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<h3>
Nilesh Patra pushed to branch upstream
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/0cc446a02dd7fc78ac0e1f3aad38788bf24a98ce">0cc446a0</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-04-19T17:10:36+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.2.0+dfsg</pre>
</li>
</ul>
<h4>16 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#3251d7a8143ce2e789f0468513df8f285f842c3a">
CHANGES.txt
</a>
</li>
<li class="file-stats">
<a href="#14789896d7d3663d4b2dd496146049d6798d139e">
DOCUMENTATION.md
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
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<li class="file-stats">
<a href="#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>
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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
</a>
</li>
<li class="file-stats">
<a href="#b624eb6adf41991d65d443e842dbcef853777899">
<span class="new-file">
+
plip/test/test_intra.py
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</a>
</li>
<li class="file-stats">
<a href="#2525073c8fbdbd4c496cc540b74b251789f6c700">
plip/test/test_literature_validated.py
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<li class="file-stats">
<a href="#7af7ba0f20f7cc7cc84eaf2bb6be9042e9aeca25">
plip/test/test_metal_coordination.py
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<li class="file-stats">
<a href="#9f67ebbb5ec813295c50bdbd1c02e865215420cd">
plip/test/test_remote_services.py
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<li class="file-stats">
<a href="#39a55f5514122e772e551dfe1a697052fe0d8bab">
plip/test/test_xml_parser.py
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</li>
<li class="file-stats">
<a href="#e380c6d288ff4e672ad4665145e8773ede9205d0">
<span class="new-file">
+
plip/test/test_xml_writer.py
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</li>
<li class="file-stats">
<a href="#3bbce20a5f639a39b0f6555b6d1039c2a7419a6c">
plip/visualization/pymol.py
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</li>
<li class="file-stats">
<a href="#814e5fbe237dcc3e3aabaee96b3a65b231d08b1c">
plip/visualization/visualize.py
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</li>
</ul>
<h4>Changes:</h4>
<li id="3251d7a8143ce2e789f0468513df8f285f842c3a">
<a href="https://salsa.debian.org/med-team/plip/-/commit/0cc446a02dd7fc78ac0e1f3aad38788bf24a98ce#3251d7a8143ce2e789f0468513df8f285f842c3a"><strong>CHANGES.txt</strong></a>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Changelog</span>
</pre>
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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">---------</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"># 2.2.0</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">* new minor release</span>
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<td class="old_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">* increased detail level of report (individual atoms on protein side)</span>
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<td class="old_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">* improved handling of multi-model structures</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">* minor bug fixes and code optimizations</span>
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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"># 2.1.9</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">* fixes issues with DNA receptor handling</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"># 2.1.8</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">* report of individual binding site atoms</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"># 2.1.7</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">* bug fixes</span>
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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(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="LC18" class="line" lang="plaintext"># 2.1.6</span>
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<td class="new_line diff-line-num" 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">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">* fetch URL for PDB files updated to avoid issues with RCSB API changes</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<li id="14789896d7d3663d4b2dd496146049d6798d139e">
<a href="https://salsa.debian.org/med-team/plip/-/commit/0cc446a02dd7fc78ac0e1f3aad38788bf24a98ce#14789896d7d3663d4b2dd496146049d6798d139e"><strong>DOCUMENTATION.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -115,11 +115,11 @@ $ plip -i 5b2m --intra A -yv</td>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="markdown">Please note that detection within a chain takes much longer than detection of protein-ligand interactions, especially for large structures.</span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Interactions of Molecules with DNA/RNA</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="markdown">PLIP can characterize interactions between ligands and DNA/RNA. A special mode allows to switch from <span class="idiff left">protein to DNA/RNA as</span> the receptor <span class="idiff">molecule </span>in the structure. <span class="idiff right">To change the receptor</span> mode, start PLIP with the option <span class="sb" style="color: #d14;">`--dnareceptor`</span>.</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="markdown">PLIP can characterize interactions between ligands and DNA/RNA. A special mode allows to switch from <span class="idiff left">treating DNA/RNA molecules as ligands to treating them as part of</span> the receptor in the structure. <span class="idiff right">If a protein is present, too, interactions of the ligand with both, protein and nucleic acids, will be shown. To use this</span> mode, start PLIP with the option <span class="sb" style="color: #d14;">`--dnareceptor`</span>.</span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Changing detection thresholds</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="markdown">The PLIP algorithm uses a rule-based detection to report non-covalent interaction between proteins and their partners. The current settings are based on literature values and have been refined based on extensive testing with independent cases from mainly crystallography journals, covering a broad range of structure resolutions. For most users, it is not recommended to change the standard settings. However, there may be cases where changing detection thresholds is advisable (e.g. sets with multiple very low resolution structures).</span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="markdown"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="markdown">PLIP allows you to change the setting permanently or for one run.