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GitLab

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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/a390324dd12ca8dccd970ab27aa8d7ecadcf1acc">a390324d</a></strong>

<div>

<span>by Alexandre Mestiashvili</span>

<i>at 2018-06-07T20:04:11+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.4.2+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/plip/commit/dfc68c30c2673293bccfb8ef05f9aac2a87f46e9">dfc68c30</a></strong>

<div>

<span>by Alexandre Mestiashvili</span>

<i>at 2018-06-07T20:04:11+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.4.2+dfsg'

Update to upstream version '1.4.2+dfsg'

with Debian dir bea40d4cce0e3e13b81e76ba4f0279762f1b6fcf</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/plip/commit/5b8735d8202fdf271d2e6ac7693c538d3f072871">5b8735d8</a></strong>

<div>

<span>by Alexandre Mestiashvili</span>

<i>at 2018-06-07T20:05:51+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog

Gbp-Dch: Ignore

</pre>

</li>

</ul>

<h4>9 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#3251d7a8143ce2e789f0468513df8f285f842c3a">

CHANGES.txt

</a>

</li>

<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#0ebacb04510ce4a5c58aafbe80203eb2da3b1fcf">

plip/modules/config.py

</a>

</li>

<li class="file-stats">

<a href="#df212bd3edccb5c6cb6e3ffe48ce9304993d81ff">

plip/modules/plipxml.py

</a>

</li>

<li class="file-stats">

<a href="#3b337656bf3a34912a29016ac837c4dfecada0e5">

plip/modules/preparation.py

</a>

</li>

<li class="file-stats">

<a href="#86a2fcb72e262191b5bad9c18b91b7cba3b7ea36">

plip/modules/report.py

</a>

</li>

<li class="file-stats">

<a href="#df20c64fcda0c0211e8d65f6fb353c8b81b85b51">

plip/plipcmd

</a>

</li>

<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/23b74ed79058a03cb56204bad72032d259596a65...5b8735d8202fdf271d2e6ac7693c538d3f072871#3251d7a8143ce2e789f0468513df8f285f842c3a"><strong>CHANGES.txt</strong></a>

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<td class="diff-line-num old_line" data-linenumber="1" 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">

1

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<td class="diff-line-num new_line" data-linenumber="1" 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">

1

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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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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2" 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">

2

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<td class="diff-line-num new_line" data-linenumber="2" 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">

2

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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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" 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">

3

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<td class="diff-line-num new_line" data-linenumber="3" 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">

3

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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="LC3" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_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="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">

4

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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"># 1.4.2</span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="5" 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">

5

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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="LC5" class="line" lang="plaintext">* Adds "--name" option to change name of output files</span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="6" 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">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">* Adds "--nopdbcanmap" option to skip calculation of canonical->PDB mapping which can lead to segfaults with OpenBabel</span>

</pre>

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<td class="diff-line-num new old_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="diff-line-num new new_line" data-linenumber="7" 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">

7

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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="LC7" class="line" lang="plaintext">* Improved handling of ligand names</span>

</pre>

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<td class="diff-line-num new old_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="diff-line-num new new_line" data-linenumber="8" 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">

8

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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="LC8" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" 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">

4

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<td class="diff-line-num new_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">

9

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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="LC9" class="line" lang="plaintext"># 1.4.1</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" 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">

5

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<td class="diff-line-num new_line" data-linenumber="10" 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">

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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="LC10" class="line" lang="plaintext">* Improved import of modules</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6" 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">

6

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<td class="diff-line-num new_line" data-linenumber="11" 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">

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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="LC11" class="line" lang="plaintext">* Corrections for README and documentation</span>

</pre>

</td>

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</table>

<br>

</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/plip/compare/23b74ed79058a03cb56204bad72032d259596a65...5b8735d8202fdf271d2e6ac7693c538d3f072871#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="33" 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="33" 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">@@ -33,7 +33,7 @@ pymol 1VSN_NFT_A_283.pse</td>

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<td class="diff-line-num old_line" data-linenumber="33" 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">

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<td class="diff-line-num new_line" data-linenumber="33" 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">

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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="LC33" class="line" lang="markdown">In your terminal, add the PLIP repository to your PYTHONPATH variable.</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="34" 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">

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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="LC34" class="line" lang="markdown">For our example, we also download a PDB file for testing.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="35" 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">

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<td class="diff-line-num new_line" data-linenumber="35" 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">

