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<h3>
Nilesh Patra 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/73f80a44c718c38d52cedf7f56ace899c15db8ca">73f80a44</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-19T02:52:56+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add myself to uploaders
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plip/-/commit/b85030abb773b4b1e54d427e0f96ab587dfd1b41">b85030ab</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-19T02:53:31+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plip/-/commit/393877e4a916749d393f71c0b38cd402d1990976">393877e4</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-19T02:53:32+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.1.7+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plip/-/commit/983c82538505d05271099c85107b4b1df0873d93">983c8253</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-19T02:53:32+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.1.7+dfsg'
Update to upstream version '2.1.7+dfsg'
with Debian dir ebc6081eb30dea03d7f86c1a37ee908e6dc15e9f</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plip/-/commit/bf7a672c5026b3c838ff3d471ef5102e009b7827">bf7a672c</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-19T02:53:32+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plip/-/commit/f35e7c00f5f5b2b7c7fd825a8953388f0edd6e95">f35e7c00</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-19T02:53:37+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#6b5252720edd1a79305a8187c9b25ca0b1651838">
plip/basic/supplemental.py
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<li class="file-stats">
<a href="#7a4c9b79c2f1bb441895d677413efbc1cb536c35">
plip/plipcmd.py
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<li class="file-stats">
<a href="#b72517a8cd7dbc6709d05fdad49ae468ebf79126">
plip/structure/preparation.py
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<li class="file-stats">
<a href="#57c07e057e19c12594e381911c4c7605005fcb83">
plip/test/test_structure_processing.py
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<li class="file-stats">
<a href="#beb8269fe80c40f1503173f33cea803608600305">
<span class="new-file">
+
plip/test/test_visualization.py
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<li class="file-stats">
<a href="#814e5fbe237dcc3e3aabaee96b3a65b231d08b1c">
plip/visualization/visualize.py
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</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/plip/-/compare/100be1392e5ba13088463cbaa491d23d40117d2b...f35e7c00f5f5b2b7c7fd825a8953388f0edd6e95#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">plip (2.1.7+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Standards-Version: 4.5.1 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com> Sat, 19 Dec 2020 02:53:37 +0530</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">plip (2.1.6+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/plip/-/compare/100be1392e5ba13088463cbaa491d23d40117d2b...f35e7c00f5f5b2b7c7fd825a8953388f0edd6e95#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: plip</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Uploaders: Alexandre Mestiashvili <mestia@debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Alexandre Mestiashvili <mestia@debian.org><span class="idiff left right">, Nilesh Patra <npatra974@gmail.com></span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: python</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,7 +12,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> python3-numpy,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> python3-openbabel,</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> python3-setuptools</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/plip</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/plip.git</span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Homepage: https://projects.biotec.tu-dresden.de/plip-web/plip/</span>
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<li id="6b5252720edd1a79305a8187c9b25ca0b1651838">
<a href="https://salsa.debian.org/med-team/plip/-/compare/100be1392e5ba13088463cbaa491d23d40117d2b...f35e7c00f5f5b2b7c7fd825a8953388f0edd6e95#6b5252720edd1a79305a8187c9b25ca0b1651838"><strong>plip/basic/supplemental.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="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">gzip</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">itertools</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></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;">platform</span></span>
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5
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4
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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;">re</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">subprocess</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,14 +16,6 @@ from plip.basic import config, logger</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">get_logger</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Windows and MacOS</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'nt'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">platform</span><span class="p">.</span><span class="n" style="color: #333;">system</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'Darwin'</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># Resource module not available for Windows</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">resource</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Settings</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">seterr</span><span class="p">(</span><span class="nb" style="color: #0086b3;">all</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'ignore'</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># No runtime warnings</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tmpfile</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">direc</span><span class="p">):</span></span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">"""Returns the path to a newly created temporary file."""</span></span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tempfile</span><span class="p">.</span><span class="n" style="color: #333;">mktemp</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">suffix</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'.pdb'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">dir</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">direc</span><span class="p">)</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="369" style="width: 35px; color: rgba(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">@@ -378,10 +369,6 @@ def int32_to_negative(int32):</td>
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378
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369
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read_pdb</span><span class="p">(</span><span class="n" style="color: #333;">pdbfname</span><span class="p">,</span> <span class="n" style="color: #333;">as_string</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>
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379
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="python"> <span class="s" style="color: #d14;">"""Reads a given PDB file and returns a Pybel Molecule."""</span></span>
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380
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371
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="python"> <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;">obErrorLog</span><span class="p">.</span><span class="n" style="color: #333;">StopLogging</span><span class="p">()</span> <span class="c1" style="color: #998; font-style: italic;"># Suppress all OpenBabel warnings</span></span>
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381
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'nt'</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># Resource module not available for Windows</span></span>
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382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="python"> <span class="n" style="color: #333;">maxsize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">resource</span><span class="p">.</span><span class="n" style="color: #333;">getrlimit</span><span class="p">(</span><span class="n" style="color: #333;">resource</span><span class="p">.</span><span class="n" style="color: #333;">RLIMIT_STACK</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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383
