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<h3>
Alexandre Mestiashvili pushed to branch master
at <a href="https://salsa.debian.org/med-team/plip">Debian Med / plip</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/plip/commit/57f173a8f0787d128f7583e9392f5306789875c6">57f173a8</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-09-25T09:36:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update Files-Excluded section in d/copyright
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plip/commit/175430d3ec44ef096c06082e18cd3f2ad0256bd8">175430d3</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-09-25T09:38:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.4.3~b+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plip/commit/c480af3e6a10eeef49c839ca23861931ae4d8b80">c480af3e</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-09-25T09:38:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.4.3_b+dfsg'
Update to upstream version '1.4.3~b+dfsg'
with Debian dir 93fd86deb27d2502735fbc17c609d6d74e3c0b4d</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plip/commit/f111ca06743a4700130c22552af010c42616ea59">f111ca06</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-09-25T09:38:35Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Check for nocheck in DEB_BUILD_OPTIONS for tests, s/plipcmd.py/plipcmd/
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plip/commit/70d5820d24d89f8135793db6944a04cfb42e830f">70d5820d</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-09-25T09:38:50Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump Policy to 4.2.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plip/commit/1549568ef24d351577628567a87eaa5c72bd3c96">1549568e</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-09-25T09:39:43Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
Gbp-Dch: Ignore
</pre>
</li>
</ul>
<h4>15 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#3251d7a8143ce2e789f0468513df8f285f842c3a">
CHANGES.txt
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</li>
<li class="file-stats">
<a href="#14789896d7d3663d4b2dd496146049d6798d139e">
DOCUMENTATION.md
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
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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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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#cd40fd0de26cf1f45321f4d2ad6a6bf3f25c8942">
plip/modules/detection.py
</a>
</li>
<li class="file-stats">
<a href="#df212bd3edccb5c6cb6e3ffe48ce9304993d81ff">
plip/modules/plipxml.py
</a>
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<li class="file-stats">
<a href="#86a2fcb72e262191b5bad9c18b91b7cba3b7ea36">
plip/modules/report.py
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<li class="file-stats">
<a href="#7a4c9b79c2f1bb441895d677413efbc1cb536c35">
plip/plipcmd
→
plip/plipcmd.py
</a>
</li>
<li class="file-stats">
<a href="#5b3b2ebd2d2f9d1847d59542eb2bffec18170cf5">
plip/test/test_special_cases.py
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</li>
<li class="file-stats">
<a href="#39a55f5514122e772e551dfe1a697052fe0d8bab">
plip/test/test_xml_parser.py
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</li>
<li class="file-stats">
<a href="#cae6f4308d8842e4ac596c953911fc711597e2ed">
plip/test/xml/1vsn.report.xml
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="3251d7a8143ce2e789f0468513df8f285f842c3a">
<a href="https://salsa.debian.org/med-team/plip/compare/5b8735d8202fdf271d2e6ac7693c538d3f072871...1549568ef24d351577628567a87eaa5c72bd3c96#3251d7a8143ce2e789f0468513df8f285f842c3a"><strong>CHANGES.txt</strong></a>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Changelog</span>
</pre>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">---------</span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"># Next version</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">* Adds information on covalent linkages to XML files</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">* __Anaconda package__ (provided by `Ikagami`)</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"># 1.4.2</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">* Adds "--name" option to change name of output files</span>
</pre>
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<br>
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<li id="14789896d7d3663d4b2dd496146049d6798d139e">
<a href="https://salsa.debian.org/med-team/plip/compare/5b8735d8202fdf271d2e6ac7693c538d3f072871...1549568ef24d351577628567a87eaa5c72bd3c96#14789896d7d3663d4b2dd496146049d6798d139e"><strong>DOCUMENTATION.md</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -44,7 +44,7 @@ and should be executed with Python 2.7.x.</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="markdown">Example command for Ubuntu using apt-get</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">sudo </span>apt-get <span class="nb" style="color: #0086b3;">install </span>pymol openbabel python-openbabel imagemagick</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">sudo </span>apt-get <span class="nb" style="color: #0086b3;">install </span>pymol openbabel python-openbabel imagemagick<span class="idiff left right"> swig</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="markdown"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -67,7 +67,7 @@ You can use any other user directory, but we will use the one given above for th</td>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="markdown">The package manager <span class="sb" style="color: #d14;">`pip`</span> will create symlinks for you so you can call PLIP using <span class="sb" style="color: #d14;">`plip`</span> in the command line. If you cloned from Github, use the following command to do the same:</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">alias </span><span class="nv" style="color: teal;">plip</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'<span class="idiff left right">~/pliptool/plip/plipcmd</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">alias </span><span class="nv" style="color: teal;">plip</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'<span class="idiff left right">python ~/pliptool/plip/plipcmd.py</span>'</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Analyze a PDB structure with PLIP</span></span>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/plip/compare/5b8735d8202fdf271d2e6ac7693c538d3f072871...1549568ef24d351577628567a87eaa5c72bd3c96#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,11 +18,11 @@ git clone https://github.com/ssalentin/plip.git ~/pliptool</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">##### As a command line tool</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="markdown">Run the <span class="sb" style="color: #d14;">`plipcmd`</span> script inside the PLIP folder to detect, report, and visualize interactions. The following example creates a PYMOL visualization for the interactions</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown">Run the <span class="sb" style="color: #d14;">`plipcmd<span class="idiff left right">.py</span>`</span> script inside the PLIP folder to detect, report, and visualize interactions. The following example creates a PYMOL visualization for the interactions</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown">between the inhibitor NFT and its target protein in the PDB structure 1VSN.</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">alias </span><span class="nv" style="color: teal;">plip</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'<span class="idiff left right">~/pliptool/plip/plipcmd</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">alias </span><span class="nv" style="color: teal;">plip</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'<span class="idiff left right">python ~/pliptool/plip/plipcmd.py</span>'</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">mkdir</span> /tmp/1vsn <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> /tmp/1vsn</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown">plip <span class="nt" style="color: navy;">-i</span> 1vsn <span class="nt" style="color: navy;">-yv</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown">pymol 1VSN_NFT_A_283.pse</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -61,7 +61,7 @@ For a full documentation of running options and output formats, please refear to</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Versions and Branches</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="markdown">For production environments, you should use the latest versioned commit from the stable branch.</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="markdown">Newer commits from the stable and development branch may contain<span class="idiff left right">s</span> new but untested and not documented features.</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown">Newer commits from the stable and development branch may contain new but untested and not documented features.</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Requirements</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="markdown">Previous to using PLIP, make sure you have the following tools and libraries installed:</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -93,3 +93,11 @@ If you are unsure about usage options, don't hesitate to contact me.</td>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="markdown">If you are using PLIP in your work, please cite</span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="markdown"><span class="gt" style="color: #a00;">> Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler.</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="markdown"><span class="gt" style="color: #a00;">> Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## FAQ</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="markdown"><span class="gt" style="color: #a00;">> I try to run PLIP, but I'm getting an error message saying:</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="markdown"><span class="gt" style="color: #a00;">> ValueError: [...] is not a recognised Open Babel descriptor type</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="markdown">Make sure Open Babel is correctly installed. This error can occur if the installed Python bindings don't match the OpenBabel version on your machine.</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="markdown">We don't offer technical support for installation of third-party packages.</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="markdown">For an instruction how to install Open Babel, please refer to their <span class="p">[</span><span class="nv" style="color: teal;">website</span><span class="p">](</span><span class="sx" style="color: #d14;">https://openbabel.org/docs/dev/Installation/install.html</span><span class="p">)</span>.</span></pre>
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<a href="https://salsa.debian.org/med-team/plip/compare/5b8735d8202fdf271d2e6ac7693c538d3f072871...1549568ef24d351577628567a87eaa5c72bd3c96#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">plip (1.4.3~b+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Update Files-Excluded section in d/copyright</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version 1.4.3~b+dfsg</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Check for nocheck in DEB_BUILD_OPTIONS for tests, s/plipcmd.py/plipcmd/</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Bump Policy to 4.2.1</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Alexandre Mestiashvili <mestia@debian.org> Tue, 25 Sep 2018 09:38:55 +0000</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">plip (1.4.2+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * New upstream version 1.4.2+dfsg</span>
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<a href="https://salsa.debian.org/med-team/plip/compare/5b8735d8202fdf271d2e6ac7693c538d3f072871...1549568ef24d351577628567a87eaa5c72bd3c96#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,7 +12,7 @@ Build-Depends: debhelper (>= 11),</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> python-openbabel,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> python-setuptools,</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> python-future</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.4</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2.1</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/plip</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/plip.git</span>
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<pre style="margin: 0;"> <span id="LC18" 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/5b8735d8202fdf271d2e6ac7693c538d3f072871...1549568ef24d351577628567a87eaa5c72bd3c96#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,6 +4,8 @@ Source: https://github.com/ssalentin/plip</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Files-Excluded:</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> plip/test/pdb/*</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> pliplogo*</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> setup_conda.py</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> recipe/*</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Files: *</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Copyright: 2016 Sebastian Salentin <sebastian.salentin@biotec.tu-dresden.de></span>
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<a href="https://salsa.debian.org/med-team/plip/compare/5b8735d8202fdf271d2e6ac7693c538d3f072871...1549568ef24d351577628567a87eaa5c72bd3c96#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,6 +12,8 @@ PYTHON_DEFAULT_VERSION := $(shell pyversions -d)</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">override_dh_auto_install:</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> dh_auto_install</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> mv $(CURDIR)/debian/$(PYBUILD_NAME)/usr/bin/plipcmd.py \</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> $(CURDIR)/debian/$(PYBUILD_NAME)/usr/bin/plipcmd</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> mkdir -p $(mandir)</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> export PYTHONPATH=$(CURDIR)/debian/$(PYBUILD_NAME)/usr/lib/$(PYTHON_DEFAULT_VERSION)/dist-packages/:\</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> $(CURDIR)/plip/modules; \</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,4 +21,6 @@ override_dh_auto_install:</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> $(CURDIR)/debian/$(PYBUILD_NAME)/usr/bin/plipcmd > $(mandir)/plipcmd.1</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> debian/tests/special-cases</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">endif</span></pre>
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<li id="cd40fd0de26cf1f45321f4d2ad6a6bf3f25c8942">
<a href="https://salsa.debian.org/med-team/plip/compare/5b8735d8202fdf271d2e6ac7693c538d3f072871...1549568ef24d351577628567a87eaa5c72bd3c96#cd40fd0de26cf1f45321f4d2ad6a6bf3f25c8942"><strong>plip/modules/detection.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,26 +17,25 @@ def filter_contacts(pairings):</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"> <span class="s" style="color: #d14;">"""Filter interactions by two criteria:</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="s" style="color: #d14;"> 1. No interactions between the same residue (important for intra mode).</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;"> 2. No duplicate interactions (A with B and B with A, also important for intra mode)."""</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">INTRA</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">filtered1_pairings</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">p</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">pairings</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reschain</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reschain_l</span><span class="p">)]</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">already_considered</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">filtered2_pairings</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">contact</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">filtered1_pairings</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC20" 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: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">INTRA</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pairings</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">filtered1_pairings</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">p</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">pairings</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reschain</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reschain_l</span><span class="p">)]</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">already_considered</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">filtered2_pairings</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">contact</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">filtered1_pairings</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'D{}'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">distance</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'D{}'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">distance</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'D{}'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">distance<span class="idiff left right">_ah</span></span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'D{}'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">distance_ah</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'D{}'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">distance_aw</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">res1</span><span class="p">,</span> <span class="n" style="color: #333;">res2</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">resnr</span><span class="p">),</span> <span class="n" style="color: #333;">contact</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reschain</span><span class="p">]),</span> <span class="s" style="color: #d14;">''</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">resnr_l</span><span class="p">),</span> <span class="n" style="color: #333;">contact</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reschain_l</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">([</span><span class="n" style="color: #333;">res1</span><span class="p">,</span> <span class="n" style="color: #333;">res2</span><span class="p">,</span> <span class="n" style="color: #333;">dist</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">data</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">already_considered</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">filtered2_pairings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">already_considered</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">filtered2_pairings</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pairings</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'D{}'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">distance_aw</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">res1</span><span class="p">,</span> <span class="n" style="color: #333;">res2</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">resnr</span><span class="p">),</span> <span class="n" style="color: #333;">contact</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reschain</span><span class="p">]),</span> <span class="s" style="color: #d14;">''</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">resnr_l</span><span class="p">),</span> <span class="n" style="color: #333;">contact</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reschain_l</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">res1</span><span class="p">,</span> <span class="n" style="color: #333;">res2</span><span class="p">,</span> <span class="n" style="color: #333;">dist</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">data</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">already_considered</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">filtered2_pairings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">already_considered</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">filtered2_pairings</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">##################################################</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -54,14 +53,15 @@ def hydrophobic_interactions(atom_set_a, atom_set_b):</td>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_idx</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">euclidean3d</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MIN_DIST</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HYDROPH_DIST_MAX</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">reschain</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atom</span><span class="p">),</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atom</span><span class="p">),</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atom</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">restype_l</span><span class="p">,</span> <span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">reschain_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atom</span><span class="p">),</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atom</span><span class="p">),</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atom</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">contact</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">(</span><span class="n" style="color: #333;">bsatom</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atom</span><span class="p">,</span> <span class="n" style="color: #333;">bsatom_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_idx</span><span class="p">,</span> <span class="n" style="color: #333;">ligatom</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atom</span><span class="p">,</span> <span class="n" style="color: #333;">ligatom_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_idx</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">distance</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">restype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">resnr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">reschain</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain</span><span class="p">,</span> <span class="n" style="color: #333;">restype_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">resnr_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">reschain_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain_l</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">pairings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC56" 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: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MIN_DIST</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HYDROPH_DIST_MAX</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">reschain</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atom</span><span class="p">),</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atom</span><span class="p">),</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atom</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">restype_l</span><span class="p">,</span> <span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">reschain_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atom</span><span class="p">),</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atom</span><span class="p">),</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atom</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">contact</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">(</span><span class="n" style="color: #333;">bsatom</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atom</span><span class="p">,</span> <span class="n" style="color: #333;">bsatom_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_idx</span><span class="p">,</span> <span class="n" style="color: #333;">ligatom</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atom</span><span class="p">,</span> <span class="n" style="color: #333;">ligatom_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_idx</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">distance</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">restype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">resnr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">reschain</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain</span><span class="p">,</span> <span class="n" style="color: #333;">restype_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">resnr_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">reschain_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain_l</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">pairings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">filter_contacts</span><span class="p">(</span><span class="n" style="color: #333;">pairings</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -75,32 +75,36 @@ def hbonds(acceptors, donor_pairs, protisdon, typ):</td>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="s" style="color: #d14;">'restype reschain resnr_l restype_l reschain_l sidechain atype dtype'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">pairings</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">acc</span><span class="p">,</span> <span class="n" style="color: #333;">don</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">itertools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">product</span><span class="p">(</span><span class="n" style="color: #333;">acceptors</span><span class="p">,</span> <span class="n" style="color: #333;">donor_pairs</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">typ</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'strong'</span><span class="p">:</span> <span class="c" style="color: #998; font-style: italic;"># Regular (strong) hydrogen bonds</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">dist_ah</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">euclidean3d</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">dist_ad</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">euclidean3d</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MIN_DIST</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">dist_ad</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HBOND_DIST_MAX</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">vec1</span><span class="p">,</span> <span class="n" style="color: #333;">vec2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vector</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">),</span> <span class="n" style="color: #333;">vector</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecangle</span><span class="p">(</span><span class="n" style="color: #333;">vec1</span><span class="p">,</span> <span class="n" style="color: #333;">vec2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HBOND_DON_ANGLE_MIN</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">protatom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OBAtom</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protisdon</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OBAtom</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">ligatom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OBAtom</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">protisdon</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OBAtom</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">is_sidechain_hbond</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">protatom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GetResidue</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GetAtomProperty</span><span class="p">(</span><span class="n" style="color: #333;">protatom</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">)</span> <span class="c" style="color: #998; font-style: italic;"># Check if sidechain atom</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">resnr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protisdon</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">resnr_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a_orig_atom</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protisdon</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d_orig_atom</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">restype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protisdon</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">restype_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a_orig_atom</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protisdon</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d_orig_atom</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">reschain</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protisdon</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">rechain_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a_orig_atom</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protisdon</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d_orig_atom</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Next line prevents H-Bonds within amino acids in intermolecular interactions</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">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: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="p">):</span> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Next line prevents backbone-backbone H-Bonds</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">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: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">protatom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GetResidue</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GetAtomProperty</span><span class="p">(</span><span class="n" style="color: #333;">protatom</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">ligatom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GetResidue</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GetAtomProperty</span><span class="p">(</span><span class="n" style="color: #333;">ligatom</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">):</span> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">contact</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">a_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a_orig_idx</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">d_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d_orig_idx</span><span class="p">,</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">h</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">distance_ah</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dist_ah</span><span class="p">,</span> <span class="n" style="color: #333;">distance_ad</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dist_ad</span><span class="p">,</span> <span class="n" style="color: #333;">angle</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">v</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: #333;">typ</span><span class="p">,</span> <span class="n" style="color: #333;">protisdon</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">protisdon</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">resnr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">restype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">reschain</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain</span><span class="p">,</span> <span class="n" style="color: #333;">resnr_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">restype_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span> <span class="n" style="color: #333;">reschain_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">rechain_l</span><span class="p">,</span> <span class="n" style="color: #333;">sidechain</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">is_sidechain_hbond</span><span class="p">,</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">atype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span><span class="p">)</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">pairings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC78" 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: #333;">typ</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'strong'</span><span class="p">:</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Regular (strong) hydrogen bonds</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">dist_ah</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">euclidean3d</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">)</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">dist_ad</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">euclidean3d</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
83
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<pre style="margin: 0;">+<span id="LC83" 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: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MIN_DIST</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">dist_ad</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HBOND_DIST_MAX</span><span class="p">:</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">vec1</span><span class="p">,</span> <span class="n" style="color: #333;">vec2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vector</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">),</span> <span class="n" style="color: #333;">vector</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">)</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecangle</span><span class="p">(</span><span class="n" style="color: #333;">vec1</span><span class="p">,</span> <span class="n" style="color: #333;">vec2</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
87
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<pre style="margin: 0;">+<span id="LC87" 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: #333;">v</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HBOND_DON_ANGLE_MIN</span><span class="p">:</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">protatom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OBAtom</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protisdon</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OBAtom</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">ligatom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OBAtom</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">protisdon</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OBAtom</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">is_sidechain_hbond</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">protatom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GetResidue</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GetAtomProperty</span><span class="p">(</span><span class="n" style="color: #333;">protatom</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">)</span> <span class="c" style="color: #998; font-style: italic;"># Check if sidechain atom</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">resnr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protisdon</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">resnr_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a_orig_atom</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protisdon</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d_orig_atom</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">restype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protisdon</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">restype_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a_orig_atom</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protisdon</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d_orig_atom</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">reschain</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protisdon</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">rechain_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a_orig_atom</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protisdon</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d_orig_atom</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Next line prevents H-Bonds within amino acids in intermolecular interactions</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">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: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="p">):</span> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Next line prevents backbone-backbone H-Bonds</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">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: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">protatom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GetResidue</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GetAtomProperty</span><span class="p">(</span><span class="n" style="color: #333;">protatom</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">ligatom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GetResidue</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GetAtomProperty</span><span class="p">(</span><span class="n" style="color: #333;">ligatom</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">):</span> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">contact</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">a_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a_orig_idx</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">d_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d_orig_idx</span><span class="p">,</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">h</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">distance_ah</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dist_ah</span><span class="p">,</span> <span class="n" style="color: #333;">distance_ad</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dist_ad</span><span class="p">,</span> <span class="n" style="color: #333;">angle</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">v</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: #333;">typ</span><span class="p">,</span> <span class="n" style="color: #333;">protisdon</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">protisdon</span><span class="p">,</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">resnr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">restype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">reschain</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain</span><span class="p">,</span> <span class="n" style="color: #333;">resnr_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">restype_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span> <span class="n" style="color: #333;">reschain_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">rechain_l</span><span class="p">,</span> <span class="n" style="color: #333;">sidechain</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">is_sidechain_hbond</span><span class="p">,</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">atype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">pairings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="p">)</span></span>
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104
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">filter_contacts</span><span class="p">(</span><span class="n" style="color: #333;">pairings</span><span class="p">)</span></span>
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -125,18 +129,19 @@ def pistacking(rings_bs, rings_lig):</td>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># SELECTION BY DISTANCE, ANGLE AND OFFSET</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">passed</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MIN_DIST</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PISTACK_DIST_MAX</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PISTACK_ANG_DEV</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PISTACK_OFFSET_MAX</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">ptype</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'P'</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">passed</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="mi" style="color: #099;">90</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PISTACK_ANG_DEV</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">90</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PISTACK_ANG_DEV</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PISTACK_OFFSET_MAX</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">ptype</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'T'</span></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">passed</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">passed</span><span class="p">:</span></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">contact</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">(</span><span class="n" style="color: #333;">proteinring</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">ligandring</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">distance</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">angle</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">offset</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">offset</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ptype</span><span class="p">,</span> <span class="n" style="color: #333;">resnr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">restype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">reschain</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain</span><span class="p">,</span></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">resnr_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">restype_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span> <span class="n" style="color: #333;">reschain_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain_l</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">pairings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="p">)</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" 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: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MIN_DIST</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PISTACK_DIST_MAX</span><span class="p">:</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PISTACK_ANG_DEV</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PISTACK_OFFSET_MAX</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">ptype</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'P'</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">passed</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="mi" style="color: #099;">90</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PISTACK_ANG_DEV</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">90</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PISTACK_ANG_DEV</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PISTACK_OFFSET_MAX</span><span class="p">:</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">ptype</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'T'</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">passed</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">passed</span><span class="p">:</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">contact</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">(</span><span class="n" style="color: #333;">proteinring</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">ligandring</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">distance</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">angle</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">offset</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">offset</span><span class="p">,</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ptype</span><span class="p">,</span> <span class="n" style="color: #333;">resnr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">restype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">reschain</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain</span><span class="p">,</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">resnr_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">restype_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span> <span class="n" style="color: #333;">reschain_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain_l</span><span class="p">)</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">pairings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">filter_contacts</span><span class="p">(</span><span class="n" style="color: #333;">pairings</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -146,46 +151,48 @@ def pication(rings, pos_charged, protcharged):</td>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">namedtuple</span><span class="p">(</span><span class="s" style="color: #d14;">'pication'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ring charge distance offset type restype resnr reschain restype_l resnr_l reschain_l protcharged'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">pairings</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">rings</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">pos_charged</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ring</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rings</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">center</span></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">pos_charged</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">euclidean3d</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">center</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Project the center of charge into the ring and measure distance to ring center</span></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">proj</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">projection</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">normal</span><span class="p">,</span> <span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">center</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">center</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">euclidean3d</span><span class="p">(</span><span class="n" style="color: #333;">proj</span><span class="p">,</span> <span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">center</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MIN_DIST</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PICATION_DIST_MAX</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PISTACK_OFFSET_MAX</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'lcharge'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fgroup</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'tertamine'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Special case here if the ligand has a tertiary amine, check an additional angle</span></span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Otherwise, we might have have a pi-cation interaction 'through' the ligand</span></span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">n_atoms</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">a_neighbor</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">a_neighbor</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">OBAtomAtomIter</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OBAtom</span><span class="p">)]</span></span>
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">n_atoms_coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">x</span><span class="p">(),</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">y</span><span class="p">(),</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">z</span><span class="p">())</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">n_atoms</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">amine_normal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cross</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="p">(</span><span class="n" style="color: #333;">n_atoms_coords</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">n_atoms_coords</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">vector</span><span class="p">(</span><span class="n" style="color: #333;">n_atoms_coords</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">n_atoms_coords</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]))</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecangle</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">normal</span><span class="p">,</span> <span class="n" style="color: #333;">amine_normal</span><span class="p">)</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Smallest of two angles, depending on direction of normal</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="mi" style="color: #099;">180</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">b</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="mi" style="color: #099;">180</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">b</span><span class="p">)</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" 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: #333;">a</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">30.0</span><span class="p">:</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">restype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]),</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python"> <span class="n" style="color: #333;">reschain</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">restype_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]),</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">reschain_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">contact</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ring</span><span class="p">,</span> <span class="n" style="color: #333;">charge</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">distance</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">offset</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'regular'</span><span class="p">,</span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">restype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">resnr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">reschain</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain</span><span class="p">,</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="python"> <span class="n" style="color: #333;">restype_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span> <span class="n" style="color: #333;">resnr_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">reschain_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain_l</span><span class="p">,</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">protcharged</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">protcharged</span><span class="p">)</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">pairings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="python"> <span class="n" style="color: #333;">resnr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protcharged</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="python"> <span class="n" style="color: #333;">resnr_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protcharged</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">restype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protcharged</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">restype_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protcharged</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">reschain</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protcharged</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">reschain_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protcharged</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">contact</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ring</span><span class="p">,</span> <span class="n" style="color: #333;">charge</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">distance</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">offset</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'regular'</span><span class="p">,</span> <span class="n" style="color: #333;">restype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">resnr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">reschain</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain</span><span class="p">,</span> <span class="n" style="color: #333;">restype_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span> <span class="n" style="color: #333;">resnr_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">reschain_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain_l</span><span class="p">,</span> <span class="n" style="color: #333;">protcharged</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">protcharged</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">rings</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">pos_charged</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pairings</span></span>
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<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ring</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rings</span><span class="p">:</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">center</span></span>