35

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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="LC35" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="36" 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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<td class="diff-line-num new_line old" data-linenumber="36" 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="LC36" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: teal;">PYTHONPATH</span><span class="o" style="font-weight: 600;">=</span>~/pliptool<span class="idiff left right">/plip</span>:<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">PYTHONPATH</span><span class="k" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: teal;">PYTHONPATH</span><span class="o" style="font-weight: 600;">=</span>~/pliptool:<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">PYTHONPATH</span><span class="k" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">cd</span> /tmp <span class="o" style="font-weight: 600;">&&</span> wget http://files.rcsb.org/download/1EVE.pdb</span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown">python</span>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="markdown"><span class="p">```</span></span>

</pre>

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<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/plip/compare/23b74ed79058a03cb56204bad72032d259596a65...5b8735d8202fdf271d2e6ac7693c538d3f072871#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">plip (1.4.2+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">  * New upstream version 1.4.2+dfsg</span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Alexandre Mestiashvili <mestia@debian.org>  Thu, 07 Jun 2018 20:05:34 +0200</span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></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="LC7" class="line" lang="plaintext">plip (1.4.1+dfsg-1) unstable; urgency=medium</span>

</pre>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">  * New upstream version 1.4.1+dfsg</span>

</pre>

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<br>

</li>

<li id="0ebacb04510ce4a5c58aafbe80203eb2da3b1fcf">

<a href="https://salsa.debian.org/med-team/plip/compare/23b74ed79058a03cb56204bad72032d259596a65...5b8735d8202fdf271d2e6ac7693c538d3f072871#0ebacb04510ce4a5c58aafbe80203eb2da3b1fcf"><strong>plip/modules/config.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="23" 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="23" 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">@@ -23,6 +23,8 @@ PEPTIDES = []  # Definition which chains should be considered as peptide ligands</td>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="n" style="color: #333;">INTRA</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="n" style="color: #333;">KEEPMOD</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="n" style="color: #333;">DNARECEPTOR</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<td class="diff-line-num new old_line" data-linenumber="26" 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="26" 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="LC26" class="line" lang="python"><span class="n" style="color: #333;">OUTPUTFILENAME</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"report"</span> <span class="c" style="color: #998; font-style: italic;"># Naming for the TXT and XML report files</span></span>

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<td class="diff-line-num new new_line" data-linenumber="27" 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="LC27" class="line" lang="python"><span class="n" style="color: #333;">NOPDBCANMAP</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span> <span class="c" style="color: #998; font-style: italic;"># Skip calculation of mapping canonical atom order: PDB atom order</span></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Configuration file for Protein-Ligand Interaction Profiler (PLIP)</span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Set thresholds for detection of interactions</span></span>

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<br>

</li>

<li id="df212bd3edccb5c6cb6e3ffe48ce9304993d81ff">

<a href="https://salsa.debian.org/med-team/plip/compare/23b74ed79058a03cb56204bad72032d259596a65...5b8735d8202fdf271d2e6ac7693c538d3f072871#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">@@ -53,10 +53,10 @@ class Interaction(XMLStorage):</td>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">interaction_part</span><span class="p">):</span></span>

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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="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">interaction_part</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'id'</span><span class="p">)</span></span>

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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;">resnr</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="n" style="color: #333;">interaction_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'resnr'</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;">restype</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="n" style="color: #333;">interaction_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'restype'</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;">restype</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="n" style="color: #333;">interaction_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'restype'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">force_string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</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;">reschain</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="n" style="color: #333;">interaction_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'reschain'</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;">True</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC58" 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;">resnr_lig</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="n" style="color: #333;">interaction_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'resnr_lig'</span><span class="p">)</span></span>

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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;">restype_lig</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="n" style="color: #333;">interaction_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'restype_lig'</span><span class="p">)</span></span>

</pre>

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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;">restype_lig</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="n" style="color: #333;">interaction_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'restype_lig'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">force_string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">)</span></span>

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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;">reschain_lig</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="n" style="color: #333;">interaction_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'reschain_lig'</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;">True</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC61" 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;">ligcoo</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;">getcoordinates</span><span class="p">(</span><span class="n" style="color: #333;">interaction_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'ligcoo'</span><span class="p">)</span></span>

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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;">protcoo</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;">getcoordinates</span><span class="p">(</span><span class="n" style="color: #333;">interaction_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'protcoo'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="87" 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="87" 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">@@ -87,8 +87,8 @@ class HydrogenBond(Interaction):</td>

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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;">protisdon</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="n" style="color: #333;">hbond_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'protisdon'</span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="88" 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">

