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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/a5f37548e65717ab3e899f3aef0ff258c35d1221">a5f37548</a></strong>

<div>

<span>by Alexandre Mestiashvili</span>

<i>at 2020-09-09T13:30:18+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.1.4+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/plip/-/commit/429e7091be4e6d1cdbc952a15876a06e160a027b">429e7091</a></strong>

<div>

<span>by Alexandre Mestiashvili</span>

<i>at 2020-09-09T13:30:19+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.1.4+dfsg'

Update to upstream version '2.1.4+dfsg'

with Debian dir ed925162949b714480efabe48514a4a087cc32ec</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/plip/-/commit/846be8bfe96967d42dd14d8b56c2189d754e538a">846be8bf</a></strong>

<div>

<span>by Alexandre Mestiashvili</span>

<i>at 2020-09-09T13:32:35+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/control: move pymol from Depends to Recommends

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/plip/-/commit/586eea80730c8d056ffd0a471658d8d71870f924">586eea80</a></strong>

<div>

<span>by Alexandre Mestiashvili</span>

<i>at 2020-09-09T13:35:35+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="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

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<li class="file-stats">

<a href="#e0bdfb93722bb0bccd3faf9d5cbf446297ff47c4">

plip/basic/config.py

</a>

</li>

<li class="file-stats">

<a href="#67d4980fce23584951cb46902ae74ffca7500b93">

plip/exchange/report.py

</a>

</li>

<li class="file-stats">

<a href="#65da37aabb52e08df77545976cc2684a5df1de5f">

plip/exchange/xml.py

</a>

</li>

<li class="file-stats">

<a href="#b72517a8cd7dbc6709d05fdad49ae468ebf79126">

plip/structure/preparation.py

</a>

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<li class="file-stats">

<a href="#696ac07ae5eed397a25b82f16361e894a7d1b19b">

plip/test/test_basic_functions.py

</a>

</li>

<li class="file-stats">

<a href="#3bbce20a5f639a39b0f6555b6d1039c2a7419a6c">

plip/visualization/pymol.py

</a>

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<li class="file-stats">

<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">

setup.py

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/plip/-/compare/0d942ce3cffb19d14db1ecdd88a8d0bc68c90bfb...586eea80730c8d056ffd0a471658d8d71870f924#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">plip (2.1.4+dfsg-1) unstable; urgency=medium</span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * New upstream version 2.1.4+dfsg</span>

</pre>

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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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * d/control: move pymol from Depends to Recommends</span>

</pre>

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

<td class="diff-line-num new old_line" data-linenumber="1" 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="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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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Alexandre Mestiashvili <mestia@debian.org>  Wed, 09 Sep 2020 13:34:11 +0200</span>

</pre>

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7

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

</pre>

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1

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">plip (2.1.3+dfsg-1) unstable; urgency=medium</span>

</pre>

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2

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>

</pre>

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3

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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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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">  * Add build-mulit.sh to Files-Excluded list in d/copyright</span>

</pre>

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</table>

<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/plip/-/compare/0d942ce3cffb19d14db1ecdd88a8d0bc68c90bfb...586eea80730c8d056ffd0a471658d8d71870f924#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" 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="19" 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">@@ -19,7 +19,8 @@ Homepage: https://projects.biotec.tu-dresden.de/plip-web/plip/</td>

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19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Package: plip</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="21" 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">

21

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Architecture: all</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="22" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">Depends: pymol, python3-openbabel, ${misc:Depends}, ${python3:Depends}</span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Depends: python3-openbabel, ${misc:Depends}, ${python3:Depends}</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Recommends: pymol</span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Description: fully automated protein-ligand interaction profiler</span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> The Protein-Ligand Interaction Profiler (PLIP) is a tool to analyze</span>

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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> and visualize protein-ligand interactions in PDB files.</span>

</pre>

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<li id="e0bdfb93722bb0bccd3faf9d5cbf446297ff47c4">

<a href="https://salsa.debian.org/med-team/plip/-/compare/0d942ce3cffb19d14db1ecdd88a8d0bc68c90bfb...586eea80730c8d056ffd0a471658d8d71870f924#e0bdfb93722bb0bccd3faf9d5cbf446297ff47c4"><strong>plip/basic/config.py</strong></a>

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1

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<pre style="margin: 0;">-<span id="LC1" 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;">'2.1.<span class="idiff left right">3</span>'</span></span>