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<td class="diff-line-num new new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">pos_charged</span><span class="p">:</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">euclidean3d</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">center</span><span class="p">)</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Project the center of charge into the ring and measure distance to ring center</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">proj</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">projection</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">normal</span><span class="p">,</span> <span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">center</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">center</span><span class="p">)</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">euclidean3d</span><span class="p">(</span><span class="n" style="color: #333;">proj</span><span class="p">,</span> <span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">center</span><span class="p">)</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" 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: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MIN_DIST</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PICATION_DIST_MAX</span> <span class="ow" style="font-weight: 600;">or</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PISTACK_OFFSET_MAX</span><span class="p">:</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'lcharge'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fgroup</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'tertamine'</span><span class="p">:</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Special case here if the ligand has a tertiary amine, check an additional angle</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Otherwise, we might have have a pi-cation interaction 'through' the ligand</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="n" style="color: #333;">n_atoms</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">a_neighbor</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">a_neighbor</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">OBAtomAtomIter</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OBAtom</span><span class="p">)]</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">n_atoms_coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">x</span><span class="p">(),</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">y</span><span class="p">(),</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">z</span><span class="p">())</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">n_atoms</span><span class="p">]</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="n" style="color: #333;">amine_normal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cross</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="p">(</span><span class="n" style="color: #333;">n_atoms_coords</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">n_atoms_coords</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">vector</span><span class="p">(</span><span class="n" style="color: #333;">n_atoms_coords</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">n_atoms_coords</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]))</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecangle</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">normal</span><span class="p">,</span> <span class="n" style="color: #333;">amine_normal</span><span class="p">)</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Smallest of two angles, depending on direction of normal</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="mi" style="color: #099;">180</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">b</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="mi" style="color: #099;">180</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">b</span><span class="p">)</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" 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: #333;">a</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">30.0</span><span class="p">:</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">restype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]),</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">reschain</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">restype_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]),</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="n" style="color: #333;">reschain_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="n" style="color: #333;">contact</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ring</span><span class="p">,</span> <span class="n" style="color: #333;">charge</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">distance</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">offset</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'regular'</span><span class="p">,</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">restype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">resnr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">reschain</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain</span><span class="p">,</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">restype_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span> <span class="n" style="color: #333;">resnr_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">reschain_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain_l</span><span class="p">,</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">protcharged</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">protcharged</span><span class="p">)</span></span>
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188
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">pairings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="p">)</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">resnr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protcharged</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">resnr_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protcharged</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">restype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protcharged</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">restype_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protcharged</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">reschain</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protcharged</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">reschain_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protcharged</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">contact</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">(</span><span class="n" style="color: #333;">ring</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ring</span><span class="p">,</span> <span class="n" style="color: #333;">charge</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">distance</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">offset</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'regular'</span><span class="p">,</span> <span class="n" style="color: #333;">restype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">resnr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">reschain</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain</span><span class="p">,</span> <span class="n" style="color: #333;">restype_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span> <span class="n" style="color: #333;">resnr_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">reschain_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain_l</span><span class="p">,</span> <span class="n" style="color: #333;">protcharged</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">protcharged</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">pairings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">filter_contacts</span><span class="p">(</span><span class="n" style="color: #333;">pairings</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -194,17 +201,18 @@ def saltbridge(poscenter, negcenter, protispos):</td>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">namedtuple</span><span class="p">(</span><span class="s" style="color: #d14;">'saltbridge'</span><span class="p">,</span> <span class="s" style="color: #d14;">'positive negative distance protispos resnr restype reschain resnr_l restype_l reschain_l'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">pairings</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pc</span><span class="p">,</span> <span class="n" style="color: #333;">nc</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">itertools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">product</span><span class="p">(</span><span class="n" style="color: #333;">poscenter</span><span class="p">,</span> <span class="n" style="color: #333;">negcenter</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MIN_DIST</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">euclidean3d</span><span class="p">(</span><span class="n" style="color: #333;">pc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">center</span><span class="p">,</span> <span class="n" style="color: #333;">nc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">center</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SALTBRIDGE_DIST_MAX</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">resnr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">resnr</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protispos</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">nc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">resnr</span></span>
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">resnr_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">nc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protispos</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">pc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">restype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">restype</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protispos</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">nc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">restype</span></span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">restype_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">nc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protispos</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">pc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">reschain</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reschain</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protispos</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">nc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reschain</span></span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">reschain_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">nc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protispos</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">pc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">contact</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">(</span><span class="n" style="color: #333;">positive</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pc</span><span class="p">,</span> <span class="n" style="color: #333;">negative</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="n" style="color: #333;">distance</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">euclidean3d</span><span class="p">(</span><span class="n" style="color: #333;">pc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">center</span><span class="p">,</span> <span class="n" style="color: #333;">nc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">center</span><span class="p">),</span> <span class="n" style="color: #333;">protispos</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">protispos</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">resnr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">restype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">reschain</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain</span><span class="p">,</span> <span class="n" style="color: #333;">resnr_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">restype_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">reschain_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain_l</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">pairings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC204" 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: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MIN_DIST</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">euclidean3d</span><span class="p">(</span><span class="n" style="color: #333;">pc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">center</span><span class="p">,</span> <span class="n" style="color: #333;">nc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">center</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SALTBRIDGE_DIST_MAX</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">resnr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">resnr</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protispos</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">nc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">resnr</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">resnr_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">nc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protispos</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">pc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">restype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">restype</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protispos</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">nc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">restype</span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">restype_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">nc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protispos</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">pc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">reschain</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reschain</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protispos</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">nc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reschain</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">reschain_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">nc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">protispos</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">pc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_atoms</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">contact</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">(</span><span class="n" style="color: #333;">positive</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pc</span><span class="p">,</span> <span class="n" style="color: #333;">negative</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="n" style="color: #333;">distance</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">euclidean3d</span><span class="p">(</span><span class="n" style="color: #333;">pc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">center</span><span class="p">,</span> <span class="n" style="color: #333;">nc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">center</span><span class="p">),</span> <span class="n" style="color: #333;">protispos</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">protispos</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">resnr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">restype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">reschain</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain</span><span class="p">,</span> <span class="n" style="color: #333;">resnr_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">restype_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">reschain_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain_l</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"> <span class="n" style="color: #333;">pairings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">filter_contacts</span><span class="p">(</span><span class="n" style="color: #333;">pairings</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -215,24 +223,27 @@ def halogen(acceptor, donor):</td>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">pairings</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">acc</span><span class="p">,</span> <span class="n" style="color: #333;">don</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">itertools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">product</span><span class="p">(</span><span class="n" style="color: #333;">acceptor</span><span class="p">,</span> <span class="n" style="color: #333;">donor</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">euclidean3d</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MIN_DIST</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HALOGEN_DIST_MAX</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python"> <span class="n" style="color: #333;">vec1</span><span class="p">,</span> <span class="n" style="color: #333;">vec2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vector</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">),</span> <span class="n" style="color: #333;">vector</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">vec3</span><span class="p">,</span> <span class="n" style="color: #333;">vec4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vector</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">),</span> <span class="n" style="color: #333;">vector</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"> <span class="n" style="color: #333;">acc_angle</span><span class="p">,</span> <span class="n" style="color: #333;">don_angle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecangle</span><span class="p">(</span><span class="n" style="color: #333;">vec1</span><span class="p">,</span> <span class="n" style="color: #333;">vec2</span><span class="p">),</span> <span class="n" style="color: #333;">vecangle</span><span class="p">(</span><span class="n" style="color: #333;">vec3</span><span class="p">,</span> <span class="n" style="color: #333;">vec4</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">is_sidechain_hal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OBAtom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GetResidue</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GetAtomProperty</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OBAtom</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">)</span> <span class="c" style="color: #998; font-style: italic;"># Check if sidechain atom</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HALOGEN_ACC_ANGLE</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HALOGEN_ANGLE_DEV</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">acc_angle</span> \</span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="python"> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HALOGEN_ACC_ANGLE</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HALOGEN_ANGLE_DEV</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HALOGEN_DON_ANGLE</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HALOGEN_ANGLE_DEV</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">don_angle</span> \</span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="python"> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HALOGEN_DON_ANGLE</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HALOGEN_ANGLE_DEV</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">reschain</span><span class="p">,</span> <span class="n" style="color: #333;">resnr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">o</span><span class="p">),</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">o</span><span class="p">),</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">o</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">restype_l</span><span class="p">,</span> <span class="n" style="color: #333;">reschain_l</span><span class="p">,</span> <span class="n" style="color: #333;">resnr_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_x</span><span class="p">),</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_x</span><span class="p">),</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_x</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="python"> <span class="n" style="color: #333;">contact</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc</span><span class="p">,</span> <span class="n" style="color: #333;">acc_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">o_orig_idx</span><span class="p">,</span> <span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="p">,</span> <span class="n" style="color: #333;">don_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">x_orig_idx</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="python"> <span class="n" style="color: #333;">distance</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dist</span><span class="p">,</span> <span class="n" style="color: #333;">don_angle</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don_angle</span><span class="p">,</span> <span class="n" style="color: #333;">acc_angle</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc_angle</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="python"> <span class="n" style="color: #333;">restype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">resnr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">reschain</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain</span><span class="p">,</span> <span class="n" style="color: #333;">restype_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="python"> <span class="n" style="color: #333;">reschain_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain_l</span><span class="p">,</span> <span class="n" style="color: #333;">resnr_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">donortype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OBAtom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GetType</span><span class="p">(),</span> <span class="n" style="color: #333;">acctype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="python"> <span class="n" style="color: #333;">sidechain</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">is_sidechain_hal</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="python"> <span class="n" style="color: #333;">pairings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC226" 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: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MIN_DIST</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HALOGEN_DIST_MAX</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">vec1</span><span class="p">,</span> <span class="n" style="color: #333;">vec2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vector</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">),</span> <span class="n" style="color: #333;">vector</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"> <span class="n" style="color: #333;">vec3</span><span class="p">,</span> <span class="n" style="color: #333;">vec4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vector</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">),</span> <span class="n" style="color: #333;">vector</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"> <span class="n" style="color: #333;">acc_angle</span><span class="p">,</span> <span class="n" style="color: #333;">don_angle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecangle</span><span class="p">(</span><span class="n" style="color: #333;">vec1</span><span class="p">,</span> <span class="n" style="color: #333;">vec2</span><span class="p">),</span> <span class="n" style="color: #333;">vecangle</span><span class="p">(</span><span class="n" style="color: #333;">vec3</span><span class="p">,</span> <span class="n" style="color: #333;">vec4</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"> <span class="n" style="color: #333;">is_sidechain_hal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OBAtom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GetResidue</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GetAtomProperty</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OBAtom</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">)</span> <span class="c" style="color: #998; font-style: italic;"># Check if sidechain atom</span></span>
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<pre style="margin: 0;">+<span id="LC232" 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: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HALOGEN_ACC_ANGLE</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HALOGEN_ANGLE_DEV</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">acc_angle</span> \</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HALOGEN_ACC_ANGLE</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HALOGEN_ANGLE_DEV</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC235" 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: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HALOGEN_DON_ANGLE</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HALOGEN_ANGLE_DEV</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">don_angle</span> \</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HALOGEN_DON_ANGLE</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HALOGEN_ANGLE_DEV</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"> <span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">reschain</span><span class="p">,</span> <span class="n" style="color: #333;">resnr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">o</span><span class="p">),</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">o</span><span class="p">),</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">o</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="n" style="color: #333;">restype_l</span><span class="p">,</span> <span class="n" style="color: #333;">reschain_l</span><span class="p">,</span> <span class="n" style="color: #333;">resnr_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_x</span><span class="p">),</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_x</span><span class="p">),</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_x</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">contact</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc</span><span class="p">,</span> <span class="n" style="color: #333;">acc_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">o_orig_idx</span><span class="p">,</span> <span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="p">,</span> <span class="n" style="color: #333;">don_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">x_orig_idx</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">distance</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dist</span><span class="p">,</span> <span class="n" style="color: #333;">don_angle</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don_angle</span><span class="p">,</span> <span class="n" style="color: #333;">acc_angle</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc_angle</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">restype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">resnr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"> <span class="n" style="color: #333;">reschain</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain</span><span class="p">,</span> <span class="n" style="color: #333;">restype_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">reschain_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain_l</span><span class="p">,</span> <span class="n" style="color: #333;">resnr_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">donortype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OBAtom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GetType</span><span class="p">(),</span> <span class="n" style="color: #333;">acctype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="n" style="color: #333;">sidechain</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">is_sidechain_hal</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"> <span class="n" style="color: #333;">pairings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">filter_contacts</span><span class="p">(</span><span class="n" style="color: #333;">pairings</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -269,32 +280,38 @@ def water_bridges(bs_hba, lig_hba, bs_hbd, lig_hbd, water):</td>