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<pre style="margin: 0;"> <span id="LC88" 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;">donoridx</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="n" style="color: #333;">hbond_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'donoridx'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC89" 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;">acceptoridx</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="n" style="color: #333;">hbond_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'acceptoridx'</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC90" 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;">donortype</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="n" style="color: #333;">hbond_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'donortype'</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC91" 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;">acceptortype</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="n" style="color: #333;">hbond_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'acceptortype'</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC90" 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;">donortype</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="n" style="color: #333;">hbond_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'donortype'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">force_string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="92" 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="LC91" 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;">acceptortype</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="n" style="color: #333;">hbond_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'acceptortype'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">force_string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="92" 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">

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="93" 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">

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<td class="diff-line-num new_line" data-linenumber="93" 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">

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="94" 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">

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">WaterBridge</span><span class="p">(</span><span class="n" style="color: #333;">Interaction</span><span class="p">):</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="105" 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="105" 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">@@ -105,8 +105,8 @@ class WaterBridge(Interaction):</td>

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC106" 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;">donor_idx</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="n" style="color: #333;">wbridge_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'donor_idx'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC107" 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;">acceptor_idx</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="n" style="color: #333;">wbridge_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'acceptor_idx'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="108" 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">

108

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<td class="diff-line-num new_line old" data-linenumber="108" 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="LC108" 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;">donortype</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="n" style="color: #333;">wbridge_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'donortype'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="108" 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="LC109" 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;">acceptortype</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="n" style="color: #333;">wbridge_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'acceptortype'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="110" 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="108" 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="LC108" 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;">donortype</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="n" style="color: #333;">wbridge_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'donortype'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">force_string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="110" 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="109" 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="LC109" 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;">acceptortype</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="n" style="color: #333;">wbridge_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'acceptortype'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">force_string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC110" 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;">water_idx</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="n" style="color: #333;">wbridge_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'water_idx'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC111" 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;">watercoo</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;">getcoordinates</span><span class="p">(</span><span class="n" style="color: #333;">wbridge_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'watercoo'</span><span class="p">)</span></span>

</pre>

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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">

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -118,7 +118,7 @@ class SaltBridge(Interaction):</td>

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<td class="diff-line-num old_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">

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python">        <span class="n" style="color: #333;">Interaction</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">sbridge_part</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="119" 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">

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<pre style="margin: 0;"> <span id="LC119" 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;">dist</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="n" style="color: #333;">sbridge_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'dist'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="120" 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">

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<pre style="margin: 0;"> <span id="LC120" 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;">protispos</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="n" style="color: #333;">sbridge_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'protispos'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="121" 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="LC121" 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;">lig_group</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="n" style="color: #333;">sbridge_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'lig_group'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="122" 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">

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<pre style="margin: 0;">+<span id="LC121" 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;">lig_group</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="n" style="color: #333;">sbridge_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'lig_group'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">force_string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC122" 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;">lig_idx_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">tagpart</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">text</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tagpart</span> <span class="ow" style="font-weight: 600;">in</span></span>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python">                             <span class="n" style="color: #333;">sbridge_part</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;">'lig_idx_list/idx'</span><span class="p">)]</span></span>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="157" 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="157" 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">@@ -157,8 +157,8 @@ class HalogenBond(Interaction):</td>

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<td class="diff-line-num old_line" data-linenumber="157" 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">

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<pre style="margin: 0;"> <span id="LC157" 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;">dist</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="n" style="color: #333;">halogen_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'dist'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC158" 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;">don_angle</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="n" style="color: #333;">halogen_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'don_angle'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC159" 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;">acc_angle</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="n" style="color: #333;">halogen_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'acc_angle'</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC160" 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;">donortype</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="n" style="color: #333;">halogen_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'donortype'</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC161" 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;">acceptortype</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="n" style="color: #333;">halogen_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'acceptortype'</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC160" 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;">donortype</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="n" style="color: #333;">halogen_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'donortype'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">force_string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="162" 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="LC161" 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;">acceptortype</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="n" style="color: #333;">halogen_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'acceptortype'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">force_string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC162" 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;">don_idx</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="n" style="color: #333;">halogen_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'don_idx'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC163" 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;">acc_idx</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="n" style="color: #333;">halogen_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'acc_idx'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC164" 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;">sidechain</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="n" style="color: #333;">halogen_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'sidechain'</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold new_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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -170,14 +170,14 @@ class MetalComplex(Interaction):</td>

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">metalcomplex_part</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="171" 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">

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="python">        <span class="n" style="color: #333;">Interaction</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">metalcomplex_part</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="172" 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">