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="python"> <span class="n" style="color: #333;">resource</span><span class="p">.</span><span class="n" style="color: #333;">setrlimit</span><span class="p">(</span><span class="n" style="color: #333;">resource</span><span class="p">.</span><span class="n" style="color: #333;">RLIMIT_STACK</span><span class="p">,</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">**</span> <span class="mi" style="color: #099;">28</span><span class="p">,</span> <span class="n" style="color: #333;">maxsize</span><span class="p">),</span> <span class="n" style="color: #333;">maxsize</span><span class="p">))</span></span>
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384
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">setrecursionlimit</span><span class="p">(</span><span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">**</span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># increase Python recursion limit</span></span>
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385
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372
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">readmol</span><span class="p">(</span><span class="n" style="color: #333;">pdbfname</span><span class="p">,</span> <span class="n" style="color: #333;">as_string</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">as_string</span><span class="p">)</span></span>
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386
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373
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="python"></span>
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387
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374
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/plip/-/compare/100be1392e5ba13088463cbaa491d23d40117d2b...f35e7c00f5f5b2b7c7fd825a8953388f0edd6e95#7a4c9b79c2f1bb441895d677413efbc1cb536c35"><strong>plip/plipcmd.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">@@ -225,9 +225,8 @@ def main():</td>
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225
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225
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--nohydro"</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"nohydro"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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226
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226
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Do not add polar hydrogens in case your structure already contains hydrogens."</span><span class="p">,</span></span>
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227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--model"</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"model"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Model number to be used for multi-model structures."</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--model"</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"model"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Model number to be used for multi-model structures."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Optional threshold arguments, not shown in help</span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python"> <span class="n" style="color: #333;">thr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">namedtuple</span><span class="p">(</span><span class="s" style="color: #d14;">'threshold'</span><span class="p">,</span> <span class="s" style="color: #d14;">'name type'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">thresholds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">thr</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'aromatic_planarity'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'angle'</span><span class="p">),</span></span>
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<a href="https://salsa.debian.org/med-team/plip/-/compare/100be1392e5ba13088463cbaa491d23d40117d2b...f35e7c00f5f5b2b7c7fd825a8953388f0edd6e95#b72517a8cd7dbc6709d05fdad49ae468ebf79126"><strong>plip/structure/preparation.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">@@ -63,6 +63,8 @@ class PDBParser:</td>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">corrected_line</span><span class="p">,</span> <span class="n" style="color: #333;">newnum</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fix_pdbline</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">lastnum</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">corrected_line</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="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">corrected_line</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'MODEL'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># reset atom number when new model is encountered</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">lastnum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># Get number of MODEL (1,2,3)</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">model_num</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">corrected_line</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">:</span><span class="mi" style="color: #099;">14</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># initialize storage for new model</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -72,7 +74,8 @@ class PDBParser:</td>
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72
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">other_models</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</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;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">f'ignoring invalid MODEL entry: </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">corrected_line</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">lastnum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newnum</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">lastnum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newnum</span></span>
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76
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">model_dict</span><span class="p">[</span><span class="n" style="color: #333;">current_model</span><span class="p">].</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">corrected_line</span><span class="p">)</span></span>
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77
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># select model</span></span>
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78
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<li id="57c07e057e19c12594e381911c4c7605005fcb83">
<a href="https://salsa.debian.org/med-team/plip/-/compare/100be1392e5ba13088463cbaa491d23d40117d2b...f35e7c00f5f5b2b7c7fd825a8953388f0edd6e95#57c07e057e19c12594e381911c4c7605005fcb83"><strong>plip/test/test_structure_processing.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,10 +22,10 @@ class StructureProcessingTestCase(unittest.TestCase):</td>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">all_hbonds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">interactions</span><span class="p">.</span><span class="n" style="color: #333;">hbonds_ldon</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">interactions</span><span class="p">.</span><span class="n" style="color: #333;">hbonds_pdon</span></span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">all_hydrogen_bonds</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">all_hbonds</span><span class="p">))</span></span>
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24
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># models contain from 0-2 hydrogen bonds</span></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual<span class="idiff left right">s</span></span><span class="p">(</span><span class="n" style="color: #333;">all_hydrogen_bonds</span><span class="p">,</span> <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">})</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">all_hydrogen_bonds</span><span class="p">,</span> <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">})</span></span>
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26
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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27
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_nmr_invalid_model</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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28
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">MODEL</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">11</span></span>