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">itertools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">product</span><span class="p">(</span><span class="n" style="color: #333;">lig_aw</span><span class="p">,</span> <span class="n" style="color: #333;">prot_hw</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"> <span class="n" style="color: #333;">acc</span><span class="p">,</span> <span class="n" style="color: #333;">wl</span><span class="p">,</span> <span class="n" style="color: #333;">distance_aw</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">l</span></span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python"> <span class="n" style="color: #333;">don</span><span class="p">,</span> <span class="n" style="color: #333;">wd</span><span class="p">,</span> <span class="n" style="color: #333;">distance_dw</span><span class="p">,</span> <span class="n" style="color: #333;">d_angle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">wl</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oxy</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">wd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oxy</span><span class="p">:</span> <span class="c" style="color: #998; font-style: italic;"># Same water molecule and angle within omega</span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="python"> <span class="n" style="color: #333;">w_angle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecangle</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">wl</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oxy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">),</span> <span class="n" style="color: #333;">vector</span><span class="p">(</span><span class="n" style="color: #333;">wl</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oxy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">WATER_BRIDGE_OMEGA_MIN</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">w_angle</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">WATER_BRIDGE_OMEGA_MAX</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">reschain</span><span class="p">,</span> <span class="n" style="color: #333;">restype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="p">),</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="p">),</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="python"> <span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">reschain_l</span><span class="p">,</span> <span class="n" style="color: #333;">restype_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a_orig_atom</span><span class="p">),</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a_orig_atom</span><span class="p">),</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a_orig_atom</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="python"> <span class="n" style="color: #333;">contact</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">a_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a_orig_idx</span><span class="p">,</span> <span class="n" style="color: #333;">atype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">d_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d_orig_idx</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="python"> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span><span class="p">,</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="n" style="color: #333;">water</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wl</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oxy</span><span class="p">,</span> <span class="n" style="color: #333;">water_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wl</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oxy_orig_idx</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python"> <span class="n" style="color: #333;">distance_aw</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">distance_aw</span><span class="p">,</span> <span class="n" style="color: #333;">distance_dw</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">distance_dw</span><span class="p">,</span> <span class="n" style="color: #333;">d_angle</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">d_angle</span><span class="p">,</span> <span class="n" style="color: #333;">w_angle</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">w_angle</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'first_deg'</span><span class="p">,</span> <span class="n" style="color: #333;">resnr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">restype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="python"> <span class="n" style="color: #333;">reschain</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain</span><span class="p">,</span> <span class="n" style="color: #333;">restype_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span> <span class="n" style="color: #333;">resnr_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">reschain_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain_l</span><span class="p">,</span> <span class="n" style="color: #333;">protisdon</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="python"> <span class="n" style="color: #333;">pairings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC283" 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: #333;">wl</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oxy</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">wd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oxy</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Same water molecule and angle within omega</span></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"> <span class="n" style="color: #333;">w_angle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecangle</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">wl</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oxy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">),</span> <span class="n" style="color: #333;">vector</span><span class="p">(</span><span class="n" style="color: #333;">wl</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oxy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC287" 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: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">WATER_BRIDGE_OMEGA_MIN</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">w_angle</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">WATER_BRIDGE_OMEGA_MAX</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"> <span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">reschain</span><span class="p">,</span> <span class="n" style="color: #333;">restype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="p">),</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="p">),</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="python"> <span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">reschain_l</span><span class="p">,</span> <span class="n" style="color: #333;">restype_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a_orig_atom</span><span class="p">),</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a_orig_atom</span><span class="p">),</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a_orig_atom</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">contact</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">a_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a_orig_idx</span><span class="p">,</span> <span class="n" style="color: #333;">atype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">d_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d_orig_idx</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span><span class="p">,</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="n" style="color: #333;">water</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wl</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oxy</span><span class="p">,</span> <span class="n" style="color: #333;">water_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wl</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oxy_orig_idx</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python"> <span class="n" style="color: #333;">distance_aw</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">distance_aw</span><span class="p">,</span> <span class="n" style="color: #333;">distance_dw</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">distance_dw</span><span class="p">,</span> <span class="n" style="color: #333;">d_angle</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">d_angle</span><span class="p">,</span> <span class="n" style="color: #333;">w_angle</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">w_angle</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'first_deg'</span><span class="p">,</span> <span class="n" style="color: #333;">resnr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">restype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python"> <span class="n" style="color: #333;">reschain</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain</span><span class="p">,</span> <span class="n" style="color: #333;">restype_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span> <span class="n" style="color: #333;">resnr_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">reschain_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain_l</span><span class="p">,</span> <span class="n" style="color: #333;">protisdon</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python"> <span class="n" style="color: #333;">pairings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="p">)</span></span>
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283
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">l</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">itertools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">product</span><span class="p">(</span><span class="n" style="color: #333;">prot_aw</span><span class="p">,</span> <span class="n" style="color: #333;">lig_dw</span><span class="p">):</span></span>
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284
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="python"> <span class="n" style="color: #333;">acc</span><span class="p">,</span> <span class="n" style="color: #333;">wl</span><span class="p">,</span> <span class="n" style="color: #333;">distance_aw</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span></span>
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285
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="python"> <span class="n" style="color: #333;">don</span><span class="p">,</span> <span class="n" style="color: #333;">wd</span><span class="p">,</span> <span class="n" style="color: #333;">distance_dw</span><span class="p">,</span> <span class="n" style="color: #333;">d_angle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">l</span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">wl</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oxy</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">wd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oxy</span><span class="p">:</span> <span class="c" style="color: #998; font-style: italic;"># Same water molecule and angle within omega</span></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="python"> <span class="n" style="color: #333;">w_angle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecangle</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">wl</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oxy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">),</span> <span class="n" style="color: #333;">vector</span><span class="p">(</span><span class="n" style="color: #333;">wl</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oxy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">WATER_BRIDGE_OMEGA_MIN</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">w_angle</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">WATER_BRIDGE_OMEGA_MAX</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="python"> <span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">reschain</span><span class="p">,</span> <span class="n" style="color: #333;">restype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="p">),</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="p">),</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="p">)</span></span>
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290
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="python"> <span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">reschain_l</span><span class="p">,</span> <span class="n" style="color: #333;">restype_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d_orig_atom</span><span class="p">),</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d_orig_atom</span><span class="p">),</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d_orig_atom</span><span class="p">)</span></span>
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291
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">contact</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">a_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a_orig_idx</span><span class="p">,</span> <span class="n" style="color: #333;">atype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">d_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d_orig_idx</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="python"> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span><span class="p">,</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="n" style="color: #333;">water</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wl</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oxy</span><span class="p">,</span> <span class="n" style="color: #333;">water_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wl</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oxy_orig_idx</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="python"> <span class="n" style="color: #333;">distance_aw</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">distance_aw</span><span class="p">,</span> <span class="n" style="color: #333;">distance_dw</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">distance_dw</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="python"> <span class="n" style="color: #333;">d_angle</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">d_angle</span><span class="p">,</span> <span class="n" style="color: #333;">w_angle</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">w_angle</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'first_deg'</span><span class="p">,</span> <span class="n" style="color: #333;">resnr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="python"> <span class="n" style="color: #333;">restype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">reschain</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="python"> <span class="n" style="color: #333;">restype_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span> <span class="n" style="color: #333;">reschain_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain_l</span><span class="p">,</span> <span class="n" style="color: #333;">resnr_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">protisdon</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="python"> <span class="n" style="color: #333;">pairings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC300" 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: #333;">wl</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oxy</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">wd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oxy</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Same water molecule and angle within omega</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">w_angle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecangle</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">wl</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oxy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">),</span> <span class="n" style="color: #333;">vector</span><span class="p">(</span><span class="n" style="color: #333;">wl</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oxy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC304" 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: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">WATER_BRIDGE_OMEGA_MIN</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">w_angle</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">WATER_BRIDGE_OMEGA_MAX</span><span class="p">:</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="python"> <span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">reschain</span><span class="p">,</span> <span class="n" style="color: #333;">restype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="p">),</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="p">),</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="python"> <span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">reschain_l</span><span class="p">,</span> <span class="n" style="color: #333;">restype_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">whichresnumber</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d_orig_atom</span><span class="p">),</span> <span class="n" style="color: #333;">whichchain</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d_orig_atom</span><span class="p">),</span> <span class="n" style="color: #333;">whichrestype</span><span class="p">(</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d_orig_atom</span><span class="p">)</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="python"> <span class="n" style="color: #333;">contact</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">a_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a_orig_idx</span><span class="p">,</span> <span class="n" style="color: #333;">atype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">d_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d_orig_idx</span><span class="p">,</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="python"> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span><span class="p">,</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">don</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="n" style="color: #333;">water</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wl</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oxy</span><span class="p">,</span> <span class="n" style="color: #333;">water_orig_idx</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wl</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oxy_orig_idx</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="python"> <span class="n" style="color: #333;">distance_aw</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">distance_aw</span><span class="p">,</span> <span class="n" style="color: #333;">distance_dw</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">distance_dw</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="python"> <span class="n" style="color: #333;">d_angle</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">d_angle</span><span class="p">,</span> <span class="n" style="color: #333;">w_angle</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">w_angle</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'first_deg'</span><span class="p">,</span> <span class="n" style="color: #333;">resnr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="python"> <span class="n" style="color: #333;">restype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">reschain</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="python"> <span class="n" style="color: #333;">restype_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span> <span class="n" style="color: #333;">reschain_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reschain_l</span><span class="p">,</span> <span class="n" style="color: #333;">resnr_l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">protisdon</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="python"> <span class="n" style="color: #333;">pairings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">contact</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">filter_contacts</span><span class="p">(</span><span class="n" style="color: #333;">pairings</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -310,13 +327,14 @@ def metal_complexation(metals, metal_binding_lig, metal_binding_bs):</td>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="python"> <span class="n" style="color: #333;">metal_to_orig_atom</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">metal</span><span class="p">,</span> <span class="n" style="color: #333;">target</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">itertools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">product</span><span class="p">(</span><span class="n" style="color: #333;">metals</span><span class="p">,</span> <span class="n" style="color: #333;">metal_binding_lig</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">metal_binding_bs</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="python"> <span class="n" style="color: #333;">distance</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">euclidean3d</span><span class="p">(</span><span class="n" style="color: #333;">metal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coords</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">distance</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">METAL_DIST_MAX</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">metal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">m</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">pairings_dict</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="python"> <span class="n" style="color: #333;">pairings_dict</span><span class="p">[</span><span class="n" style="color: #333;">metal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">m</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="n" style="color: #333;">target</span><span class="p">,</span> <span class="n" style="color: #333;">distance</span><span class="p">),</span> <span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="python"> <span class="n" style="color: #333;">metal_to_id</span><span class="p">[</span><span class="n" style="color: #333;">metal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">m</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">m_orig_idx</span></span>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="python"> <span class="n" style="color: #333;">metal_to_orig_atom</span><span class="p">[</span><span class="n" style="color: #333;">metal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">m</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_m</span></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="python"> <span class="n" style="color: #333;">pairings_dict</span><span class="p">[</span><span class="n" style="color: #333;">metal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">m</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">target</span><span class="p">,</span> <span class="n" style="color: #333;">distance</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC330" 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: #333;">distance</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">METAL_DIST_MAX</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">metal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">m</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">pairings_dict</span><span class="p">:</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python"> <span class="n" style="color: #333;">pairings_dict</span><span class="p">[</span><span class="n" style="color: #333;">metal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">m</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="n" style="color: #333;">target</span><span class="p">,</span> <span class="n" style="color: #333;">distance</span><span class="p">),</span> <span class="p">]</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="python"> <span class="n" style="color: #333;">metal_to_id</span><span class="p">[</span><span class="n" style="color: #333;">metal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">m</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">m_orig_idx</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="python"> <span class="n" style="color: #333;">metal_to_orig_atom</span><span class="p">[</span><span class="n" style="color: #333;">metal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">m</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">orig_m</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="python"> <span class="n" style="color: #333;">pairings_dict</span><span class="p">[</span><span class="n" style="color: #333;">metal</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">m</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">target</span><span class="p">,</span> <span class="n" style="color: #333;">distance</span><span class="p">))</span></span>