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<pre style="margin: 0;"> <span id="LC172" 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_idx</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="n" style="color: #333;">metalcomplex_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'metal_idx'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="173" 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="LC173" 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_type</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="n" style="color: #333;">metalcomplex_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'metal_type'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="174" 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="173" 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="LC173" 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_type</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="n" style="color: #333;">metalcomplex_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'metal_type'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">force_string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="174" 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">

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<td class="diff-line-num new_line" data-linenumber="174" 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">

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<pre style="margin: 0;"> <span id="LC174" 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;">target_idx</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="n" style="color: #333;">metalcomplex_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'target_idx'</span><span class="p">)</span></span>

</pre>

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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">

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC175" 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;">target_type</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="n" style="color: #333;">metalcomplex_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'target_type'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="176" 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="175" 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="LC175" 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;">target_type</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="n" style="color: #333;">metalcomplex_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'target_type'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">force_string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="176" 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">

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<pre style="margin: 0;"> <span id="LC176" 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;">coordination</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="n" style="color: #333;">metalcomplex_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'coordination'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_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">

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC177" 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;">dist</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="n" style="color: #333;">metalcomplex_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'dist'</span><span class="p">)</span></span>

</pre>

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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">

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC178" 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;">location</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="n" style="color: #333;">metalcomplex_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'location'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="179" 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="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">

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<pre style="margin: 0;">+<span id="LC178" 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;">location</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="n" style="color: #333;">metalcomplex_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'location'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">force_string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="179" 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">

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<td class="diff-line-num new_line" data-linenumber="179" 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">

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<pre style="margin: 0;"> <span id="LC179" 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;">rms</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="n" style="color: #333;">metalcomplex_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'rms'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="180" 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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<td class="diff-line-num new_line old" data-linenumber="180" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC180" 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;">geometry</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="n" style="color: #333;">metalcomplex_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'geometry'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC180" 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;">geometry</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="n" style="color: #333;">metalcomplex_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'geometry'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">force_string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC181" 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;">complexnum</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="n" style="color: #333;">metalcomplex_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'complexnum'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC182" 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;">targetcoo</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;">getcoordinates</span><span class="p">(</span><span class="n" style="color: #333;">metalcomplex_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'targetcoo'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC183" 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;">metalcoo</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;">getcoordinates</span><span class="p">(</span><span class="n" style="color: #333;">metalcomplex_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'metalcoo'</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="190" 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="190" 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">@@ -190,13 +190,13 @@ class BSite(XMLStorage):</td>

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<pre style="margin: 0;"> <span id="LC190" 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;">pdbid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pdbid</span></span>

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<pre style="margin: 0;"> <span id="LC191" 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;">bsid</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;">bindingsite</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;">'identifiers/*/text()'</span><span class="p">)[</span><span class="mi" style="color: #099;">2</span><span class="p">:</span><span class="mi" style="color: #099;">5</span><span class="p">])</span></span>

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<pre style="margin: 0;"> <span id="LC192" 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;">uniqueid</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="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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bsid</span><span class="p">])</span></span>

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<td class="diff-line-num new_line old" data-linenumber="193" 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="LC193" 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;">hetid</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="n" style="color: #333;">bindingsite</span><span class="p">,</span> <span class="s" style="color: #d14;">'identifiers/hetid'</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC194" 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;">longname</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="n" style="color: #333;">bindingsite</span><span class="p">,</span> <span class="s" style="color: #d14;">'identifiers/longname'</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC195" 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;">ligtype</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="n" style="color: #333;">bindingsite</span><span class="p">,</span> <span class="s" style="color: #d14;">'identifiers/ligtype'</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC196" 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="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="n" style="color: #333;">bindingsite</span><span class="p">,</span> <span class="s" style="color: #d14;">'identifiers/smiles'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC197" 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;">inchikey</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="n" style="color: #333;">bindingsite</span><span class="p">,</span> <span class="s" style="color: #d14;">'identifiers/inchikey'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC193" 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;">hetid</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="n" style="color: #333;">bindingsite</span><span class="p">,</span> <span class="s" style="color: #d14;">'identifiers/hetid'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">force_string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="198" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="194" 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="LC194" 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;">longname</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="n" style="color: #333;">bindingsite</span><span class="p">,</span> <span class="s" style="color: #d14;">'identifiers/longname'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">force_string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="198" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="195" 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">

195

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<pre style="margin: 0;">+<span id="LC195" 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;">ligtype</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="n" style="color: #333;">bindingsite</span><span class="p">,</span> <span class="s" style="color: #d14;">'identifiers/ligtype'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">force_string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="198" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="196" 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">