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<pre style="margin: 0;">+<span id="LC1" 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;">'2.1.<span class="idiff left right">4</span>'</span></span>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="n" style="color: #333;">__maintainer__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'PharmAI GmbH (2020) - www.pharm.ai - hello@pharm.ai'</span></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span></span>

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<li id="67d4980fce23584951cb46902ae74ffca7500b93">

<a href="https://salsa.debian.org/med-team/plip/-/compare/0d942ce3cffb19d14db1ecdd88a8d0bc68c90bfb...586eea80730c8d056ffd0a471658d8d71870f924#67d4980fce23584951cb46902ae74ffca7500b93"><strong>plip/exchange/report.py</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="287" 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">@@ -287,7 +287,8 @@ class BindingSiteReport:</td>

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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python">                 <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">location</span><span class="p">,</span> <span class="s" style="color: #d14;">'%.2f'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">rms</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">geometry</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">complexnum</span><span class="p">),</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">metal</span><span class="p">.</span><span class="n" style="color: #333;">coords</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC288" class="line" lang="python">                 <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">atom</span><span class="p">.</span><span class="n" style="color: #333;">coords</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC290" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_section</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">features</span><span class="p">,</span> <span class="n" style="color: #333;">info</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC290" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_section</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">features</span><span class="p">,</span> <span class="n" style="color: #333;">info</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python">        <span class="s" style="color: #d14;">"""Provides formatting for one section (e.g. hydrogen bonds)"""</span></span>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">info</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python">            <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n\n</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;">name</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="295" 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="296" 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">@@ -295,7 +296,8 @@ class BindingSiteReport:</td>

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<pre style="margin: 0;"> <span id="LC296" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">info</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python">                <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</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="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">)))</span></span>

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC298" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">rst_table</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">array</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">rst_table</span><span class="p">(</span><span class="n" style="color: #333;">array</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC301" class="line" lang="python">        <span class="s" style="color: #d14;">"""Given an array, the function formats and returns and table in rST format."""</span></span>

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<pre style="margin: 0;"> <span id="LC302" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Determine cell width for each column</span></span>

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<pre style="margin: 0;"> <span id="LC303" class="line" lang="python">        <span class="n" style="color: #333;">cell_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

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<br>

</li>

<li id="65da37aabb52e08df77545976cc2684a5df1de5f">

<a href="https://salsa.debian.org/med-team/plip/-/compare/0d942ce3cffb19d14db1ecdd88a8d0bc68c90bfb...586eea80730c8d056ffd0a471658d8d71870f924#65da37aabb52e08df77545976cc2684a5df1de5f"><strong>plip/exchange/xml.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">@@ -6,7 +6,8 @@ from urllib.request import urlopen</td>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">XMLStorage</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python">    <span class="s" style="color: #d14;">"""Generic class for storing XML data from PLIP XML files."""</span></span>

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

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">getdata</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">tree</span><span class="p">,</span> <span class="n" style="color: #333;">location</span><span class="p">,</span> <span class="n" style="color: #333;">force_string</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">getdata</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">,</span> <span class="n" style="color: #333;">location</span><span class="p">,</span> <span class="n" style="color: #333;">force_string</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>

</pre>

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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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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python">        <span class="s" style="color: #d14;">"""Gets XML data from a specific element and handles types."""</span></span>

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<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">

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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">

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python">        <span class="n" style="color: #333;">found</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">xpath</span><span class="p">(</span><span class="s" style="color: #d14;">'%s/text()'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">location</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="13" 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="LC13" 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;">found</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="29" 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="30" 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">@@ -29,7 +30,8 @@ class XMLStorage:</td>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># It's a string</span></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python">                    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">data</span></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="32" 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="LC32" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">getcoordinates</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">tree</span><span class="p">,</span> <span class="n" style="color: #333;">location</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">getcoordinates</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">,</span> <span class="n" style="color: #333;">location</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python">        <span class="s" style="color: #d14;">"""Gets coordinates from a specific element in PLIP XML"""</span></span>

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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="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">xpath</span><span class="p">(</span><span class="s" style="color: #d14;">'.//%s/*/text()'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">location</span><span class="p">))</span></span>

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<td class="diff-line-num new_line" data-linenumber="37" 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="LC37" class="line" lang="python"></span>