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320
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338
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cnum</span><span class="p">,</span> <span class="n" style="color: #333;">metal</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">pairings_dict</span><span class="p">):</span></span>
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321
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339
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="python"> <span class="n" style="color: #333;">rms</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span></span>
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322
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340
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="python"> <span class="n" style="color: #333;">excluded</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<a href="https://salsa.debian.org/med-team/plip/compare/5b8735d8202fdf271d2e6ac7693c538d3f072871...1549568ef24d351577628567a87eaa5c72bd3c96#df212bd3edccb5c6cb6e3ffe48ce9304993d81ff"><strong>plip/modules/plipxml.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,7 +22,7 @@ class XMLStorage:</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">getdata</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">tree</span><span class="p">,</span> <span class="n" style="color: #333;">location</span><span class="p">,</span> <span class="n" style="color: #333;">force_string</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="s" style="color: #d14;">"""Gets XML data from a specific element and handles types."""</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">found</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">xpath</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s/text()'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">location</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left">found</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">[]</span>:</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;"><span class="idiff left">not</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">found</span></span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">found</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -244,7 +244,7 @@ class BSite(XMLStorage):</td>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">halogens</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">HalogenBond</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">interactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">xpath</span><span class="p">(</span><span class="s" style="color: #d14;">'halogen_bonds/halogen_bond'</span><span class="p">)]</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metal_complexes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">MetalComplex</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">interactions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">xpath</span><span class="p">(</span><span class="s" style="color: #d14;">'metal_complexes/metal_complex'</span><span class="p">)]</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">num_contacts</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">hydrophobics</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">hbonds</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wbridges</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sbridges</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pi_stacks</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pi_cations</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">halogens</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metal_complexes</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">has_interactions</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;"><span class="idiff left">True</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">num_contacts</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">has_interactions</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">num_contacts</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_atom_mapping</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">counts</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_counts</span><span class="p">()</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -282,7 +282,7 @@ class PLIPXML(XMLStorage):</td>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filetype</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getdata</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">doc</span><span class="p">,</span> <span class="s" style="color: #d14;">'/report/filetype'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fixed</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getdata</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">doc</span><span class="p">,</span> <span class="s" style="color: #d14;">'/report/pdbfixes/'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getdata</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">doc</span><span class="p">,</span> <span class="s" style="color: #d14;">'/report/filename'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">excluded</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;"><span class="idiff left">getdata</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">doc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'/report/excluded_ligands</span>'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">excluded</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;"><span class="idiff left">doc</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">xpath</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff right">'/report/excluded_ligands/excluded_ligand/text()</span>'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Parse binding site information</span></span>
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bsites</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">BSite</span><span class="p">(</span><span class="n" style="color: #333;">bs</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pdbid</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bsid</span><span class="p">:</span> <span class="n" style="color: #333;">BSite</span><span class="p">(</span><span class="n" style="color: #333;">bs</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pdbid</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">bs</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">xpath</span><span class="p">(</span><span class="s" style="color: #d14;">'//bindingsite'</span><span class="p">)}</span></span>
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<li id="86a2fcb72e262191b5bad9c18b91b7cba3b7ea36">
<a href="https://salsa.debian.org/med-team/plip/compare/5b8735d8202fdf271d2e6ac7693c538d3f072871...1549568ef24d351577628567a87eaa5c72bd3c96#86a2fcb72e262191b5bad9c18b91b7cba3b7ea36"><strong>plip/modules/report.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,7 +19,7 @@ from . import config</td>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># External libraries</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">lxml.etree</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">et</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'1.4.<span class="idiff left right">2</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'1.4.<span class="idiff left right">3</span>'</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">StructureReport</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">"""Creates reports (xml or txt) for one structure/"""</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -61,6 +61,13 @@ class StructureReport:</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">exlig</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">excluded</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">et</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SubElement</span><span class="p">(</span><span class="n" style="color: #333;">exligs</span><span class="p">,</span> <span class="s" style="color: #d14;">'excluded_ligand'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">text</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exlig</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">covalent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">et</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SubElement</span><span class="p">(</span><span class="n" style="color: #333;">report</span><span class="p">,</span> <span class="s" style="color: #d14;">'covlinkages'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">covlinkage</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">covalent</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">et</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SubElement</span><span class="p">(</span><span class="n" style="color: #333;">covalent</span><span class="p">,</span> <span class="s" style="color: #d14;">'covlinkage'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">f1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">et</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SubElement</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="s" style="color: #d14;">'res1'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">f2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">et</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SubElement</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="s" style="color: #d14;">'res2'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">f1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">text</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">":"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">covlinkage</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">id1</span><span class="p">,</span> <span class="n" style="color: #333;">covlinkage</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chain1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">covlinkage</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pos1</span><span class="p">)])</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">f2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">text</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">":"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">covlinkage</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">id2</span><span class="p">,</span> <span class="n" style="color: #333;">covlinkage</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chain2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">covlinkage</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pos2</span><span class="p">)])</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">report</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">construct_txt_file</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/plip/compare/5b8735d8202fdf271d2e6ac7693c538d3f072871...1549568ef24d351577628567a87eaa5c72bd3c96#7a4c9b79c2f1bb441895d677413efbc1cb536c35"><strong>plip/plipcmd</strong>
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<strong>plip/plipcmd.py</strong>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#! /usr/bin/env python</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;">plipcmd - Main script for PLIP command line execution.</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;">plipcmd<span class="idiff left right">.py</span> - Main script for PLIP command line execution.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Compatibility</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,12 +9,20 @@ from __future__ import print_function</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">absolute_import</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Own modules</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.modules.preparation</span> <span class="kn" style="font-weight: 600;">import</span> <span class="o" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.modules.plipremote</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">VisualizerData</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.modules.report</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">StructureReport</span><span class="p">,</span><span class="n" style="color: #333;">__version__</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.modules</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">config</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.modules.mp</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">parallel_fn</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.modules.webservices</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">check_pdb_status</span><span class="p">,</span> <span class="n" style="color: #333;">fetch_pdb</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.modules.preparation</span> <span class="kn" style="font-weight: 600;">import</span> <span class="o" style="font-weight: 600;">*</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.modules.plipremote</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">VisualizerData</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.modules.report</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">StructureReport</span><span class="p">,</span><span class="n" style="color: #333;">__version__</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.modules</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">config</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.modules.mp</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">parallel_fn</span></span>
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<td class="diff-line-num new old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.modules.webservices</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">check_pdb_status</span><span class="p">,</span> <span class="n" style="color: #333;">fetch_pdb</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">modules.preparation</span> <span class="kn" style="font-weight: 600;">import</span> <span class="o" style="font-weight: 600;">*</span></span>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">modules.plipremote</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">VisualizerData</span></span>
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<td class="diff-line-num new old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">modules.report</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">StructureReport</span><span class="p">,</span><span class="n" style="color: #333;">__version__</span></span>
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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">modules</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">config</span></span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">modules.mp</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">parallel_fn</span></span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">modules.webservices</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">check_pdb_status</span><span class="p">,</span> <span class="n" style="color: #333;">fetch_pdb</span></span>
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18
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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19
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Python standard library</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -72,7 +80,10 @@ def process_pdb(pdbfile, outpath, as_string=False, outputprefix='report'):</td>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">######################################</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PYMOL</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PICS</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.modules.visualize</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">visualize_in_pymol</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.modules.visualize</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">visualize_in_pymol</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">modules.visualize</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">visualize_in_pymol</span></span>
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76
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">complexes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">VisualizerData</span><span class="p">(</span><span class="n" style="color: #333;">mol</span><span class="p">,</span> <span class="n" style="color: #333;">site</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">site</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">interaction_sets</span><span class="p">)</span></span>
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77
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">interaction_sets</span><span class="p">[</span><span class="n" style="color: #333;">site</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">interacting_res</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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78
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MAXTHREADS</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -166,12 +177,12 @@ def main(inputstructs, inputpdbids):</td>
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166
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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167
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">write_message</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Finished analysis. Find the result files in </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BASEPATH</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>
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170
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">##############################</span></span>
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Parse command line arguments</span></span>
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173
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">##############################</span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="python"></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main_init</span><span class="p">():</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parse command line arguments and start main script for analysis."""</span></span>
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175
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">prog</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"PLIP"</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">descript</span><span class="p">)</span></span>
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176
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">pdbstructure</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_mutually_exclusive_group</span><span class="p">(</span><span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span> <span class="c" style="color: #998; font-style: italic;"># Needs either PDB ID or file</span></span>
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177
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">pdbstructure</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-f"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--file"</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"input"</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"+"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Set input file, '-' reads from stdin"</span><span class="p">)</span> <span class="c" style="color: #998; font-style: italic;"># '-' as file name reads from stdin</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -293,3 +304,5 @@ if __name__ == '__main__':</td>
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293
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304
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"The water bridge omega minimum angle has to be smaller than the water bridge omega maximum angle"</span><span class="p">)</span></span>
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294
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<td class="diff-line-num new_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
305
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="python"> <span class="n" style="color: #333;">expanded_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tilde_expansion</span><span class="p">(</span><span class="n" style="color: #333;">arguments</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">input</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">arguments</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">input</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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295
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306
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">(</span><span class="n" style="color: #333;">expanded_path</span><span class="p">,</span> <span class="n" style="color: #333;">arguments</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pdbid</span><span class="p">)</span> <span class="c" style="color: #998; font-style: italic;"># Start main script</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="python"> <span class="n" style="color: #333;">main_init</span><span class="p">()</span></span></pre>
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<li id="5b3b2ebd2d2f9d1847d59542eb2bffec18170cf5">
<a href="https://salsa.debian.org/med-team/plip/compare/5b8735d8202fdf271d2e6ac7693c538d3f072871...1549568ef24d351577628567a87eaa5c72bd3c96#5b3b2ebd2d2f9d1847d59542eb2bffec18170cf5"><strong>plip/test/test_special_cases.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,20 +14,20 @@ class SpecialCasesTest(unittest.TestCase):</td>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_empty_input_file</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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16
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"> <span class="s" style="color: #d14;">"""Input file is empty."""</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">exitcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="s" style="color: #d14;">'<span class="idiff left right">../plipcmd</span> -f ./special/empty.pdb -o /tmp'</span><span class="p">,</span> <span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">exitcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="s" style="color: #d14;">'<span class="idiff left right">python ../plipcmd.py</span> -f ./special/empty.pdb -o /tmp'</span><span class="p">,</span> <span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">exitcode</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="c" style="color: #998; font-style: italic;"># Specific exitcode 2</span></span>
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19
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>
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20
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_invalid_pdb_id</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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21
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="s" style="color: #d14;">"""A PDB ID with no valid PDB record is provided."""</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">exitcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="s" style="color: #d14;">'<span class="idiff left right">../plipcmd</span> -i xx1x -o /tmp'</span><span class="p">,</span> <span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">exitcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="s" style="color: #d14;">'<span class="idiff left right">python ../plipcmd.py</span> -i xx1x -o /tmp'</span><span class="p">,</span> <span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">exitcode</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="c" style="color: #998; font-style: italic;"># Specific exitcode 3</span></span>
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24
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"></span>
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_invalid_input_file</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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26
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="s" style="color: #d14;">"""A file is provided which is not a PDB file."""</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">exitcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="s" style="color: #d14;">'<span class="idiff left right">../plipcmd</span> -f ./special/non-pdb.pdb -o /tmp'</span><span class="p">,</span> <span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">exitcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="s" style="color: #d14;">'<span class="idiff left right">python ../plipcmd.py</span> -f ./special/non-pdb.pdb -o /tmp'</span><span class="p">,</span> <span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">exitcode</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="c" style="color: #998; font-style: italic;"># Specific exitcode 4</span></span>
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29
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_pdb_format_not_available</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="s" style="color: #d14;">"""A valid PDB ID is provided, but there is no entry in PDB format from wwPDB"""</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">exitcode1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="s" style="color: #d14;">'<span class="idiff left right">../plipcmd</span> -i 4v59 -o /tmp'</span><span class="p">,</span> <span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">exitcode1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="s" style="color: #d14;">'<span class="idiff left right">python ../plipcmd.py</span> -i 4v59 -o /tmp'</span><span class="p">,</span> <span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">exitcode1</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="c" style="color: #998; font-style: italic;"># Specific exitcode 5</span></span></pre>
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<li id="39a55f5514122e772e551dfe1a697052fe0d8bab">
<a href="https://salsa.debian.org/med-team/plip/compare/5b8735d8202fdf271d2e6ac7693c538d3f072871...1549568ef24d351577628567a87eaa5c72bd3c96#39a55f5514122e772e551dfe1a697052fe0d8bab"><strong>plip/test/test_xml_parser.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,16 +15,15 @@ class XMLParserTest(unittest.TestCase):</td>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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16