196

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<pre style="margin: 0;">+<span id="LC196" 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="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="n" style="color: #333;">bindingsite</span><span class="p">,</span> <span class="s" style="color: #d14;">'identifiers/smiles'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">force_string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="198" 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="197" 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">

197

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<pre style="margin: 0;">+<span id="LC197" 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;">inchikey</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="n" style="color: #333;">bindingsite</span><span class="p">,</span> <span class="s" style="color: #d14;">'identifiers/inchikey'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">force_string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">)</span></span>

</pre>

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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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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC198" 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;">position</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="n" style="color: #333;">bindingsite</span><span class="p">,</span> <span class="s" style="color: #d14;">'identifiers/position'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="199" 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">

199

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<td class="diff-line-num new_line old" data-linenumber="199" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC199" 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;">chain</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="n" style="color: #333;">bindingsite</span><span class="p">,</span> <span class="s" style="color: #d14;">'identifiers/chain'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="200" 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="199" 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">

199

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<pre style="margin: 0;">+<span id="LC199" 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;">chain</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="n" style="color: #333;">bindingsite</span><span class="p">,</span> <span class="s" style="color: #d14;">'identifiers/chain'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">force_string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="200" 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">

200

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<td class="diff-line-num new_line" data-linenumber="200" 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">

200

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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="LC200" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="201" 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">

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<td class="diff-line-num new_line" data-linenumber="201" 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">

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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="LC201" class="line" lang="python">        <span class="c" style="color: #998; font-style: italic;"># Information on binding site members</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="202" 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">

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<td class="diff-line-num new_line" data-linenumber="202" 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">

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<pre style="margin: 0;"> <span id="LC202" 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;">members</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="3b337656bf3a34912a29016ac837c4dfecada0e5">

<a href="https://salsa.debian.org/med-team/plip/compare/23b74ed79058a03cb56204bad72032d259596a65...5b8735d8202fdf271d2e6ac7693c538d3f072871#3b337656bf3a34912a29016ac837c4dfecada0e5"><strong>plip/modules/preparation.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="340" 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="340" 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">@@ -340,7 +340,10 @@ class LigandFinder:</td>

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<td class="diff-line-num old_line" data-linenumber="340" 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">

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<td class="diff-line-num new_line" data-linenumber="340" 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">

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<pre style="margin: 0;"> <span id="LC340" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="341" 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">

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<td class="diff-line-num new_line" data-linenumber="341" 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">

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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python">        <span class="n" style="color: #333;">write_message</span><span class="p">(</span><span class="s" style="color: #d14;">"Renumerated molecule generated</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">mtype</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'debug'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="342" 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">

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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="LC342" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC343" class="line" lang="python">        <span class="n" style="color: #333;">atomorder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">canonicalize</span><span class="p">(</span><span class="n" style="color: #333;">lig</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC343" 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;">NOPDBCANMAP</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python">            <span class="n" style="color: #333;">atomorder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">canonicalize</span><span class="p">(</span><span class="n" style="color: #333;">lig</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC345" 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="LC346" class="line" lang="python">            <span class="n" style="color: #333;">atomorder</span> <span class="o" style="font-weight: 600;">=</span>  <span class="bp" style="color: #999;">None</span></span>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python">        <span class="n" style="color: #333;">can_to_pdb</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">atomorder</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="p">:</span></span>

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<br>

</li>

<li id="86a2fcb72e262191b5bad9c18b91b7cba3b7ea36">

<a href="https://salsa.debian.org/med-team/plip/compare/23b74ed79058a03cb56204bad72032d259596a65...5b8735d8202fdf271d2e6ac7693c538d3f072871#86a2fcb72e262191b5bad9c18b91b7cba3b7ea36"><strong>plip/modules/report.py</strong></a>

<hr>

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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">@@ -19,17 +19,18 @@ from . import config</td>

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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">1</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">2</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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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">mol</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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">mol</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">outputprefix</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff right">'report'</span></span><span class="p">):</span></span>

</pre>

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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;">mol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mol</span></span>

</pre>

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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;">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;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">excluded</span></span>

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<pre style="margin: 0;"> <span id="LC29" 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;">xmlreport</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;">construct_xml_tree</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC30" 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;">txtreport</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;">construct_txt_file</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="31" 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">

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<pre style="margin: 0;"> <span id="LC31" 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_bindingsite_data</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="32" 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">

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<pre style="margin: 0;"> <span id="LC32" 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;">outpath</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;">output_path</span></span>