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<br>

</li>

<li id="b72517a8cd7dbc6709d05fdad49ae468ebf79126">

<a href="https://salsa.debian.org/med-team/plip/-/compare/0d942ce3cffb19d14db1ecdd88a8d0bc68c90bfb...586eea80730c8d056ffd0a471658d8d71870f924#b72517a8cd7dbc6709d05fdad49ae468ebf79126"><strong>plip/structure/preparation.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="352" 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">@@ -352,7 +352,8 @@ class LigandFinder:</td>

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<pre style="margin: 0;"> <span id="LC352" class="line" lang="python">                      <span class="n" style="color: #333;">can_to_pdb</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">can_to_pdb</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC353" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ligand</span></span>

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<pre style="margin: 0;"> <span id="LC354" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC355" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">is_het_residue</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">obres</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC355" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC356" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">is_het_residue</span><span class="p">(</span><span class="n" style="color: #333;">obres</span><span class="p">):</span></span>

</pre>

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356

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<pre style="margin: 0;"> <span id="LC357" class="line" lang="python">        <span class="s" style="color: #d14;">"""Given an OBResidue, determines if the residue is indeed a possible ligand</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC358" class="line" lang="python"><span class="s" style="color: #d14;">        in the PDB file"""</span></span>

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<td class="diff-line-num new_line" data-linenumber="359" 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">

359

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<pre style="margin: 0;"> <span id="LC359" 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;">obres</span><span class="p">.</span><span class="n" style="color: #333;">GetResidueProperty</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="701" 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="702" 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">@@ -701,7 +702,8 @@ class PLInteraction:</td>

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702

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<pre style="margin: 0;"> <span id="LC702" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC703" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">unpaired_hba</span><span class="p">,</span> <span class="n" style="color: #333;">unpaired_hbd</span><span class="p">,</span> <span class="n" style="color: #333;">unpaired_hal</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="704" 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">

704

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<pre style="margin: 0;"> <span id="LC704" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="704" 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="705" 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="LC704" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">refine_hydrophobic</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">all_h</span><span class="p">,</span> <span class="n" style="color: #333;">pistacks</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="705" 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="705" 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">

705

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<pre style="margin: 0;">+<span id="LC705" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="706" 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="LC706" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">refine_hydrophobic</span><span class="p">(</span><span class="n" style="color: #333;">all_h</span><span class="p">,</span> <span class="n" style="color: #333;">pistacks</span><span class="p">):</span></span>

</pre>

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705

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<td class="diff-line-num new_line" data-linenumber="707" 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="LC707" class="line" lang="python">        <span class="s" style="color: #d14;">"""Apply several rules to reduce the number of hydrophobic interactions."""</span></span>

</pre>

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706

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<td class="diff-line-num new_line" data-linenumber="708" 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">

708

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<pre style="margin: 0;"> <span id="LC708" class="line" lang="python">        <span class="n" style="color: #333;">sel</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="707" 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="709" 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">

709

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<pre style="margin: 0;"> <span id="LC709" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#  1. Rings interacting via stacking can't have additional hydrophobic contacts between each other.</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="768" 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="770" 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">@@ -768,7 +770,8 @@ class PLInteraction:</td>

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<td class="diff-line-num old_line" data-linenumber="768" 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">

768

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<td class="diff-line-num new_line" data-linenumber="770" 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">

770

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<pre style="margin: 0;"> <span id="LC770" class="line" lang="python">            <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">f'reduced number of hydrophobic contacts from </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">before</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> to </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">reduced</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="769" 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="771" 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">

771

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<pre style="margin: 0;"> <span id="LC771" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">hydroph_final</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC772" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="773" 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="LC771" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">refine_hbonds_ldon</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">all_hbonds</span><span class="p">,</span> <span class="n" style="color: #333;">salt_lneg</span><span class="p">,</span> <span class="n" style="color: #333;">salt_pneg</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="772" 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="773" 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="LC773" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="774" 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="LC774" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">refine_hbonds_ldon</span><span class="p">(</span><span class="n" style="color: #333;">all_hbonds</span><span class="p">,</span> <span class="n" style="color: #333;">salt_lneg</span><span class="p">,</span> <span class="n" style="color: #333;">salt_pneg</span><span class="p">):</span></span>

</pre>

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772

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<td class="diff-line-num new_line" data-linenumber="775" 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="LC775" class="line" lang="python">        <span class="s" style="color: #d14;">"""Refine selection of hydrogen bonds. Do not allow groups which already form salt bridges to form H-Bonds."""</span></span>

</pre>

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773

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<td class="diff-line-num new_line" data-linenumber="776" 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="LC776" class="line" lang="python">        <span class="n" style="color: #333;">i_set</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="774" 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">