</span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Permanent change</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">@@ -147,7 +147,7 @@ PLIP offers further command line options which enables you to switch advanced se</td>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Web Service</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="markdown">A web service for analysis of protein-ligand complexes using PLIP is available at</span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">plip.biotec.tu-dresden.de</span><span class="p">](</span><span class="sx" style="color: #d14;">http://plip.biotec.tu-dresden.de/</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="markdown"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="markdown">The web site offers advanced functions to search for specific entries from PDB and lists the interaction results in the browser. Additionally, the service used the BioLiP database to annotate biologically relevant ligands. The option to change threshold, ligand filtering, and batch processing is only available in the command line tool and with the Python modules.</span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Algorithm</span></span>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/plip/-/commit/0cc446a02dd7fc78ac0e1f3aad38788bf24a98ce#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,8 +18,6 @@ Analyze noncovalent protein-ligand interactions in 3D structures with ease.</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown">| "I love the Linux command line and want to build a workflow around PLIP!" | :x: | :heavy_check_mark: | :heavy_check_mark: | :yellow_circle: |</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown">| "I'm a Python programmer and want to use PLIP in my project!" | :x: | :yellow_circle: | :yellow_circle: | :heavy_check_mark: |</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="markdown">:exclamation: <span class="gs" style="font-weight: 600;">**Note:**</span> The web server is currently running an outdated version of PLIP, which will be replaced soon. For production use and data analysis we highly recommend to use the current command line release. :exclamation:</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown"><span class="p">---</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Quickstart</span></span>
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<a href="https://salsa.debian.org/med-team/plip/-/commit/0cc446a02dd7fc78ac0e1f3aad38788bf24a98ce#e0bdfb93722bb0bccd3faf9d5cbf446297ff47c4"><strong>plip/basic/config.py</strong></a>
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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.<span class="idiff left right">1.6</span>'</span></span>
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2
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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="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.<span class="idiff left right">2.0</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<span class="idiff left right">-2021</span>) - 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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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/plip/-/commit/0cc446a02dd7fc78ac0e1f3aad38788bf24a98ce#67d4980fce23584951cb46902ae74ffca7500b93"><strong>plip/exchange/report.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -40,6 +40,8 @@ class StructureReport:</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">mode</span><span class="p">.</span><span class="n" style="color: #333;">text</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'default'</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">pdbid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">et</span><span class="p">.</span><span class="n" style="color: #333;">SubElement</span><span class="p">(</span><span class="n" style="color: #333;">report</span><span class="p">,</span> <span class="s" style="color: #d14;">'pdbid'</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;">pdbid</span><span class="p">.</span><span class="n" style="color: #333;">text</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;">mol</span><span class="p">.</span><span class="n" style="color: #333;">pymol_name</span><span class="p">.</span><span class="n" style="color: #333;">upper</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">et</span><span class="p">.</span><span class="n" style="color: #333;">SubElement</span><span class="p">(</span><span class="n" style="color: #333;">report</span><span class="p">,</span> <span class="s" style="color: #d14;">'model'</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;">model</span><span class="p">.</span><span class="n" style="color: #333;">text</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">MODEL</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;">filetype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">et</span><span class="p">.</span><span class="n" style="color: #333;">SubElement</span><span class="p">(</span><span class="n" style="color: #333;">report</span><span class="p">,</span> <span class="s" style="color: #d14;">'filetype'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">filetype</span><span class="p">.</span><span class="n" style="color: #333;">text</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;">mol</span><span class="p">.</span><span class="n" style="color: #333;">filetype</span><span class="p">.</span><span class="n" style="color: #333;">upper</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">pdbfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">et</span><span class="p">.</span><span class="n" style="color: #333;">SubElement</span><span class="p">(</span><span class="n" style="color: #333;">report</span><span class="p">,</span> <span class="s" style="color: #d14;">'pdbfile'</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -72,7 +74,8 @@ class StructureReport:</td>
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">excluded</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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73
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">textlines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">'Excluded molecules as ligands: %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="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">lig</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">lig</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">excluded</span><span class="p">]))</span></span>
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74
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76