</pre>

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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;">outputprefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outputprefix</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">construct_xml_tree</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="36" 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">

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python">        <span class="s" style="color: #d14;">"""Construct the basic XML tree"""</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="95" 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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -95,7 +96,7 @@ class StructureReport:</td>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_xml</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">as_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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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python">        <span class="s" style="color: #d14;">"""Write the XML report"""</span></span>

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<pre style="margin: 0;"> <span id="LC98" 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;">as_string</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python">            <span class="n" style="color: #333;">et</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ElementTree</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;">xmlreport</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;"><span class="idiff left">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s/report.xml'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</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 right">outpath</span></span><span class="p">,</span> <span class="n" style="color: #333;">pretty_print</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">xml_declaration</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="LC99" class="line" lang="python">            <span class="n" style="color: #333;">et</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ElementTree</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;">xmlreport</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'<span class="idiff left">{}/{}.xml'</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">format</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">outpath</span></span><span class="p"><span class="idiff">,</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">outputprefix</span></span><span class="p"><span class="idiff right">)</span>,</span> <span class="n" style="color: #333;">pretty_print</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">xml_declaration</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="LC100" 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="LC101" class="line" lang="python">            <span class="n" style="color: #333;">output</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;">tostring</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;">xmlreport</span><span class="p">,</span> <span class="n" style="color: #333;">pretty_print</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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<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">

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<pre style="margin: 0;"> <span id="LC102" 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;">RAWSTRING</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="105" 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="106" 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">@@ -105,7 +106,7 @@ class StructureReport:</td>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_txt</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">as_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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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python">        <span class="s" style="color: #d14;">"""Write the TXT report"""</span></span>

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<pre style="margin: 0;"> <span id="LC108" 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;">as_string</span><span class="p">:</span></span>

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<td class="diff-line-num old old_line" data-linenumber="108" 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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<td class="diff-line-num new_line old" data-linenumber="109" 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="LC108" class="line" lang="python">            <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;"><span class="idiff left">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s/report.txt'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</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 right">outpath</span></span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>

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<td class="diff-line-num new new_line" data-linenumber="109" 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="LC109" class="line" lang="python">            <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'<span class="idiff left">{}/{}.txt'</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">format</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">outpath</span></span><span class="p"><span class="idiff">,</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">outputprefix</span></span><span class="p"><span class="idiff right">)</span>,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python">                <span class="p">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">textline</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">textline</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;">txtreport</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC111" 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="LC112" class="line" lang="python">            <span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">txtreport</span><span class="p">)</span></span>

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<a href="https://salsa.debian.org/med-team/plip/compare/23b74ed79058a03cb56204bad72032d259596a65...5b8735d8202fdf271d2e6ac7693c538d3f072871#df20c64fcda0c0211e8d65f6fb353c8b81b85b51"><strong>plip/plipcmd</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 @@ def threshold_limiter(aparser, arg):</td>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">process_pdb</span><span class="p">(</span><span class="n" style="color: #333;">pdbfile</span><span class="p">,</span> <span class="n" style="color: #333;">outpath</span><span class="p">,</span> <span class="n" style="color: #333;">as_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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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">process_pdb</span><span class="p">(</span><span class="n" style="color: #333;">pdbfile</span><span class="p">,</span> <span class="n" style="color: #333;">outpath</span><span class="p">,</span> <span class="n" style="color: #333;">as_string</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">outputprefix</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff right">'report'</span></span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python">    <span class="s" style="color: #d14;">"""Analysis of a single PDB file. Can generate textual reports XML, PyMOL session files and images as output."""</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC49" 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;">as_string</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python">        <span class="n" style="color: #333;">startmessage</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Starting analysis of </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">pdbfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'/'</span><span class="p">)[</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 new_line" data-linenumber="62" 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">@@ -62,7 +62,7 @@ def process_pdb(pdbfile, outpath, as_string=False):</td>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python">    <span class="n" style="color: #333;">create_folder_if_not_exists</span><span class="p">(</span><span class="n" style="color: #333;">outpath</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python">    <span class="c" style="color: #998; font-style: italic;"># Generate the report files</span></span>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python">    <span class="n" style="color: #333;">streport</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StructureReport</span><span class="p">(</span><span class="n" style="color: #333;">mol</span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="66" 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="LC65" class="line" lang="python">    <span class="n" style="color: #333;">streport</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StructureReport</span><span class="p">(</span><span class="n" style="color: #333;">mol</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">outputprefix</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">outputprefix</span></span><span class="p">)</span></span>