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">px</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PLIPXML</span><span class="p">(</span><span class="s" style="color: #d14;">'./xml/1vsn.report.xml'</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
17
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bsite</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">px</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bsites</span><span class="p">[</span><span class="s" style="color: #d14;">'NFT:A:283'</span><span class="p">]</span></span>
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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">smiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">N=CCNC(=O)[C@H](CC(C)C)N[C@H](C(F)(F)F)c1ccc(cc1)c1ccc(cc1)S(=O)(=O)</span>N'</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">smiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">CC(C)CC(NC(c1ccc(cc1)c1ccc(cc1)S(N)(=O)=O)C(F)(F)F)C(=O)NCC=</span>N'</span></span>
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19
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>
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20
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_general_information</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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21
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test if general information is correctly parsed."""</span></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">px</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</span><span class="p">,</span> <span class="s" style="color: #d14;">'1.<span class="idiff left right">3</span>.2'</span><span class="p">)</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">px</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</span><span class="p">,</span> <span class="s" style="color: #d14;">'1.<span class="idiff left right">4</span>.2'</span><span class="p">)</span></span>
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23
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">px</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pdbid</span><span class="p">,</span> <span class="s" style="color: #d14;">'1VSN'</span><span class="p">)</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">px</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filetype</span><span class="p">,</span> <span class="s" style="color: #d14;">'PDB'</span><span class="p">)</span></span>
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25
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertFalse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">px</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fixed</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
26
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">px</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">'1vsn.pdb'</span><span class="p">)</span></span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">px</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">excluded</span><span class="p">,</span> <span class="bp" style="color: #999;"><span class="idiff left right">None</span></span><span class="p">)</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">px</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">excluded</span><span class="p">,</span> <span class="p"><span class="idiff left right">[]</span>)</span></span>
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28
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"></span>
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29
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_bsite_information</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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30
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test if the binding site information is correctly parsed."""</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -47,17 +46,17 @@ class XMLParserTest(unittest.TestCase):</td>
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47
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bsite</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unpaired_hal</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
48
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bsite</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rings</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
49
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<td class="diff-line-num new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bsite</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rotatable_bonds</span><span class="p">,</span> <span class="mi" style="color: #099;">12</span><span class="p">)</span></span>
</pre>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert<span class="idiff left">Equal</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">bsite</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">molweight</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff right">484.5349896</span></span><span class="p">)</span></span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert<span class="idiff left">Equal</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">bsite</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">logp</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff right">6.0371</span></span><span class="p">)</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert<span class="idiff left">AlmostEqual</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">bsite</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">molweight</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">484</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">)</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert<span class="idiff left">AlmostEqual</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">bsite</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">logp</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">6</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Atom mappings (non-exhaustive test)</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">lmap</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bsite</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mappings</span><span class="p">[</span><span class="s" style="color: #d14;">'pdb_to_smiles'</span><span class="p">]</span></span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">lmap</span><span class="p">[</span><span class="mi" style="color: #099;">1625</span><span class="p">],</span> <span class="mi" style="color: #099;"><span class="idiff left right">9</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">lmap</span><span class="p">[</span><span class="mi" style="color: #099;">1649</span><span class="p">],</span> <span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">lmap</span><span class="p">[</span><span class="mi" style="color: #099;">1617</span><span class="p">],</span> <span class="mi" style="color: #099;">1<span class="idiff left right">9</span></span><span class="p">)</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">lmap</span><span class="p">[</span><span class="mi" style="color: #099;">1625</span><span class="p">],</span> <span class="mi" style="color: #099;"><span class="idiff left right">24</span></span><span class="p">)</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">lmap</span><span class="p">[</span><span class="mi" style="color: #099;">1649</span><span class="p">],</span> <span class="mi" style="color: #099;"><span class="idiff left right">33</span></span><span class="p">)</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">lmap</span><span class="p">[</span><span class="mi" style="color: #099;">1617</span><span class="p">],</span> <span class="mi" style="color: #099;">1<span class="idiff left right">4</span></span><span class="p">)</span></span>
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"></span>
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59
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Binding site residues</span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bsite</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bs_res</span><span class="p">),</span> <span class="mi" style="color: #099;">3<span class="idiff left right">6</span></span><span class="p">)</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bsite</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bs_res</span><span class="p">),</span> <span class="mi" style="color: #099;">3<span class="idiff left right">5</span></span><span class="p">)</span></span>
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"></span>
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62
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Interacting chains</span></span>
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63
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bsite</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">interacting_chains</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'A'</span><span class="p">])</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -82,7 +81,7 @@ class XMLParserTest(unittest.TestCase):</td>
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82
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"></span>
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83
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"></span>
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84
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Hydrogen Bonds</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bsite</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">hbonds</span><span class="p">),</span> <span class="mi" style="color: #099;"><span class="idiff left right">7</span></span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bsite</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">hbonds</span><span class="p">),</span> <span class="mi" style="color: #099;"><span class="idiff left right">6</span></span><span class="p">)</span></span>
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86
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">hbond1</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bsite</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">hbonds</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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87
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">hbond1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="mi" style="color: #099;">19</span><span class="p">)</span></span>
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88
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">hbond1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="s" style="color: #d14;">'GLN'</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -100,7 +99,7 @@ class XMLParserTest(unittest.TestCase):</td>
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100
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<td class="diff-line-num new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">hbond1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">protcoo</span><span class="p">,</span> <span class="p">(</span><span class="mf" style="color: #099;">3.976</span><span class="p">,</span> <span class="mf" style="color: #099;">15.409</span><span class="p">,</span> <span class="mf" style="color: #099;">7.712</span><span class="p">))</span></span>
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101
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"></span>
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102
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Water Bridges</span></span>
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103
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<td class="diff-line-num new_line old" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bsite</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wbridges</span><span class="p">),</span> <span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bsite</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wbridges</span><span class="p">),</span> <span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span></span>
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104
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<td class="diff-line-num new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">wbridge1</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bsite</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wbridges</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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105
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<td class="diff-line-num new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">wbridge1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="mi" style="color: #099;">159</span><span class="p">)</span></span>
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106
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">wbridge1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="s" style="color: #d14;">'HIS'</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/plip/compare/5b8735d8202fdf271d2e6ac7693c538d3f072871...1549568ef24d351577628567a87eaa5c72bd3c96#cae6f4308d8842e4ac596c953911fc711597e2ed"><strong>plip/test/xml/1vsn.report.xml</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;"><?xml version='1.0' encoding='ASCII'?></span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="xml"><span class="nt" style="color: navy;"><report></span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="xml"> <span class="nt" style="color: navy;"><plipversion></span>1.<span class="idiff left right">3</span>.2<span class="nt" style="color: navy;"></plipversion></span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="xml"> <span class="nt" style="color: navy;"><plipversion></span>1.<span class="idiff left right">4</span>.2<span class="nt" style="color: navy;"></plipversion></span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="xml"> <span class="nt" style="color: navy;"><bindingsite</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"1"</span> <span class="na" style="color: teal;">has_interactions=</span><span class="s" style="color: #d14;">"True"</span><span class="nt" style="color: navy;">></span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="xml"> <span class="nt" style="color: navy;"><identifiers></span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="xml"> <span class="nt" style="color: navy;"><longname></span>NFT<span class="nt" style="color: navy;"></longname></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,7 +12,8 @@</td>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="xml"> <span class="nt" style="color: navy;"><members></span></span>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="xml"> <span class="nt" style="color: navy;"><member</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: navy;">></span>NFT:A:283<span class="nt" style="color: navy;"></member></span></span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="xml"> <span class="nt" style="color: navy;"></members></span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="xml"> <span class="nt" style="color: navy;"><smiles></span>N=CCNC(=O)[C@H](CC(C)C)N[C@H](C(F)(F)F)c1ccc(cc1)c1ccc(cc1)S(=O)(=O)N<span class="nt" style="color: navy;"></smiles></span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="xml"> <span class="nt" style="color: navy;"><smiles></span>CC(C)CC(NC(c1ccc(cc1)c1ccc(cc1)S(N)(=O)=O)C(F)(F)F)C(=O)NCC=N<span class="nt" style="color: navy;"></smiles></span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="xml"> <span class="nt" style="color: navy;"><inchikey></span>LUFZQYFBEDDLGO-UHFFFAOYSA-N<span class="nt" style="color: navy;"></inchikey></span></span>
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16
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="xml"> <span class="nt" style="color: navy;"></identifiers></span></span>
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17
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="xml"> <span class="nt" style="color: navy;"><lig_properties></span></span>
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18
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="xml"> <span class="nt" style="color: navy;"><num_heavy_atoms></span>33<span class="nt" style="color: navy;"></num_heavy_atoms></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,8 +25,8 @@</td>
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24
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="xml"> <span class="nt" style="color: navy;"><num_unpaired_hal></span>1<span class="nt" style="color: navy;"></num_unpaired_hal></span></span>
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25
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="xml"> <span class="nt" style="color: navy;"><num_aromatic_rings></span>2<span class="nt" style="color: navy;"></num_aromatic_rings></span></span>
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26
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="xml"> <span class="nt" style="color: navy;"><num_rotatable_bonds></span>12<span class="nt" style="color: navy;"></num_rotatable_bonds></span></span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="xml"> <span class="nt" style="color: navy;"><molweight></span>48<span class="idiff left right">4.53498</span>96<span class="nt" style="color: navy;"></molweight></span></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="xml"> <span class="nt" style="color: navy;"><logp></span><span class="idiff left right">6.037</span>1<span class="nt" style="color: navy;"></logp></span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="xml"> <span class="nt" style="color: navy;"><molweight></span>48<span class="idiff left right">3.52704</span>96<span class="nt" style="color: navy;"></molweight></span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="xml"> <span class="nt" style="color: navy;"><logp></span><span class="idiff left right">5.914</span>1<span class="nt" style="color: navy;"></logp></span></span>
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="xml"> <span class="nt" style="color: navy;"></lig_properties></span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="xml"> <span class="nt" style="color: navy;"><interacting_chains></span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="xml"> <span class="nt" style="color: navy;"><interacting_chain</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: navy;">></span>A<span class="nt" style="color: navy;"></interacting_chain></span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -50,23 +51,22 @@</td>
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50
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"PHE"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"False"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"17"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"7.4"</span><span class="nt" style="color: navy;">></span>28A<span class="nt" style="color: navy;"></bs_residue></span></span>
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51
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"LEU"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"False"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"18"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"4.2"</span><span class="nt" style="color: navy;">></span>205A<span class="nt" style="color: navy;"></bs_residue></span></span>
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52
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53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"THR"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"False"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"19"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"7.3"</span><span class="nt" style="color: navy;">></span>69A<span class="nt" style="color: navy;"></bs_residue></span></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"TRP"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"<span class="idiff left right">Tru</span>e"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"20"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"5.8"</span><span class="nt" style="color: navy;">></span>177A<span class="nt" style="color: navy;"></bs_residue></span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"TRP"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"<span class="idiff left right">Fals</span>e"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"20"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"5.8"</span><span class="nt" style="color: navy;">></span>177A<span class="nt" style="color: navy;"></bs_residue></span></span>
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54
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55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"HIS"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"True"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"21"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"4.0"</span><span class="nt" style="color: navy;">></span>159A<span class="nt" style="color: navy;"></bs_residue></span></span>
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55
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"ASN"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"True"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"22"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"2.9"</span><span class="nt" style="color: navy;">></span>158A<span class="nt" style="color: navy;"></bs_residue></span></span>
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56
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"VAL"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"False"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"23"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"6.9"</span><span class="nt" style="color: navy;">></span>161A<span class="nt" style="color: navy;"></bs_residue></span></span>
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57
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"ALA"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"False"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"24"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"6.8"</span><span class="nt" style="color: navy;">></span>27A<span class="nt" style="color: navy;"></bs_residue></span></span>
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58
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"ALA"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"False"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"25"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"6.8"</span><span class="nt" style="color: navy;">></span>1156A<span class="nt" style="color: navy;"></bs_residue></span></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"CYS"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"True"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"26"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"1.7"</span><span class="nt" style="color: navy;">></span>25A<span class="nt" style="color: navy;"></bs_residue></span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"GLY"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"False"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"27"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"3.4"</span><span class="nt" style="color: navy;">></span>23A<span class="nt" style="color: navy;"></bs_residue></span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"GLU"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"False"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"28"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"3.3"</span><span class="nt" style="color: navy;">></span>59A<span class="nt" style="color: navy;"></bs_residue></span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"GLY"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"False"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"29"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"5.8"</span><span class="nt" style="color: navy;">></span>62A<span class="nt" style="color: navy;"></bs_residue></span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"VAL"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"False"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"30"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"6.0"</span><span class="nt" style="color: navy;">></span>132A<span class="nt" style="color: navy;"></bs_residue></span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"ASN"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"False"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"31"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"3.0"</span><span class="nt" style="color: navy;">></span>60A<span class="nt" style="color: navy;"></bs_residue></span></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"ILE"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"False"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"32"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"5.7"</span><span class="nt" style="color: navy;">></span>134A<span class="nt" style="color: navy;"></bs_residue></span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"VAL"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"False"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"33"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"6.3"</span><span class="nt" style="color: navy;">></span>57A<span class="nt" style="color: navy;"></bs_residue></span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"GLN"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"True"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"34"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"3.1"</span><span class="nt" style="color: navy;">></span>19A<span class="nt" style="color: navy;"></bs_residue></span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"ASN"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"False"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"35"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"5.9"</span><span class="nt" style="color: navy;">></span>70A<span class="nt" style="color: navy;"></bs_residue></span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"GLY"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"True"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"36"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"2.9"</span><span class="nt" style="color: navy;">></span>66A<span class="nt" style="color: navy;"></bs_residue></span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"GLY"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"False"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"26"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"3.4"</span><span class="nt" style="color: navy;">></span>23A<span class="nt" style="color: navy;"></bs_residue></span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"GLU"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"False"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"27"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"3.3"</span><span class="nt" style="color: navy;">></span>59A<span class="nt" style="color: navy;"></bs_residue></span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"GLY"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"False"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"28"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"5.8"</span><span class="nt" style="color: navy;">></span>62A<span class="nt" style="color: navy;"></bs_residue></span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"VAL"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"False"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"29"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"6.0"</span><span class="nt" style="color: navy;">></span>132A<span class="nt" style="color: navy;"></bs_residue></span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"ASN"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"False"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"30"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"3.0"</span><span class="nt" style="color: navy;">></span>60A<span class="nt" style="color: navy;"></bs_residue></span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"ILE"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"False"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"31"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"5.7"</span><span class="nt" style="color: navy;">></span>134A<span class="nt" style="color: navy;"></bs_residue></span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"VAL"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"False"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"32"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"6.3"</span><span class="nt" style="color: navy;">></span>57A<span class="nt" style="color: navy;"></bs_residue></span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"GLN"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"True"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"33"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"3.1"</span><span class="nt" style="color: navy;">></span>19A<span class="nt" style="color: navy;"></bs_residue></span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"ASN"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"False"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"34"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"5.9"</span><span class="nt" style="color: navy;">></span>70A<span class="nt" style="color: navy;"></bs_residue></span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="xml"> <span class="nt" style="color: navy;"><bs_residue</span> <span class="na" style="color: teal;">aa=</span><span class="s" style="color: #d14;">"GLY"</span> <span class="na" style="color: teal;">contact=</span><span class="s" style="color: #d14;">"True"</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"35"</span> <span class="na" style="color: teal;">min_dist=</span><span class="s" style="color: #d14;">"2.9"</span><span class="nt" style="color: navy;">></span>66A<span class="nt" style="color: navy;"></bs_residue></span></span>