774

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<td class="diff-line-num new_line" data-linenumber="777" 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">

777

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<pre style="margin: 0;"> <span id="LC777" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">hbond</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">all_hbonds</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="793" 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="796" 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">@@ -793,7 +796,8 @@ class PLInteraction:</td>

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<td class="diff-line-num old_line" data-linenumber="793" 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="796" 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">

796

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<pre style="margin: 0;"> <span id="LC796" class="line" lang="python">                    <span class="n" style="color: #333;">second_set</span><span class="p">[</span><span class="n" style="color: #333;">hbl</span><span class="p">.</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">hbl</span><span class="p">.</span><span class="n" style="color: #333;">angle</span><span class="p">,</span> <span class="n" style="color: #333;">hbl</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="794" 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">

794

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<td class="diff-line-num new_line" data-linenumber="797" 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">

797

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<pre style="margin: 0;"> <span id="LC797" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">hb</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">hb</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">second_set</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">()]</span></span>

</pre>

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795

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<td class="diff-line-num new_line" data-linenumber="798" 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="LC798" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="799" 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="LC796" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">refine_hbonds_pdon</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">all_hbonds</span><span class="p">,</span> <span class="n" style="color: #333;">salt_lneg</span><span class="p">,</span> <span class="n" style="color: #333;">salt_pneg</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="797" 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="799" 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">

799

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<pre style="margin: 0;">+<span id="LC799" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="797" 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="800" 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="LC800" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">refine_hbonds_pdon</span><span class="p">(</span><span class="n" style="color: #333;">all_hbonds</span><span class="p">,</span> <span class="n" style="color: #333;">salt_lneg</span><span class="p">,</span> <span class="n" style="color: #333;">salt_pneg</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="797" 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">

797

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<td class="diff-line-num new_line" data-linenumber="801" 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">

801

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<pre style="margin: 0;"> <span id="LC801" class="line" lang="python">        <span class="s" style="color: #d14;">"""Refine selection of hydrogen bonds. Do not allow groups which already form salt bridges to form H-Bonds with</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="798" 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">

798

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<td class="diff-line-num new_line" data-linenumber="802" 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">

802

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<pre style="margin: 0;"> <span id="LC802" class="line" lang="python"><span class="s" style="color: #d14;">        atoms of the same group.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="799" 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="803" 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">

803

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<pre style="margin: 0;"> <span id="LC803" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="820" 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="824" 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">@@ -820,7 +824,8 @@ class PLInteraction:</td>

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820

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824

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<pre style="margin: 0;"> <span id="LC824" class="line" lang="python">                    <span class="n" style="color: #333;">second_set</span><span class="p">[</span><span class="n" style="color: #333;">hbp</span><span class="p">.</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">hbp</span><span class="p">.</span><span class="n" style="color: #333;">angle</span><span class="p">,</span> <span class="n" style="color: #333;">hbp</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="821" 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">

821

</td>

<td class="diff-line-num new_line" data-linenumber="825" 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">

825

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC825" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">hb</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">hb</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">second_set</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">()]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="822" 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">

822

</td>

<td class="diff-line-num new_line" data-linenumber="826" 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">

826

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC826" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="823" 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">

823

</td>

<td class="diff-line-num new_line old" data-linenumber="827" 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="LC823" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">refine_pi_cation_laro</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">all_picat</span><span class="p">,</span> <span class="n" style="color: #333;">stacks</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="824" 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="827" 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">

827

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<pre style="margin: 0;">+<span id="LC827" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="824" 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="828" 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">

828

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<pre style="margin: 0;">+<span id="LC828" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">refine_pi_cation_laro</span><span class="p">(</span><span class="n" style="color: #333;">all_picat</span><span class="p">,</span> <span class="n" style="color: #333;">stacks</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="824" 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">

824

</td>

<td class="diff-line-num new_line" data-linenumber="829" 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">

829

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<pre style="margin: 0;"> <span id="LC829" class="line" lang="python">        <span class="s" style="color: #d14;">"""Just important for constellations with histidine involved. If the histidine ring is positioned in stacking</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="825" 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">

825

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<td class="diff-line-num new_line" data-linenumber="830" 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">

830

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<pre style="margin: 0;"> <span id="LC830" class="line" lang="python"><span class="s" style="color: #d14;">        position to an aromatic ring in the ligand, there is in most cases stacking and pi-cation interaction reported</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="826" 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">