</pre>

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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 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="nb" style="color: #0086b3;">min</span><span class="p">(</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="p">,</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>

</pre>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="127" 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="127" 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">@@ -127,6 +127,7 @@ def main(inputstructs, inputpdbids):</td>

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<pre style="margin: 0;"> <span id="LC127" 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;">'</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="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">title</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python">    <span class="n" style="color: #333;">write_message</span><span class="p">(</span><span class="n" style="color: #333;">title</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC129" 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;">'</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="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">title</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">'</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;">outputprefix</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;">OUTPUTFILENAME</span></span>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"></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="n" style="color: #333;">inputstructs</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span>  <span class="c" style="color: #998; font-style: italic;"># Process PDB file(s)</span></span>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python">        <span class="n" style="color: #333;">num_structures</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">inputstructs</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold new_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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -147,7 +148,8 @@ def main(inputstructs, inputpdbids):</td>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">num_structures</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="LC149" class="line" lang="python">                    <span class="n" style="color: #333;">basename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inputstruct</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'/'</span><span class="p">)[</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="LC150" class="line" lang="python">                    <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OUTPATH</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;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BASEPATH</span><span class="p">,</span> <span class="n" style="color: #333;">basename</span><span class="p">])</span></span>

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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python">            <span class="n" style="color: #333;">process_pdb</span><span class="p">(</span><span class="n" style="color: #333;">inputstruct</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OUTPATH</span><span class="p">,</span> <span class="n" style="color: #333;">as_string</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">read_from_stdin</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;">outputprefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'report'</span></span>

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python">            <span class="n" style="color: #333;">process_pdb</span><span class="p">(</span><span class="n" style="color: #333;">inputstruct</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OUTPATH</span><span class="p">,</span> <span class="n" style="color: #333;">as_string</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">read_from_stdin</span><span class="p">,</span> <span class="n" style="color: #333;">outputprefix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outputprefix</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span>  <span class="c" style="color: #998; font-style: italic;"># Try to fetch the current PDB structure(s) directly from the RCBS server</span></span>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python">        <span class="n" style="color: #333;">num_pdbids</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">inputpdbids</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python">        <span class="n" style="color: #333;">inputpdbids</span> <span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">remove_duplicates</span><span class="p">(</span><span class="n" style="color: #333;">inputpdbids</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="155" 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="157" 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">@@ -155,7 +157,8 @@ def main(inputstructs, inputpdbids):</td>

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python">            <span class="n" style="color: #333;">pdbpath</span><span class="p">,</span> <span class="n" style="color: #333;">pdbid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">download_structure</span><span class="p">(</span><span class="n" style="color: #333;">inputpdbid</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="n" style="color: #333;">num_pdbids</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="LC159" class="line" lang="python">                <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OUTPATH</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;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BASEPATH</span><span class="p">,</span> <span class="n" style="color: #333;">pdbid</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">3</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">upper</span><span class="p">(),</span> <span class="n" style="color: #333;">pdbid</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">upper</span><span class="p">()])</span></span>

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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python">            <span class="n" style="color: #333;">process_pdb</span><span class="p">(</span><span class="n" style="color: #333;">pdbpath</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OUTPATH</span><span class="p">)</span></span>

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<td class="diff-line-num new new_line" data-linenumber="160" 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="LC160" class="line" lang="python">                <span class="n" style="color: #333;">outputprefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'report'</span></span>

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python">            <span class="n" style="color: #333;">process_pdb</span><span class="p">(</span><span class="n" style="color: #333;">pdbpath</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OUTPATH</span><span class="p">,</span> <span class="n" style="color: #333;">outputprefix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outputprefix</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="162" 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">

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"></span>

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<td class="diff-line-num new_line" data-linenumber="163" 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">

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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="p">(</span><span class="n" style="color: #333;">pdbid</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;">or</span> <span class="n" style="color: #333;">inputstructs</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</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="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="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC164" 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;">BASEPATH</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'./'</span><span class="p">]:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="204" 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="207" 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">@@ -204,9 +207,14 @@ if __name__ == '__main__':</td>

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<pre style="margin: 0;"> <span id="LC207" 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;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--nofixfile"</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;">"nofixfile"</span><span class="p">,</span> <span class="n" style="color: #333;">default</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="LC208" class="line" lang="python">                        <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Turns off writing files for fixed PDB files."</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python">                        <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">)</span></span>