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70
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="xml"> <span class="nt" style="color: navy;"></bs_residues></span></span>
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71
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="xml"> <span class="nt" style="color: navy;"><interactions></span></span>
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72
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="xml"> <span class="nt" style="color: navy;"><hydrophobic_interactions></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -74,6 +74,9 @@</td>
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74
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr></span>61<span class="nt" style="color: navy;"></resnr></span></span>
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75
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype></span>ASP<span class="nt" style="color: navy;"></restype></span></span>
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76
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain></span>A<span class="nt" style="color: navy;"></reschain></span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr_lig></span>283<span class="nt" style="color: navy;"></resnr_lig></span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype_lig></span>NFT<span class="nt" style="color: navy;"></restype_lig></span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain_lig></span>A<span class="nt" style="color: navy;"></reschain_lig></span></span>
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77
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="xml"> <span class="nt" style="color: navy;"><dist></span>3.67<span class="nt" style="color: navy;"></dist></span></span>
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78
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="xml"> <span class="nt" style="color: navy;"><ligcarbonidx></span>1639<span class="nt" style="color: navy;"></ligcarbonidx></span></span>
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79
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="xml"> <span class="nt" style="color: navy;"><protcarbonidx></span>448<span class="nt" style="color: navy;"></protcarbonidx></span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -92,6 +95,9 @@</td>
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92
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr></span>67<span class="nt" style="color: navy;"></resnr></span></span>
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93
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype></span>TYR<span class="nt" style="color: navy;"></restype></span></span>
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94
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain></span>A<span class="nt" style="color: navy;"></reschain></span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr_lig></span>283<span class="nt" style="color: navy;"></resnr_lig></span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype_lig></span>NFT<span class="nt" style="color: navy;"></restype_lig></span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain_lig></span>A<span class="nt" style="color: navy;"></reschain_lig></span></span>
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95
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<td class="diff-line-num new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="xml"> <span class="nt" style="color: navy;"><dist></span>3.73<span class="nt" style="color: navy;"></dist></span></span>
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<td class="diff-line-num old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
96
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<td class="diff-line-num new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="xml"> <span class="nt" style="color: navy;"><ligcarbonidx></span>1622<span class="nt" style="color: navy;"></ligcarbonidx></span></span>
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<td class="diff-line-num old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
97
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<td class="diff-line-num new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="xml"> <span class="nt" style="color: navy;"><protcarbonidx></span>482<span class="nt" style="color: navy;"></protcarbonidx></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -110,6 +116,9 @@</td>
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110
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr></span>67<span class="nt" style="color: navy;"></resnr></span></span>
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<td class="diff-line-num old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
111
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<td class="diff-line-num new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype></span>TYR<span class="nt" style="color: navy;"></restype></span></span>
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<td class="diff-line-num old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
112
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<td class="diff-line-num new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain></span>A<span class="nt" style="color: navy;"></reschain></span></span>
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<td class="diff-line-num new old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr_lig></span>283<span class="nt" style="color: navy;"></resnr_lig></span></span>
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<td class="diff-line-num new old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype_lig></span>NFT<span class="nt" style="color: navy;"></restype_lig></span></span>
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<td class="diff-line-num new old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain_lig></span>A<span class="nt" style="color: navy;"></reschain_lig></span></span>
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<td class="diff-line-num old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
113
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="xml"> <span class="nt" style="color: navy;"><dist></span>3.84<span class="nt" style="color: navy;"></dist></span></span>
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<td class="diff-line-num old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
114
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="xml"> <span class="nt" style="color: navy;"><ligcarbonidx></span>1636<span class="nt" style="color: navy;"></ligcarbonidx></span></span>
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<td class="diff-line-num old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
115
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="xml"> <span class="nt" style="color: navy;"><protcarbonidx></span>481<span class="nt" style="color: navy;"></protcarbonidx></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -128,6 +137,9 @@</td>
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<td class="diff-line-num old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
128
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr></span>133<span class="nt" style="color: navy;"></resnr></span></span>
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<td class="diff-line-num old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
129
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<td class="diff-line-num new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype></span>ALA<span class="nt" style="color: navy;"></restype></span></span>
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<td class="diff-line-num old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
130
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<td class="diff-line-num new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain></span>A<span class="nt" style="color: navy;"></reschain></span></span>
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<td class="diff-line-num new old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr_lig></span>283<span class="nt" style="color: navy;"></resnr_lig></span></span>
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<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype_lig></span>NFT<span class="nt" style="color: navy;"></restype_lig></span></span>
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<td class="diff-line-num new old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain_lig></span>A<span class="nt" style="color: navy;"></reschain_lig></span></span>
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<td class="diff-line-num old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
131
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<td class="diff-line-num new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="xml"> <span class="nt" style="color: navy;"><dist></span>3.97<span class="nt" style="color: navy;"></dist></span></span>
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<td class="diff-line-num old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
132
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<td class="diff-line-num new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
144
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC144" class="line" lang="xml"> <span class="nt" style="color: navy;"><ligcarbonidx></span>1636<span class="nt" style="color: navy;"></ligcarbonidx></span></span>
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<td class="diff-line-num old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
133
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<td class="diff-line-num new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
145
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC145" class="line" lang="xml"> <span class="nt" style="color: navy;"><protcarbonidx></span>994<span class="nt" style="color: navy;"></protcarbonidx></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -148,6 +160,9 @@</td>
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<td class="diff-line-num old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
148
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr></span>19<span class="nt" style="color: navy;"></resnr></span></span>
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149
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype></span>GLN<span class="nt" style="color: navy;"></restype></span></span>
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150
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain></span>A<span class="nt" style="color: navy;"></reschain></span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr_lig></span>283<span class="nt" style="color: navy;"></resnr_lig></span></span>
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<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype_lig></span>NFT<span class="nt" style="color: navy;"></restype_lig></span></span>
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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain_lig></span>A<span class="nt" style="color: navy;"></reschain_lig></span></span>
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151
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="xml"> <span class="nt" style="color: navy;"><sidechain></span>True<span class="nt" style="color: navy;"></sidechain></span></span>
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<td class="diff-line-num old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
152
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="xml"> <span class="nt" style="color: navy;"><dist_h-a></span>2.16<span class="nt" style="color: navy;"></dist_h-a></span></span>
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153
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="xml"> <span class="nt" style="color: navy;"><dist_d-a></span>3.11<span class="nt" style="color: navy;"></dist_d-a></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -169,33 +184,12 @@</td>
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169
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="xml"> <span class="nt" style="color: navy;"></protcoo></span></span>
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<td class="diff-line-num old_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
170
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="xml"> <span class="nt" style="color: navy;"></hydrogen_bond></span></span>
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171
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="xml"> <span class="nt" style="color: navy;"><hydrogen_bond</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"2"</span><span class="nt" style="color: navy;">></span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr></span>25<span class="nt" style="color: navy;"></resnr></span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype></span>CYS<span class="nt" style="color: navy;"></restype></span></span>
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<td class="diff-line-num old old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain></span>A<span class="nt" style="color: navy;"></reschain></span></span>
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<td class="diff-line-num old old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="xml"> <span class="nt" style="color: navy;"><sidechain></span>False<span class="nt" style="color: navy;"></sidechain></span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="xml"> <span class="nt" style="color: navy;"><dist_h-a></span>2.21<span class="nt" style="color: navy;"></dist_h-a></span></span>
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<td class="diff-line-num old old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="xml"> <span class="nt" style="color: navy;"><dist_d-a></span>3.09<span class="nt" style="color: navy;"></dist_d-a></span></span>
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<td class="diff-line-num old old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="xml"> <span class="nt" style="color: navy;"><don_angle></span>146.90<span class="nt" style="color: navy;"></don_angle></span></span>
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<td class="diff-line-num old old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="xml"> <span class="nt" style="color: navy;"><protisdon></span>True<span class="nt" style="color: navy;"></protisdon></span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="xml"> <span class="nt" style="color: navy;"><donoridx></span>183<span class="nt" style="color: navy;"></donoridx></span></span>
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<td class="diff-line-num old old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="xml"> <span class="nt" style="color: navy;"><donortype></span>Nam<span class="nt" style="color: navy;"></donortype></span></span>
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<td class="diff-line-num old old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="xml"> <span class="nt" style="color: navy;"><acceptoridx></span>1649<span class="nt" style="color: navy;"></acceptoridx></span></span>
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<td class="diff-line-num old old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="xml"> <span class="nt" style="color: navy;"><acceptortype></span>N2<span class="nt" style="color: navy;"></acceptortype></span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="xml"> <span class="nt" style="color: navy;"><ligcoo></span></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="xml"> <span class="nt" style="color: navy;"><x></span>2.820<span class="nt" style="color: navy;"></x></span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="xml"> <span class="nt" style="color: navy;"><y></span>18.145<span class="nt" style="color: navy;"></y></span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="xml"> <span class="nt" style="color: navy;"><z></span>6.806<span class="nt" style="color: navy;"></z></span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="xml"> <span class="nt" style="color: navy;"></ligcoo></span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="xml"> <span class="nt" style="color: navy;"><protcoo></span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="xml"> <span class="nt" style="color: navy;"><x></span>3.306<span class="nt" style="color: navy;"></x></span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="xml"> <span class="nt" style="color: navy;"><y></span>18.620<span class="nt" style="color: navy;"></y></span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="xml"> <span class="nt" style="color: navy;"><z></span>9.817<span class="nt" style="color: navy;"></z></span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="xml"> <span class="nt" style="color: navy;"></protcoo></span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="xml"> <span class="nt" style="color: navy;"></hydrogen_bond></span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="xml"> <span class="nt" style="color: navy;"><hydrogen_bond</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"3"</span><span class="nt" style="color: navy;">></span></span>
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196
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr></span>61<span class="nt" style="color: navy;"></resnr></span></span>
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197
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype></span>ASP<span class="nt" style="color: navy;"></restype></span></span>
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<td class="diff-line-num old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
198
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain></span>A<span class="nt" style="color: navy;"></reschain></span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr_lig></span>283<span class="nt" style="color: navy;"></resnr_lig></span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype_lig></span>NFT<span class="nt" style="color: navy;"></restype_lig></span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain_lig></span>A<span class="nt" style="color: navy;"></reschain_lig></span></span>
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199
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="xml"> <span class="nt" style="color: navy;"><sidechain></span>True<span class="nt" style="color: navy;"></sidechain></span></span>
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200
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="xml"> <span class="nt" style="color: navy;"><dist_h-a></span>2.26<span class="nt" style="color: navy;"></dist_h-a></span></span>
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201
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="xml"> <span class="nt" style="color: navy;"><dist_d-a></span>2.99<span class="nt" style="color: navy;"></dist_d-a></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -216,10 +210,13 @@</td>
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216
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="xml"> <span class="nt" style="color: navy;"><z></span>9.223<span class="nt" style="color: navy;"></z></span></span>
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217
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="xml"> <span class="nt" style="color: navy;"></protcoo></span></span>
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218
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="xml"> <span class="nt" style="color: navy;"></hydrogen_bond></span></span>
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219
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="xml"> <span class="nt" style="color: navy;"><hydrogen_bond</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"<span class="idiff left right">4</span>"</span><span class="nt" style="color: navy;">></span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="xml"> <span class="nt" style="color: navy;"><hydrogen_bond</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"<span class="idiff left right">3</span>"</span><span class="nt" style="color: navy;">></span></span>
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220
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr></span>61<span class="nt" style="color: navy;"></resnr></span></span>
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221
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype></span>ASP<span class="nt" style="color: navy;"></restype></span></span>
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222
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216
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain></span>A<span class="nt" style="color: navy;"></reschain></span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr_lig></span>283<span class="nt" style="color: navy;"></resnr_lig></span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype_lig></span>NFT<span class="nt" style="color: navy;"></restype_lig></span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain_lig></span>A<span class="nt" style="color: navy;"></reschain_lig></span></span>
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223
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220
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="xml"> <span class="nt" style="color: navy;"><sidechain></span>True<span class="nt" style="color: navy;"></sidechain></span></span>
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224
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221
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="xml"> <span class="nt" style="color: navy;"><dist_h-a></span>1.98<span class="nt" style="color: navy;"></dist_h-a></span></span>
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225
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222
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="xml"> <span class="nt" style="color: navy;"><dist_d-a></span>2.99<span class="nt" style="color: navy;"></dist_d-a></span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -240,10 +237,13 @@</td>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="xml"> <span class="nt" style="color: navy;"><z></span>9.223<span class="nt" style="color: navy;"></z></span></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="xml"> <span class="nt" style="color: navy;"></protcoo></span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="xml"> <span class="nt" style="color: navy;"></hydrogen_bond></span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="xml"> <span class="nt" style="color: navy;"><hydrogen_bond</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"<span class="idiff left right">5</span>"</span><span class="nt" style="color: navy;">></span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="xml"> <span class="nt" style="color: navy;"><hydrogen_bond</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"<span class="idiff left right">4</span>"</span><span class="nt" style="color: navy;">></span></span>
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244
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr></span>66<span class="nt" style="color: navy;"></resnr></span></span>
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242