826

</td>

<td class="diff-line-num new_line" data-linenumber="831" 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">

831

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC831" class="line" lang="python"><span class="s" style="color: #d14;">        as histidine also carries a positive charge in the ring. For such cases, only report stacking.</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="835" 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="840" 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">@@ -835,7 +840,8 @@ class PLInteraction:</td>

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<td class="diff-line-num old_line" data-linenumber="835" 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">

835

</td>

<td class="diff-line-num new_line" data-linenumber="840" 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">

840

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<pre style="margin: 0;"> <span id="LC840" class="line" lang="python">                <span class="n" style="color: #333;">i_set</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">picat</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="836" 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">

836

</td>

<td class="diff-line-num new_line" data-linenumber="841" 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">

841

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<pre style="margin: 0;"> <span id="LC841" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">i_set</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="837" 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">

837

</td>

<td class="diff-line-num new_line" data-linenumber="842" 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">

842

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC842" class="line" lang="python"></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="838" 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">

838

</td>

<td class="diff-line-num new_line old" data-linenumber="843" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC838" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">refine_water_bridges</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">wbridges</span><span class="p">,</span> <span class="n" style="color: #333;">hbonds_ldon</span><span class="p">,</span> <span class="n" style="color: #333;">hbonds_pdon</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="839" 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="843" 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">

843

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<pre style="margin: 0;">+<span id="LC843" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="839" 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="844" 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">

844

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<pre style="margin: 0;">+<span id="LC844" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">refine_water_bridges</span><span class="p">(</span><span class="n" style="color: #333;">wbridges</span><span class="p">,</span> <span class="n" style="color: #333;">hbonds_ldon</span><span class="p">,</span> <span class="n" style="color: #333;">hbonds_pdon</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="839" 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">

839

</td>

<td class="diff-line-num new_line" data-linenumber="845" 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">

845

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<pre style="margin: 0;"> <span id="LC845" class="line" lang="python">        <span class="s" style="color: #d14;">"""A donor atom already forming a hydrogen bond is not allowed to form a water bridge. Each water molecule</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="840" 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">

840

</td>

<td class="diff-line-num new_line" data-linenumber="846" 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">

846

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<pre style="margin: 0;"> <span id="LC846" class="line" lang="python"><span class="s" style="color: #d14;">        can only be donor for two water bridges, selecting the constellation with the omega angle closest to 110 deg."""</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="841" 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">

841

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<td class="diff-line-num new_line" data-linenumber="847" 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">

847

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<pre style="margin: 0;"> <span id="LC847" class="line" lang="python">        <span class="n" style="color: #333;">donor_atoms_hbonds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">hb</span><span class="p">.</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">idx</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">hb</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">hbonds_ldon</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">hbonds_pdon</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1064" 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="1070" 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">@@ -1064,7 +1070,8 @@ class Ligand(Mol):</td>

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1070

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<pre style="margin: 0;"> <span id="LC1070" class="line" lang="python">        <span class="s" style="color: #d14;">"""Converts internal atom ID into canonical atom ID. Agrees with Canonical SMILES in XML."""</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1065" 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">

1065

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<td class="diff-line-num new_line" data-linenumber="1071" 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">

1071

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<pre style="margin: 0;"> <span id="LC1071" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">atomorder</span><span class="p">[</span><span class="n" style="color: #333;">atomnum</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1066" 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">

1066

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<td class="diff-line-num new_line" data-linenumber="1072" 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">

1072

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<pre style="margin: 0;"> <span id="LC1072" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1067" 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">

1067

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<td class="diff-line-num new_line old" data-linenumber="1073" 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="LC1067" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">is_functional_group</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">atom</span><span class="p">,</span> <span class="n" style="color: #333;">group</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1068" 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="LC1073" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1068" 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="1074" 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">

1074

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<pre style="margin: 0;">+<span id="LC1074" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">is_functional_group</span><span class="p">(</span><span class="n" style="color: #333;">atom</span><span class="p">,</span> <span class="n" style="color: #333;">group</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1075" 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">

1075

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<pre style="margin: 0;"> <span id="LC1075" class="line" lang="python">        <span class="s" style="color: #d14;">"""Given a pybel atom, look up if it belongs to a function group"""</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1069" 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">

1069

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<td class="diff-line-num new_line" data-linenumber="1076" 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">

