
37
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333333;">versfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">obtmpdir</span><span class="o" style="font-weight: 600;">+</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">/openbabel-3.1.1.1/openbabel/__init__.py</span><span class="sh" style="color: #dd1144;">'</span></span>
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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
38
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC38" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="39" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
39
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333333;">tarfile</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333333;">obtmp</span><span class="p">,</span><span class="n" style="color: #333333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">r</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333333;">tf</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
40
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333333;">tf</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">extractall</span><span class="p">(</span><span class="n" style="color: #333333;">obtmpdir</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
41
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC41" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
42
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC42" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">print </span><span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">Fix versions: s/3.1.1.1/3.1.1/ to make StrictVersion() in openbabel</span><span class="se" style="color: #dd1144;">\'</span><span class="s" style="color: #dd1144;">s setup.py happy</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
43
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC43" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">print </span><span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">See https://github.com/openbabel/openbabel/issues/2408 for more details</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
44
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333333;">fileinput</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">input</span><span class="p">(</span><span class="n" style="color: #333333;">files</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">versfile</span><span class="p">,</span><span class="n" style="color: #333333;">inplace</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999999;">True</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333333;">f</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="45" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
45
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333333;">f</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
46
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333333;">op</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333333;">line</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">replace</span><span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">__version__ = </span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">3.1.1.1</span><span class="sh" style="color: #dd1144;">"'</span><span class="p">,</span> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">__version__ = </span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">3.1.1</span><span class="sh" style="color: #dd1144;">"'</span><span class="p">)</span></span>
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47
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC47" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333333;">op</span><span class="p">,</span> <span class="n" style="color: #333333;">end</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">''</span><span class="p">)</span></span>
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48
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC48" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
49
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC49" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">install_pkg_via_pip</span><span class="p">(</span><span class="n" style="color: #333333;">obtmpdir</span><span class="o" style="font-weight: 600;">+</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">/openbabel-3.1.1.1/</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
50
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC50" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">print </span><span class="p">(</span><span class="sa">f</span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">Cleanup tmpdir: </span><span class="si" style="color: #dd1144;">{</span><span class="n" style="color: #333333;">obtmpdir</span><span class="si" style="color: #dd1144;">}</span><span class="sh" style="color: #dd1144;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="51" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
51
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333333;">shutil</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">rmtree</span><span class="p">(</span><span class="n" style="color: #333333;">obtmpdir</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="52" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
52
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC52" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
53
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC53" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #445588; font-weight: 600;">CustomBuild</span><span class="p">(</span><span class="n" style="color: #333333;">build</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
54
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC54" class="line" lang="python"> <span class="sh" style="color: #dd1144;">"""</span><span class="s" style="color: #dd1144;">Ensure build_ext runs first in build command.</span><span class="sh" style="color: #dd1144;">"""</span></span>
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<td class="new_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
55
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #990000; font-weight: 600;">run</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="56" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
56
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">run_command</span><span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">build_ext</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="57" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
57
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333333;">build</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">run</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
58
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC58" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="59" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
59
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC59" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #445588; font-weight: 600;">CustomInstall</span><span class="p">(</span><span class="n" style="color: #333333;">install</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
60
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC60" class="line" lang="python"> <span class="sh" style="color: #dd1144;">"""</span><span class="s" style="color: #dd1144;">Ensure build_ext runs first in install command.</span><span class="sh" style="color: #dd1144;">"""</span></span>
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<td class="new_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
61
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #990000; font-weight: 600;">run</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="62" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
62
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333333;">self</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">run_command</span><span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">build_ext</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
63
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333333;">install</span><span class="p">.</span><span class="nf" style="color: #990000; font-weight: 600;">run</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">)</span></span>
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64
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC64" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
65
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC65" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #445588; font-weight: 600;">CustomBuildExt</span><span class="p">(</span><span class="n" style="color: #333333;">build_ext</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
66
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC66" class="line" lang="python"> <span class="sh" style="color: #dd1144;">"""</span><span class="s" style="color: #dd1144;"> Check if openbabel bindings are installed || build them </span><span class="sh" style="color: #dd1144;">"""</span></span>
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<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
67
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #990000; font-weight: 600;">run</span><span class="p">(</span><span class="n" style="color: #333333;">self</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
68
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">openbabel</span></span>
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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
69