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<td class="diff-line-num new new_line" data-linenumber="210" 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="LC210" 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;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--nopdbcanmap"</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;">"nopdbcanmap"</span><span class="p">,</span> <span class="n" style="color: #333;">default</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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<td class="diff-line-num new old_line" data-linenumber="207" 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="211" 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="LC211" class="line" lang="python">                        <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Turns off calculation of mapping between canonical and PDB atom order for ligands."</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="207" 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="212" 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="LC212" class="line" lang="python">                        <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="207" 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">

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<td class="diff-line-num new_line" data-linenumber="213" 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">

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<pre style="margin: 0;"> <span id="LC213" 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;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--dnareceptor"</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;">"dnareceptor"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="208" 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">

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<td class="diff-line-num new_line" data-linenumber="214" 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">

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python">                        <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Uses the DNA instead of the protein as a receptor for interactions."</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="209" 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">

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python">                        <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" 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="216" 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="LC216" 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;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--name"</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;">"outputfilename"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"report"</span><span class="p">,</span></span>

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<td class="diff-line-num new new_line" data-linenumber="217" 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="LC217" class="line" lang="python">                        <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Set a filename for the report TXT and XML files. Will only work when processing single structures."</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="218" 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">

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python">    <span class="n" style="color: #333;">ligandtype</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="c" style="color: #998; font-style: italic;"># Either peptide/inter or intra mode</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="211" 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">

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<td class="diff-line-num new_line" data-linenumber="219" 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">

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="python">    <span class="n" style="color: #333;">ligandtype</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;">"--peptides"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--inter"</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;">"peptides"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="212" 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">

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<td class="diff-line-num new_line" data-linenumber="220" 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">

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="python">                        <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Allows to define one or multiple chains as peptide ligands or to detect inter-chain contacts"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="251" 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="259" 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">@@ -251,8 +259,10 @@ if __name__ == '__main__':</td>

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<pre style="margin: 0;"> <span id="LC259" class="line" lang="python">    <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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arguments</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">intra</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="252" 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">

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="python">    <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">NOFIX</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arguments</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nofix</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="python">    <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">NOFIXFILE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arguments</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nofixfile</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="262" 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="LC262" class="line" lang="python">    <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">NOPDBCANMAP</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arguments</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nopdbcanmap</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC263" class="line" lang="python">    <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">KEEPMOD</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arguments</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keepmod</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python">    <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DNARECEPTOR</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arguments</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dnareceptor</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="256" 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="265" 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="LC265" class="line" lang="python">    <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">OUTPUTFILENAME</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arguments</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">outputfilename</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="256" 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">

256

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<td class="diff-line-num new_line" data-linenumber="266" 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">

266

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="python">    <span class="c" style="color: #998; font-style: italic;"># Make sure we have pymol with --pics and --pymol</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="257" 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">

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<td class="diff-line-num new_line" data-linenumber="267" 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">

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<pre style="margin: 0;"> <span id="LC267" 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;">PICS</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;">PYMOL</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="258" 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">

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<td class="diff-line-num new_line" data-linenumber="268" 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">

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<br>

</li>

<li id="8e2edce0d507e1297474f25c00cae94258db38d8">

<a href="https://salsa.debian.org/med-team/plip/compare/23b74ed79058a03cb56204bad72032d259596a65...5b8735d8202fdf271d2e6ac7693c538d3f072871#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" 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="6" 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">@@ -6,7 +6,7 @@ setup.py - Setup configuration file for pip, etc.</td>

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<td class="diff-line-num old_line" data-linenumber="6" 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">

6

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6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">setuptools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">setup</span></span>

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<td class="diff-line-num old_line" data-linenumber="7" 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">

7

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<td class="diff-line-num new_line" data-linenumber="7" 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">

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" 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">

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<td class="diff-line-num new_line" data-linenumber="8" 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">

8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'plip'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="9" 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">

9

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<td class="diff-line-num new_line old" data-linenumber="9" 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="LC9" 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">1</span>'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="10" 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="9" 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">

9

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<pre style="margin: 0;">+<span id="LC9" 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 class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="10" 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">

10

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<td class="diff-line-num new_line" data-linenumber="10" 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">

10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python">      <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'PLIP - Fully automated protein-ligand interaction profiler'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="11" 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">

11

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<td class="diff-line-num new_line" data-linenumber="11" 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">

11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python">      <span class="n" style="color: #333;">classifiers</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>

</pre>

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<td class="diff-line-num 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">

12

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<td class="diff-line-num 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">

12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python">          <span class="s" style="color: #d14;">'Development Status :: 5 - Production/Stable'</span><span class="p">,</span></span>

</pre>

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