1076

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<pre style="margin: 0;"> <span id="LC1076" class="line" lang="python">        <span class="n" style="color: #333;">n_atoms</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">a_neighbor</span><span class="p">.</span><span class="n" style="color: #333;">GetAtomicNum</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">a_neighbor</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">pybel</span><span class="p">.</span><span class="n" style="color: #333;">ob</span><span class="p">.</span><span class="n" style="color: #333;">OBAtomAtomIter</span><span class="p">(</span><span class="n" style="color: #333;">atom</span><span class="p">.</span><span class="n" style="color: #333;">OBAtom</span><span class="p">)]</span></span>

</pre>

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1070

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<td class="diff-line-num new_line" data-linenumber="1077" 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">

1077

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<pre style="margin: 0;"> <span id="LC1077" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1460" 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="1467" 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">@@ -1460,7 +1467,8 @@ class PDBComplex:</td>

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<pre style="margin: 0;"> <span id="LC1467" class="line" lang="python">        <span class="s" style="color: #d14;">"""Return list of ids from residues belonging to the binding site"""</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1461" 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="1468" 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="LC1468" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">obres</span><span class="p">.</span><span class="n" style="color: #333;">GetIdx</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">obres</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">resis</span> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">res_belongs_to_bs</span><span class="p">(</span><span class="n" style="color: #333;">obres</span><span class="p">,</span> <span class="n" style="color: #333;">cutoff</span><span class="p">,</span> <span class="n" style="color: #333;">ligcentroid</span><span class="p">)]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1469" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="1470" 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="LC1463" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">res_belongs_to_bs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">res</span><span class="p">,</span> <span class="n" style="color: #333;">cutoff</span><span class="p">,</span> <span class="n" style="color: #333;">ligcentroid</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1470" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1471" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">res_belongs_to_bs</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="p">,</span> <span class="n" style="color: #333;">cutoff</span><span class="p">,</span> <span class="n" style="color: #333;">ligcentroid</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC1472" class="line" lang="python">        <span class="s" style="color: #d14;">"""Check for each residue if its centroid is within a certain distance to the ligand centroid.</span></span>

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<pre style="margin: 0;"> <span id="LC1473" class="line" lang="python"><span class="s" style="color: #d14;">        Additionally checks if a residue belongs to a chain restricted by the user (e.g. by defining a peptide chain)"""</span></span>

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<pre style="margin: 0;"> <span id="LC1474" class="line" lang="python">        <span class="n" style="color: #333;">rescentroid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">centroid</span><span class="p">([(</span><span class="n" style="color: #333;">atm</span><span class="p">.</span><span class="n" style="color: #333;">x</span><span class="p">(),</span> <span class="n" style="color: #333;">atm</span><span class="p">.</span><span class="n" style="color: #333;">y</span><span class="p">(),</span> <span class="n" style="color: #333;">atm</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">())</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">atm</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">pybel</span><span class="p">.</span><span class="n" style="color: #333;">ob</span><span class="p">.</span><span class="n" style="color: #333;">OBResidueAtomIter</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="p">)])</span></span>

</pre>

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<li id="696ac07ae5eed397a25b82f16361e894a7d1b19b">

<a href="https://salsa.debian.org/med-team/plip/-/compare/0d942ce3cffb19d14db1ecdd88a8d0bc68c90bfb...586eea80730c8d056ffd0a471658d8d71870f924#696ac07ae5eed397a25b82f16361e894a7d1b19b"><strong>plip/test/test_basic_functions.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">@@ -71,7 +71,8 @@ class TestMapping(unittest.TestCase):</td>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">GeometryTest</span><span class="p">(</span><span class="n" style="color: #333;">unittest</span><span class="p">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python">    <span class="s" style="color: #d14;">"""Tests for geometrical calculations in PLIP"""</span></span>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">vector_magnitude</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">vector_magnitude</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">sqrt</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">**</span><span class="mi" style="color: #099;">2</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">v</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># noinspection PyUnusedLocal</span></span>

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<br>

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<li id="3bbce20a5f639a39b0f6555b6d1039c2a7419a6c">