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ModuleNotFoundError</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
70
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333333;">requests</span></span>
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<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
71
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ModuleNotFoundError</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
72
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC72" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">install_pkg_via_pip</span><span class="p">(</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">requests</span><span class="sh" style="color: #dd1144;">'</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
73
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC73" class="line" lang="python"> <span class="nf" style="color: #990000; font-weight: 600;">build_ob_py_bindings</span><span class="p">()</span></span>
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74
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<td class="new_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
75
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC75" class="line" lang="python"></span>
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5
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<td class="new_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
76
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC76" class="line" lang="python"><span class="nf" style="color: #990000; font-weight: 600;">setup</span><span class="p">(</span><span class="n" style="color: #333333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">plip</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
6
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="python"> <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">__version__</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
7
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC7" class="line" lang="python"> <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">PLIP - Fully automated protein-ligand interaction profiler</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
8
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC8" class="line" lang="python"> <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;">classifiers</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
9
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="python"> <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">Development Status :: 5 - Production/Stable</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
10
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10" class="line" lang="python"> <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">Intended Audience :: Science/Research</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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11
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC11" class="line" lang="python"> <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">Natural Language :: English</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
12
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC12" class="line" lang="python"> <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">License :: OSI Approved :: GNU General Public License v2 (GPLv2)</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
13
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC13" class="line" lang="python"> <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">Programming Language :: Python :: 3.6</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
14
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC14" class="line" lang="python"> <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">Topic :: Scientific/Engineering :: Bio-Informatics</span><span class="sh" style="color: #dd1144;">'</span></span>
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<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
15
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC15" class="line" lang="python"> <span class="p">],</span></span>
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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
16
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC16" class="line" lang="python"> <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">https://github.com/pharmai/plip</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
17
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC17" class="line" lang="python"> <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;">author</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">PharmAI GmbH</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
18
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC18" class="line" lang="python"> <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;">author_email</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">hello@pharm.ai</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
19
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC19" class="line" lang="python"> <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;">license</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">GPLv2</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
20
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC20" class="line" lang="python"> <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;">packages</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #990000; font-weight: 600;">find_packages</span><span class="p">(),</span></span>
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<td class="old_line diff-line-num old" data-linenumber="21" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
21
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC21" class="line" lang="python"> <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;">scripts</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">plip/plipcmd.py</span><span class="sh" style="color: #dd1144;">'</span><span class="p">],</span></span>
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<td class="old_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
22
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC22" class="line" lang="python"> <span class="idiff left deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;"><span class="idiff deletion" style="background-color: #fac5cd;">install_requires</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">=</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">[</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
23
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC23" class="line" lang="python"> <span class="idiff left deletion" style="background-color: #fac5cd;"> </span><span class="sh" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">'</span></span><span class="s" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">openbabel</span></span><span class="sh" style="color: #dd1144;"><span class="idiff deletion" style="background-color: #fac5cd;">'</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">,</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
24
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC24" class="line" lang="python"> <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">numpy</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
25
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC25" class="line" lang="python"> <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">lxml</span><span class="sh" style="color: #dd1144;">'</span></span>
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<td class="old_line diff-line-num old" data-linenumber="26" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
26
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC26" class="line" lang="python"> <span class="p">],</span></span>
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<td class="old_line diff-line-num old" data-linenumber="27" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
27
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC27" class="line" lang="python"> <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;">entry_points</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
28
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC28" class="line" lang="python"> <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">console_scripts</span><span class="sh" style="color: #dd1144;">"</span><span class="p">:</span> <span class="p">[</span></span>
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<td class="old_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
29
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC29" class="line" lang="python"> <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">plip = plip.plipcmd:main</span><span class="sh" style="color: #dd1144;">"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
30
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC30" class="line" lang="python"> <span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="31" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
31
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC31" class="line" lang="python"> <span class="p">},</span></span>
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<td class="old_line diff-line-num old" data-linenumber="32" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
32
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<td class="new_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC32" class="line" lang="python"> <span class="idiff left right deletion" style="background-color: #fac5cd;"> </span><span class="n" style="color: #333333;">zip_safe</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999999;">False</span><span class="p">)</span></span></pre></td>