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype></span>GLY<span class="nt" style="color: navy;"></restype></span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain></span>A<span class="nt" style="color: navy;"></reschain></span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr_lig></span>283<span class="nt" style="color: navy;"></resnr_lig></span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype_lig></span>NFT<span class="nt" style="color: navy;"></restype_lig></span></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain_lig></span>A<span class="nt" style="color: navy;"></reschain_lig></span></span>
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247
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247
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="xml"> <span class="nt" style="color: navy;"><sidechain></span>False<span class="nt" style="color: navy;"></sidechain></span></span>
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248
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248
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="xml"> <span class="nt" style="color: navy;"><dist_h-a></span>2.33<span class="nt" style="color: navy;"></dist_h-a></span></span>
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249
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="xml"> <span class="nt" style="color: navy;"><dist_d-a></span>3.18<span class="nt" style="color: navy;"></dist_d-a></span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -264,10 +264,13 @@</td>
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264
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="xml"> <span class="nt" style="color: navy;"><z></span>8.576<span class="nt" style="color: navy;"></z></span></span>
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265
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="xml"> <span class="nt" style="color: navy;"></protcoo></span></span>
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266
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="xml"> <span class="nt" style="color: navy;"></hydrogen_bond></span></span>
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267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="xml"> <span class="nt" style="color: navy;"><hydrogen_bond</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"<span class="idiff left right">6</span>"</span><span class="nt" style="color: navy;">></span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="xml"> <span class="nt" style="color: navy;"><hydrogen_bond</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"<span class="idiff left right">5</span>"</span><span class="nt" style="color: navy;">></span></span>
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268
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr></span>66<span class="nt" style="color: navy;"></resnr></span></span>
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269
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype></span>GLY<span class="nt" style="color: navy;"></restype></span></span>
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270
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain></span>A<span class="nt" style="color: navy;"></reschain></span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr_lig></span>283<span class="nt" style="color: navy;"></resnr_lig></span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype_lig></span>NFT<span class="nt" style="color: navy;"></restype_lig></span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain_lig></span>A<span class="nt" style="color: navy;"></reschain_lig></span></span>
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271
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274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="xml"> <span class="nt" style="color: navy;"><sidechain></span>False<span class="nt" style="color: navy;"></sidechain></span></span>
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272
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="xml"> <span class="nt" style="color: navy;"><dist_h-a></span>2.05<span class="nt" style="color: navy;"></dist_h-a></span></span>
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273
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="xml"> <span class="nt" style="color: navy;"><dist_d-a></span>2.95<span class="nt" style="color: navy;"></dist_d-a></span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -288,10 +291,13 @@</td>
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288
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291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="xml"> <span class="nt" style="color: navy;"><z></span>8.621<span class="nt" style="color: navy;"></z></span></span>
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289
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="xml"> <span class="nt" style="color: navy;"></protcoo></span></span>
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290
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="xml"> <span class="nt" style="color: navy;"></hydrogen_bond></span></span>
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291
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="xml"> <span class="nt" style="color: navy;"><hydrogen_bond</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"<span class="idiff left right">7</span>"</span><span class="nt" style="color: navy;">></span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="xml"> <span class="nt" style="color: navy;"><hydrogen_bond</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"<span class="idiff left right">6</span>"</span><span class="nt" style="color: navy;">></span></span>
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292
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295
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr></span>158<span class="nt" style="color: navy;"></resnr></span></span>
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293
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296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype></span>ASN<span class="nt" style="color: navy;"></restype></span></span>
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294
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain></span>A<span class="nt" style="color: navy;"></reschain></span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr_lig></span>283<span class="nt" style="color: navy;"></resnr_lig></span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype_lig></span>NFT<span class="nt" style="color: navy;"></restype_lig></span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain_lig></span>A<span class="nt" style="color: navy;"></reschain_lig></span></span>
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295
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301
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="xml"> <span class="nt" style="color: navy;"><sidechain></span>False<span class="nt" style="color: navy;"></sidechain></span></span>
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296
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302
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="xml"> <span class="nt" style="color: navy;"><dist_h-a></span>1.95<span class="nt" style="color: navy;"></dist_h-a></span></span>
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297
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303
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="xml"> <span class="nt" style="color: navy;"><dist_d-a></span>2.92<span class="nt" style="color: navy;"></dist_d-a></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -318,6 +324,9 @@</td>
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318
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr></span>159<span class="nt" style="color: navy;"></resnr></span></span>
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319
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325
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype></span>HIS<span class="nt" style="color: navy;"></restype></span></span>
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320
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326
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain></span>A<span class="nt" style="color: navy;"></reschain></span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr_lig></span>283<span class="nt" style="color: navy;"></resnr_lig></span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype_lig></span>NFT<span class="nt" style="color: navy;"></restype_lig></span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain_lig></span>A<span class="nt" style="color: navy;"></reschain_lig></span></span>
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321
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330
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="xml"> <span class="nt" style="color: navy;"><dist_a-w></span>3.67<span class="nt" style="color: navy;"></dist_a-w></span></span>
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322
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331
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="xml"> <span class="nt" style="color: navy;"><dist_d-w></span>3.13<span class="nt" style="color: navy;"></dist_d-w></span></span>
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323
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332
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="xml"> <span class="nt" style="color: navy;"><don_angle></span>126.73<span class="nt" style="color: navy;"></don_angle></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -344,36 +353,6 @@</td>
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344
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353
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="xml"> <span class="nt" style="color: navy;"><z></span>3.309<span class="nt" style="color: navy;"></z></span></span>
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<td class="diff-line-num old_line" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
345
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354
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="xml"> <span class="nt" style="color: navy;"></watercoo></span></span>
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<td class="diff-line-num old_line" data-linenumber="346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
346
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355
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="xml"> <span class="nt" style="color: navy;"></water_bridge></span></span>
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347
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="xml"> <span class="nt" style="color: navy;"><water_bridge</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"2"</span><span class="nt" style="color: navy;">></span></span>
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348
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr></span>177<span class="nt" style="color: navy;"></resnr></span></span>
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349
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype></span>TRP<span class="nt" style="color: navy;"></restype></span></span>
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350
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain></span>A<span class="nt" style="color: navy;"></reschain></span></span>
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351
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="xml"> <span class="nt" style="color: navy;"><dist_a-w></span>3.96<span class="nt" style="color: navy;"></dist_a-w></span></span>
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352
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="xml"> <span class="nt" style="color: navy;"><dist_d-w></span>3.04<span class="nt" style="color: navy;"></dist_d-w></span></span>
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353
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="xml"> <span class="nt" style="color: navy;"><don_angle></span>125.14<span class="nt" style="color: navy;"></don_angle></span></span>
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354
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="xml"> <span class="nt" style="color: navy;"><water_angle></span>84.15<span class="nt" style="color: navy;"></water_angle></span></span>
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355
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="xml"> <span class="nt" style="color: navy;"><protisdon></span>True<span class="nt" style="color: navy;"></protisdon></span></span>
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356
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="xml"> <span class="nt" style="color: navy;"><donor_idx></span>1380<span class="nt" style="color: navy;"></donor_idx></span></span>
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357
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="xml"> <span class="nt" style="color: navy;"><donortype></span>Nar<span class="nt" style="color: navy;"></donortype></span></span>
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358
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="xml"> <span class="nt" style="color: navy;"><acceptor_idx></span>1649<span class="nt" style="color: navy;"></acceptor_idx></span></span>
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359
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="xml"> <span class="nt" style="color: navy;"><acceptortype></span>N2<span class="nt" style="color: navy;"></acceptortype></span></span>
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360
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="xml"> <span class="nt" style="color: navy;"><water_idx></span>1735<span class="nt" style="color: navy;"></water_idx></span></span>
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361
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="xml"> <span class="nt" style="color: navy;"><ligcoo></span></span>
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362
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="xml"> <span class="nt" style="color: navy;"><x></span>2.820<span class="nt" style="color: navy;"></x></span></span>
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363
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="xml"> <span class="nt" style="color: navy;"><y></span>18.145<span class="nt" style="color: navy;"></y></span></span>
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364
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="xml"> <span class="nt" style="color: navy;"><z></span>6.806<span class="nt" style="color: navy;"></z></span></span>
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365
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="xml"> <span class="nt" style="color: navy;"></ligcoo></span></span>
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366
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="xml"> <span class="nt" style="color: navy;"><protcoo></span></span>
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367
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="xml"> <span class="nt" style="color: navy;"><x></span>7.577<span class="nt" style="color: navy;"></x></span></span>
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368
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="xml"> <span class="nt" style="color: navy;"><y></span>15.116<span class="nt" style="color: navy;"></y></span></span>
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369
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="xml"> <span class="nt" style="color: navy;"><z></span>5.463<span class="nt" style="color: navy;"></z></span></span>
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370
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="xml"> <span class="nt" style="color: navy;"></protcoo></span></span>
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371
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="xml"> <span class="nt" style="color: navy;"><watercoo></span></span>
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="xml"> <span class="nt" style="color: navy;"><x></span>4.665<span class="nt" style="color: navy;"></x></span></span>
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373
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="xml"> <span class="nt" style="color: navy;"><y></span>15.397<span class="nt" style="color: navy;"></y></span></span>
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374
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="xml"> <span class="nt" style="color: navy;"><z></span>4.635<span class="nt" style="color: navy;"></z></span></span>
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375
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="xml"> <span class="nt" style="color: navy;"></watercoo></span></span>
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376
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="xml"> <span class="nt" style="color: navy;"></water_bridge></span></span>
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377
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356
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="xml"> <span class="nt" style="color: navy;"></water_bridges></span></span>
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378
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357
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="xml"> <span class="nt" style="color: navy;"><salt_bridges/></span></span>
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379
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358
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="xml"> <span class="nt" style="color: navy;"><pi_stacks/></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -383,6 +362,9 @@</td>
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383
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362
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr></span>67<span class="nt" style="color: navy;"></resnr></span></span>
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384
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363
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype></span>TYR<span class="nt" style="color: navy;"></restype></span></span>
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385
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364
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain></span>A<span class="nt" style="color: navy;"></reschain></span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr_lig></span>283<span class="nt" style="color: navy;"></resnr_lig></span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype_lig></span>NFT<span class="nt" style="color: navy;"></restype_lig></span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain_lig></span>A<span class="nt" style="color: navy;"></reschain_lig></span></span>
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386
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368
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="xml"> <span class="nt" style="color: navy;"><sidechain></span>True<span class="nt" style="color: navy;"></sidechain></span></span>
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387
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369
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="xml"> <span class="nt" style="color: navy;"><dist></span>3.37<span class="nt" style="color: navy;"></dist></span></span>
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<td class="diff-line-num old_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
388
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="xml"> <span class="nt" style="color: navy;"><don_angle></span>156.70<span class="nt" style="color: navy;"></don_angle></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -406,6 +388,9 @@</td>
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406
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr></span>157<span class="nt" style="color: navy;"></resnr></span></span>
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407
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389
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype></span>LEU<span class="nt" style="color: navy;"></restype></span></span>
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<td class="diff-line-num old_line" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
408
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390
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain></span>A<span class="nt" style="color: navy;"></reschain></span></span>
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<td class="diff-line-num new old_line" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="xml"> <span class="nt" style="color: navy;"><resnr_lig></span>283<span class="nt" style="color: navy;"></resnr_lig></span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="xml"> <span class="nt" style="color: navy;"><restype_lig></span>NFT<span class="nt" style="color: navy;"></restype_lig></span></span>
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<td class="diff-line-num new old_line" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="xml"> <span class="nt" style="color: navy;"><reschain_lig></span>A<span class="nt" style="color: navy;"></reschain_lig></span></span>
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="xml"> <span class="nt" style="color: navy;"><sidechain></span>False<span class="nt" style="color: navy;"></sidechain></span></span>
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="xml"> <span class="nt" style="color: navy;"><dist></span>3.24<span class="nt" style="color: navy;"></dist></span></span>
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="xml"> <span class="nt" style="color: navy;"><don_angle></span>141.32<span class="nt" style="color: navy;"></don_angle></span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -429,12 +414,14 @@</td>
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="xml"> <span class="nt" style="color: navy;"><metal_complexes/></span></span>
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="xml"> <span class="nt" style="color: navy;"></interactions></span></span>
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="xml"> <span class="nt" style="color: navy;"><mappings></span></span>
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="xml"> <span class="nt" style="color: navy;"><smiles_to_pdb></span>1:16<span class="idiff left right">49,2:1648,3:1630,4:1629,5:1637,6:1632,7:1631,8:1624,9:1625,10:1626,11:1627,12:1628,13:1623,14:1621,15:1620,16:1619,17:1618,18:1622,19:1617,20:1639,21:1640,22:1641,23:1642,24:1643,25:1644,26:1645,27:1646,28:1647,29:1633,30:1634,31:1635,32:1636,33:1638</span><span class="nt" style="color: navy;"></smiles_to_pdb></span></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="xml"> <span class="nt" style="color: navy;"><smiles_to_pdb></span>1:16<span class="idiff left right">36,2:1634,3:1635,4:1633,5:1632,6:1631,7:1624,8:1623,9:1621,10:1620,11:1619,12:1618,13:1622,14:1617,15:1639,16:1640,17:1641,18:1642,19:1643,20:1644,21:1645,22:1646,23:1647,24:1625,25:1626,26:1627,27:1628,28:1637,29:1638,30:1629,31:1630,32:1648,33:1649</span><span class="nt" style="color: navy;"></smiles_to_pdb></span></span>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="xml"> <span class="nt" style="color: navy;"></mappings></span></span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="xml"> <span class="nt" style="color: navy;"></bindingsite></span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="xml"> <span class="nt" style="color: navy;"><date_of_creation></span>2018/08/07<span class="nt" style="color: navy;"></date_of_creation></span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="xml"> <span class="nt" style="color: navy;"><citation_information></span>Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler. Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315<span class="nt" style="color: navy;"></citation_information></span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="xml"> <span class="nt" style="color: navy;"><mode></span>default<span class="nt" style="color: navy;"></mode></span></span>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="xml"> <span class="nt" style="color: navy;"><pdbid></span>1VSN<span class="nt" style="color: navy;"></pdbid></span></span>
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="xml"> <span class="nt" style="color: navy;"><filetype></span>PDB<span class="nt" style="color: navy;"></filetype></span></span>
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="xml"> <span class="nt" style="color: navy;"><pdbfile></span>1vsn.pdb<span class="nt" style="color: navy;"></pdbfile></span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="xml"> <span class="nt" style="color: navy;"><pdbfile></span>./1vsn.pdb<span class="nt" style="color: navy;"></pdbfile></span></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="xml"> <span class="nt" style="color: navy;"><pdbfixes></span>False<span class="nt" style="color: navy;"></pdbfixes></span></span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="xml"> <span class="nt" style="color: navy;"><filename></span>1vsn.pdb<span class="nt" style="color: navy;"></filename></span></span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="xml"> <span class="nt" style="color: navy;"><excluded_ligands/></span></span>
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<a href="https://salsa.debian.org/med-team/plip/compare/5b8735d8202fdf271d2e6ac7693c538d3f072871...1549568ef24d351577628567a87eaa5c72bd3c96#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,7 +22,7 @@ setup(name='plip',</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">author_email</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'sebastian.salentin@tu-dresden.de'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">license</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'GPLv2'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">packages</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'plip'</span><span class="p">,</span> <span class="s" style="color: #d14;">'plip/modules'</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">scripts</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'plip/plipcmd'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">scripts</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'plip/plipcmd<span class="idiff left right">.py</span>'</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="s" style="color: #d14;">'openbabel'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="s" style="color: #d14;">'numpy'</span><span class="p">,</span></span>
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