<a href="https://salsa.debian.org/med-team/plip/-/compare/0d942ce3cffb19d14db1ecdd88a8d0bc68c90bfb...586eea80730c8d056ffd0a471658d8d71870f924#3bbce20a5f639a39b0f6555b6d1039c2a7419a6c"><strong>plip/visualization/pymol.py</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="28" 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">@@ -28,7 +28,8 @@ class PyMOLVisualizer:</td>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python">        <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">clip</span><span class="p">(</span><span class="s" style="color: #d14;">'far'</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1000</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python">        <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">clip</span><span class="p">(</span><span class="s" style="color: #d14;">'near'</span><span class="p">,</span> <span class="mi" style="color: #099;">1000</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="31" 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="31" 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="LC31" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">make_initial_selections</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 old_line" data-linenumber="32" 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="31" 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="LC31" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" 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="32" 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="LC32" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">make_initial_selections</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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<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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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python">        <span class="s" style="color: #d14;">"""Make empty selections for structures and interactions"""</span></span>

</pre>

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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="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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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">group</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'Hydrophobic-P'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Hydrophobic-L'</span><span class="p">,</span> <span class="s" style="color: #d14;">'HBondDonor-P'</span><span class="p">,</span></span>

</pre>

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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="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">

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python">                      <span class="s" style="color: #d14;">'HBondDonor-L'</span><span class="p">,</span> <span class="s" style="color: #d14;">'HBondAccept-P'</span><span class="p">,</span> <span class="s" style="color: #d14;">'HBondAccept-L'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="50" 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">@@ -49,7 +50,8 @@ class PyMOLVisualizer:</td>

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<td class="diff-line-num old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python">        <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="s" style="color: #d14;">'dash_radius'</span><span class="p">,</span> <span class="mf" style="color: #099;">0.05</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="50" 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="51" 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="LC51" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">set_custom_colorset</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="52" 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="LC52" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="52" 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="53" 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="LC52" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_custom_colorset</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 old_line" data-linenumber="53" 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="53" 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="LC53" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="53" 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="54" 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="LC54" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_custom_colorset</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="53" 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="55" 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="LC55" class="line" lang="python">        <span class="s" style="color: #d14;">"""Defines a colorset with matching colors. Provided by Joachim."""</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="54" 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="56" 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="LC56" class="line" lang="python">        <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">set_color</span><span class="p">(</span><span class="s" style="color: #d14;">'myorange'</span><span class="p">,</span> <span class="s" style="color: #d14;">'[253, 174, 97]'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="55" 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="57" 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="LC57" class="line" lang="python">        <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">set_color</span><span class="p">(</span><span class="s" style="color: #d14;">'mygreen'</span><span class="p">,</span> <span class="s" style="color: #d14;">'[171, 221, 164]'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="58" 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="60" 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">@@ -58,7 +60,8 @@ class PyMOLVisualizer:</td>

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<td class="diff-line-num old_line" data-linenumber="58" 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="60" 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="LC60" class="line" lang="python">        <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">set_color</span><span class="p">(</span><span class="s" style="color: #d14;">'mylightblue'</span><span class="p">,</span> <span class="s" style="color: #d14;">'[158, 202, 225]'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python">        <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">set_color</span><span class="p">(</span><span class="s" style="color: #d14;">'mylightgreen'</span><span class="p">,</span> <span class="s" style="color: #d14;">'[229, 245, 224]'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">select_by_ids</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">selname</span><span class="p">,</span> <span class="n" style="color: #333;">idlist</span><span class="p">,</span> <span class="n" style="color: #333;">selection_exists</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">chunksize</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="n" style="color: #333;">restrict</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">select_by_ids</span><span class="p">(</span><span class="n" style="color: #333;">selname</span><span class="p">,</span> <span class="n" style="color: #333;">idlist</span><span class="p">,</span> <span class="n" style="color: #333;">selection_exists</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">chunksize</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="n" style="color: #333;">restrict</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python">        <span class="s" style="color: #d14;">"""Selection with a large number of ids concatenated into a selection</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"><span class="s" style="color: #d14;">        list can cause buffer overflow in PyMOL. This function takes a selection</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"><span class="s" style="color: #d14;">        name and and list of IDs (list of integers) as input and makes a careful</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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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">@@ -72,7 +75,8 @@ class PyMOLVisualizer:</td>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">restrict</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="LC76" class="line" lang="python">            <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">select</span><span class="p">(</span><span class="n" style="color: #333;">selname</span><span class="p">,</span> <span class="s" style="color: #d14;">'%s and %s'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">selname</span><span class="p">,</span> <span class="n" style="color: #333;">restrict</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">object_exists</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">object_name</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">object_exists</span><span class="p">(</span><span class="n" style="color: #333;">object_name</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python">        <span class="s" style="color: #d14;">"""Checks if an object exists in the open PyMOL session."""</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">object_name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">get_names</span><span class="p">(</span><span class="s" style="color: #d14;">"objects"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="82" 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="LC82" class="line" lang="python"></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -326,7 +330,8 @@ class PyMOLVisualizer:</td>