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<td class="old_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
77
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333333;">config</span><span class="p">.</span><span class="n" style="color: #333333;">__version__</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
78
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">PLIP - Fully automated protein-ligand interaction profiler</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
79
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333333;">classifiers</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<td class="old_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="80" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
80
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC80" class="line" lang="python"> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">Development Status :: 5 - Production/Stable</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
81
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC81" class="line" lang="python"> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">Intended Audience :: Science/Research</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="82" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
82
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC82" class="line" lang="python"> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">Natural Language :: English</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="83" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
83
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC83" class="line" lang="python"> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">License :: OSI Approved :: GNU General Public License v2 (GPLv2)</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
84
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC84" class="line" lang="python"> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">Programming Language :: Python :: 3.6</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
85
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC85" class="line" lang="python"> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">Topic :: Scientific/Engineering :: Bio-Informatics</span><span class="sh" style="color: #dd1144;">'</span></span>
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<td class="new_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
86
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC86" class="line" lang="python"> <span class="idiff left right addition" style="background-color: #c7f0d2;"> </span><span class="p">],</span></span>
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<td class="old_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
87
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">https://github.com/pharmai/plip</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
88
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333333;">author</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">PharmAI GmbH</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
89
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333333;">author_email</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">hello@pharm.ai</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
90
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333333;">license</span><span class="o" style="font-weight: 600;">=</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">GPLv2</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="91" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
91
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333333;">packages</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #990000; font-weight: 600;">find_packages</span><span class="p">(),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
92
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333333;">scripts</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">plip/plipcmd.py</span><span class="sh" style="color: #dd1144;">'</span><span class="p">],</span></span>
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<td class="new_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
93
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333333;"><span class="idiff left addition" style="background-color: #c7f0d2;">cmdclass</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">{</span></span><span class="sh" style="color: #dd1144;"><span class="idiff addition" style="background-color: #c7f0d2;">'</span></span><span class="s" style="color: #dd1144;"><span class="idiff addition" style="background-color: #c7f0d2;">build</span></span><span class="sh" style="color: #dd1144;"><span class="idiff addition" style="background-color: #c7f0d2;">'</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">:</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">CustomBuild</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="sh" style="color: #dd1144;"><span class="idiff addition" style="background-color: #c7f0d2;">'</span></span><span class="s" style="color: #dd1144;"><span class="idiff addition" style="background-color: #c7f0d2;">build_ext</span></span><span class="sh" style="color: #dd1144;"><span class="idiff addition" style="background-color: #c7f0d2;">'</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">:</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">CustomBuildExt</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="sh" style="color: #dd1144;"><span class="idiff addition" style="background-color: #c7f0d2;">'</span></span><span class="s" style="color: #dd1144;"><span class="idiff addition" style="background-color: #c7f0d2;">install</span></span><span class="sh" style="color: #dd1144;"><span class="idiff addition" style="background-color: #c7f0d2;">'</span></span><span class="p"><span class="idiff addition" style="background-color: #c7f0d2;">:</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="n" style="color: #333333;"><span class="idiff addition" style="background-color: #c7f0d2;">CustomInstall</span></span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">},</span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="94" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
94
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333333;"><span class="idiff left addition" style="background-color: #c7f0d2;">install_requires</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">=</span></span><span class="p"><span class="idiff right addition" style="background-color: #c7f0d2;">[</span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
95
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC95" class="line" lang="python"> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">numpy</span><span class="sh" style="color: #dd1144;">'</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
96
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC96" class="line" lang="python"> <span class="sh" style="color: #dd1144;">'</span><span class="s" style="color: #dd1144;">lxml</span><span class="sh" style="color: #dd1144;">'</span></span>
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<td class="new_line diff-line-num new" data-linenumber="97" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
97
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC97" class="line" lang="python"> <span class="idiff left right addition" style="background-color: #c7f0d2;"> </span><span class="p">],</span></span>
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<td class="new_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
98
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333333;">entry_points</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="99" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
99
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC99" class="line" lang="python"> <span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">console_scripts</span><span class="sh" style="color: #dd1144;">"</span><span class="p">:</span> <span class="p">[</span></span>
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<td class="old_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="100" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
100
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC100" class="line" lang="python"> <span class="sh" style="color: #dd1144;">"</span><span class="s" style="color: #dd1144;">plip = plip.plipcmd:main</span><span class="sh" style="color: #dd1144;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
101
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC101" class="line" lang="python"> <span class="idiff left right addition" style="background-color: #c7f0d2;"> </span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
102
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC102" class="line" lang="python"> <span class="idiff left right addition" style="background-color: #c7f0d2;"> </span><span class="p">},</span></span>
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<td class="new_line diff-line-num new" data-linenumber="103" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
103
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #28272d; position: relative; font-family: "GitLab Mono","JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333333;">zip_safe</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999999;">False</span><span class="p">)</span></span></pre></td>
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