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<pre style="margin: 0;"> <span id="LC76" 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;">DNARECEPTOR</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;">textlines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">'DNA/RNA in structure was chosen as the receptor part.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">textlines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">'DNA/RNA in structure was chosen to be part of the receptor.'</span><span class="p">)</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">textlines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">'Analysis was done on model </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">MODEL</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">textlines</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_bindingsite_data</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -191,23 +194,28 @@ class BindingSiteReport:</td>
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191
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">################</span></span>
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"></span>
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">saltbridge_features</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"> <span class="s" style="color: #d14;">'RESNR'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESTYPE'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESCHAIN'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESNR_LIG'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESTYPE_LIG'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESCHAIN_LIG'</span><span class="p">,</span> <span class="s" style="color: #d14;">'DIST'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PROTISPOS'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="s" style="color: #d14;">'RESNR'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESTYPE'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESCHAIN'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PROT_IDX_LIST'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESNR_LIG'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESTYPE_LIG'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESCHAIN_LIG'</span><span class="p">,</span> <span class="s" style="color: #d14;">'DIST'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="s" style="color: #d14;">'PROTISPOS'</span><span class="p">,</span></span>
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195
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"> <span class="s" style="color: #d14;">'LIG_GROUP'</span><span class="p">,</span></span>
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python"> <span class="s" style="color: #d14;">'LIG_IDX_LIST'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"> <span class="s" style="color: #d14;">'LIGCOO'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PROTCOO'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">saltbridge_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sb</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">complex</span><span class="p">.</span><span class="n" style="color: #333;">saltbridge_lneg</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">complex</span><span class="p">.</span><span class="n" style="color: #333;">saltbridge_pneg</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">protispos</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="p">,</span> <span class="n" style="color: #333;">ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">negative</span><span class="p">.</span><span class="n" style="color: #333;">fgroup</span><span class="p">,</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">str</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;">sb</span><span class="p">.</span><span class="n" style="color: #333;">negative</span><span class="p">.</span><span class="n" style="color: #333;">atoms_orig_idx</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">saltbridge_info</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">reschain</span><span class="p">,</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">reschain_l</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="p">,</span> <span class="n" style="color: #333;">ligand_atom_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">negative</span><span class="p">.</span><span class="n" style="color: #333;">fgroup</span><span class="p">,</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">str</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;">sb</span><span class="p">.</span><span class="n" style="color: #333;">negative</span><span class="p">.</span><span class="n" style="color: #333;">atoms_orig_idx</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">protein_atom_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">str</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;">sb</span><span class="p">.</span><span class="n" style="color: #333;">positive</span><span class="p">.</span><span class="n" style="color: #333;">atoms_orig_idx</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">saltbridge_info</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">reschain</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;">protein_atom_ids</span><span class="p">),</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">reschain_l</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"> <span class="s" style="color: #d14;">'%.2f'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">distance</span><span class="p">,</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">protispos</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="p">.</span><span class="n" style="color: #333;">capitalize</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;">ids</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="p">.</span><span class="n" style="color: #333;">capitalize</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;"><span class="idiff left right">ligand_atom_</span>ids</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">negative</span><span class="p">.</span><span class="n" style="color: #333;">center</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">positive</span><span class="p">.</span><span class="n" style="color: #333;">center</span><span class="p">)))</span></span>