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<pre style="margin: 0;"> <span id="LC330" class="line" lang="python">            <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">override</span></span>

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<pre style="margin: 0;"> <span id="LC331" class="line" lang="python">        <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">save</span><span class="p">(</span><span class="s" style="color: #d14;">"/"</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">outfolder</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s.pse"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">filename</span><span class="p">]))</span></span>

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<pre style="margin: 0;"> <span id="LC332" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC329" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">png_workaround</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">filepath</span><span class="p">,</span> <span class="n" style="color: #333;">width</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1200</span><span class="p">,</span> <span class="n" style="color: #333;">height</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">800</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC334" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">png_workaround</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">,</span> <span class="n" style="color: #333;">width</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1200</span><span class="p">,</span> <span class="n" style="color: #333;">height</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">800</span><span class="p">):</span></span>

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<td class="diff-line-num new_line" data-linenumber="335" 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="LC335" class="line" lang="python">        <span class="s" style="color: #d14;">"""Workaround for (a) severe bug(s) in PyMOL preventing ray-traced images to be produced in command-line mode.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="python"><span class="s" style="color: #d14;">        Use this function in case neither cmd.ray() or cmd.png() work.</span></span>

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<pre style="margin: 0;"> <span id="LC337" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="378" 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="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -378,7 +383,8 @@ class PyMOLVisualizer:</td>

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<pre style="margin: 0;"> <span id="LC383" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">set_fancy_ray</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC384" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">png_workaround</span><span class="p">(</span><span class="s" style="color: #d14;">"/"</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">outfolder</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">]))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC385" class="line" lang="python"></span>

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<td class="diff-line-num new_line old" data-linenumber="386" 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="LC381" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_fancy_ray</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC386" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="387" 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="LC387" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_fancy_ray</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC388" class="line" lang="python">        <span class="s" style="color: #d14;">"""Give the molecule a flat, modern look."""</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC389" class="line" lang="python">        <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="s" style="color: #d14;">'light_count'</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">)</span></span>

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384

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<td class="diff-line-num new_line" data-linenumber="390" 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">

390

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<pre style="margin: 0;"> <span id="LC390" class="line" lang="python">        <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="s" style="color: #d14;">'spec_count'</span><span class="p">,</span> <span class="mf" style="color: #099;">1.5</span><span class="p">)</span></span>

</pre>

</td>

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<br>

</li>

<li id="8e2edce0d507e1297474f25c00cae94258db38d8">

<a href="https://salsa.debian.org/med-team/plip/-/compare/0d942ce3cffb19d14db1ecdd88a8d0bc68c90bfb...586eea80730c8d056ffd0a471658d8d71870f924#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="22" 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="22" 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">@@ -22,8 +22,7 @@ setup(name='plip',</td>

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<td class="diff-line-num old_line" data-linenumber="22" 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">

22

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<td class="diff-line-num new_line" data-linenumber="22" 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">

22

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python">      <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>

</pre>

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<td class="diff-line-num 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">

23

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<td class="diff-line-num 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">

23

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python">          <span class="s" style="color: #d14;">'openbabel'</span><span class="p">,</span></span>

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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

24

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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">

24

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python">          <span class="s" style="color: #d14;">'numpy'</span><span class="p">,</span></span>

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<td class="diff-line-num old old_line" data-linenumber="25" 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">

25

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<td class="diff-line-num new_line old" data-linenumber="25" 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="LC25" class="line" lang="python">          <span class="s" style="color: #d14;">'lxml'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="26" 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">

26

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<td class="diff-line-num new_line old" data-linenumber="25" 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="LC26" class="line" lang="python">          <span class="s" style="color: #d14;">'pymol'</span></span>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="25" 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">

25

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python">          <span class="s" style="color: #d14;">'lxml'</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="27" 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="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python">      <span class="p">],</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="28" 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">

28

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<td class="diff-line-num new_line" data-linenumber="27" 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">

27

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python">      <span class="n" style="color: #333;">entry_points</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="29" 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">

29

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<td class="diff-line-num new_line" data-linenumber="28" 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">

28

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python">          <span class="s" style="color: #d14;">"console_scripts"</span><span class="p">:</span> <span class="p">[</span></span>

</pre>

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