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29
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">interactions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">characterize_complex</span><span class="p">(</span><span class="s" style="color: #d14;">'./pdb/2ndo.pdb'</span><span class="p">,</span> <span class="s" style="color: #d14;">'SFQ:A:201'</span><span class="p">)</span></span>
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">all_hbonds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">interactions</span><span class="p">.</span><span class="n" style="color: #333;">hbonds_ldon</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">interactions</span><span class="p">.</span><span class="n" style="color: #333;">hbonds_pdon</span></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual<span class="idiff left right">s</span></span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">all_hbonds</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span></pre>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">all_hbonds</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/plip/-/compare/100be1392e5ba13088463cbaa491d23d40117d2b...f35e7c00f5f5b2b7c7fd825a8953388f0edd6e95#beb8269fe80c40f1503173f33cea803608600305"><strong>plip/test/test_visualization.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">tempfile</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">unittest</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.basic</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">config</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.basic.remote</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">VisualizerData</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.structure.preparation</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">PDBComplex</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.visualization.visualize</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">visualize_in_pymol</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">VisualizationTest</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="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</span> <span 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="LC14" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tmp_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempfile</span><span class="p">.</span><span class="n" style="color: #333;">mkdtemp</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_visualization</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</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="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">pdb_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'./pdb/2ndo.pdb'</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">binding_site_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'SFQ:A:201'</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">PYMOL</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">MODEL</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">OUTPATH</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">pdb_complex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PDBComplex</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">pdb_complex</span><span class="p">.</span><span class="n" style="color: #333;">load_pdb</span><span class="p">(</span><span class="n" style="color: #333;">pdb_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ligand</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">pdb_complex</span><span class="p">.</span><span class="n" style="color: #333;">ligands</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</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;">ligand</span><span class="p">.</span><span class="n" style="color: #333;">hetid</span><span class="p">,</span> <span class="n" style="color: #333;">ligand</span><span class="p">.</span><span class="n" style="color: #333;">chain</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">ligand</span><span class="p">.</span><span class="n" style="color: #333;">position</span><span class="p">)])</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">binding_site_id</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">pdb_complex</span><span class="p">.</span><span class="n" style="color: #333;">characterize_complex</span><span class="p">(</span><span class="n" style="color: #333;">ligand</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">visualizer_complexes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">VisualizerData</span><span class="p">(</span><span class="n" style="color: #333;">pdb_complex</span><span class="p">,</span> <span class="n" style="color: #333;">site</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">site</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">pdb_complex</span><span class="p">.</span><span class="n" style="color: #333;">interaction_sets</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <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;">pdb_complex</span><span class="p">.</span><span class="n" style="color: #333;">interaction_sets</span><span class="p">[</span><span class="n" style="color: #333;">site</span><span class="p">].</span><span class="n" style="color: #333;">interacting_res</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">visualize_in_pymol</span><span class="p">(</span><span class="n" style="color: #333;">visualizer_complexes</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">listdir</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">)))</span></span></pre>
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<li id="814e5fbe237dcc3e3aabaee96b3a65b231d08b1c">
<a href="https://salsa.debian.org/med-team/plip/-/compare/100be1392e5ba13088463cbaa491d23d40117d2b...f35e7c00f5f5b2b7c7fd825a8953388f0edd6e95#814e5fbe237dcc3e3aabaee96b3a65b231d08b1c"><strong>plip/visualization/visualize.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">@@ -8,7 +8,7 @@ logger = logger.get_logger()</td>
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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>
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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;">visualize_in_pymol</span><span class="p">(</span><span class="n" style="color: #333;">plcomplex</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"> <span class="s" style="color: #d14;">"""Visualizes the <span class="idiff left right">protein-ligand pliprofiler</span> at one site in PyMOL."""</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="s" style="color: #d14;">"""Visualizes the <span class="idiff left right">given Protein-Ligand complex</span> at one site in PyMOL."""</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">vis</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PyMOLVisualizer</span><span class="p">(</span><span class="n" style="color: #333;">plcomplex</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC14" 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">@@ -39,7 +39,8 @@ def visualize_in_pymol(plcomplex):</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">plcomplex</span><span class="p">.</span><span class="n" style="color: #333;">sourcefile</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">current_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">get_object_list</span><span class="p">(</span><span class="n" style="color: #333;">selection</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'(all)'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">f'setting current_name to </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">current_name</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> and pdbid to </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">pdbid</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">f'setting current_name to </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">current_name</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> and PDB-ID to </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">pdbid</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">set_name</span><span class="p">(</span><span class="n" style="color: #333;">current_name</span><span class="p">,</span> <span class="n" style="color: #333;">pdbid</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">hide</span><span class="p">(</span><span class="s" style="color: #d14;">'everything'</span><span class="p">,</span> <span class="s" style="color: #d14;">'all'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">PEPTIDES</span><span class="p">:</span></span>
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