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<pre style="margin: 0;"> <span id="LC212" 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="LC207" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="p">,</span> <span class="n" style="color: #333;">ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">positive</span><span class="p">.</span><span class="n" style="color: #333;">fgroup</span><span class="p">,</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">str</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;">sb</span><span class="p">.</span><span class="n" style="color: #333;">positive</span><span class="p">.</span><span class="n" style="color: #333;">atoms_orig_idx</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">saltbridge_info</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">reschain</span><span class="p">,</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">reschain_l</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="p">,</span> <span class="n" style="color: #333;">ligand_atom_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">positive</span><span class="p">.</span><span class="n" style="color: #333;">fgroup</span><span class="p">,</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">str</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;">sb</span><span class="p">.</span><span class="n" style="color: #333;">positive</span><span class="p">.</span><span class="n" style="color: #333;">atoms_orig_idx</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">protein_atom_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">str</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;">sb</span><span class="p">.</span><span class="n" style="color: #333;">negative</span><span class="p">.</span><span class="n" style="color: #333;">atoms_orig_idx</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">saltbridge_info</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">reschain</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;">protein_atom_ids</span><span class="p">),</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">reschain_l</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python"> <span class="s" style="color: #d14;">'%.2f'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">distance</span><span class="p">,</span> <span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">protispos</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="p">.</span><span class="n" style="color: #333;">capitalize</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;">ids</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="p">.</span><span class="n" style="color: #333;">capitalize</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;"><span class="idiff left right">ligand_atom_</span>ids</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="python"> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">positive</span><span class="p">.</span><span class="n" style="color: #333;">center</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">sb</span><span class="p">.</span><span class="n" style="color: #333;">negative</span><span class="p">.</span><span class="n" style="color: #333;">center</span><span class="p">)))</span></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">###############</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -215,15 +223,18 @@ class BindingSiteReport:</td>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">###############</span></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pistacking_features</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"> <span class="s" style="color: #d14;">'RESNR'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESTYPE'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESCHAIN'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESNR_LIG'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESTYPE_LIG'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESCHAIN_LIG'</span><span class="p">,</span> <span class="s" style="color: #d14;">'CENTDIST'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ANGLE'</span><span class="p">,</span> <span class="s" style="color: #d14;">'OFFSET'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="s" style="color: #d14;">'RESNR'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESTYPE'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESCHAIN'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESNR_LIG'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESTYPE_LIG'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESCHAIN_LIG'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PROT_IDX_LIST'</span><span class="p">,</span> <span class="s" style="color: #d14;">'CENTDIST'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <span class="s" style="color: #d14;">'ANGLE'</span><span class="p">,</span> <span class="s" style="color: #d14;">'OFFSET'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python"> <span class="s" style="color: #d14;">'TYPE'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python"> <span class="s" style="color: #d14;">'LIG_IDX_LIST'</span><span class="p">,</span> <span class="s" style="color: #d14;">'LIGCOO'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PROTCOO'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pistacking_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">stack</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">complex</span><span class="p">.</span><span class="n" style="color: #333;">pistacking</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">str</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;">stack</span><span class="p">.</span><span class="n" style="color: #333;">ligandring</span><span class="p">.</span><span class="n" style="color: #333;">atoms_orig_idx</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;">ligand_atom_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">str</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;">stack</span><span class="p">.</span><span class="n" style="color: #333;">ligandring</span><span class="p">.</span><span class="n" style="color: #333;">atoms_orig_idx</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"> <span class="n" style="color: #333;">protein_atom_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">str</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;">stack</span><span class="p">.</span><span class="n" style="color: #333;">proteinring</span><span class="p">.</span><span class="n" style="color: #333;">atoms_orig_idx</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pistacking_info</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">stack</span><span class="p">.</span><span class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">stack</span><span class="p">.</span><span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">stack</span><span class="p">.</span><span class="n" style="color: #333;">reschain</span><span class="p">,</span> <span class="n" style="color: #333;">stack</span><span class="p">.</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">stack</span><span class="p">.</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">stack</span><span class="p">.</span><span class="n" style="color: #333;">reschain_l</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;">stack</span><span class="p">.</span><span class="n" style="color: #333;">distance</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="python"> <span class="s" style="color: #d14;">'%.2f'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">stack</span><span class="p">.</span><span class="n" style="color: #333;">angle</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;">stack</span><span class="p">.</span><span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="n" style="color: #333;">stack</span><span class="p">.</span><span class="nb" style="color: #0086b3;">type</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;">ids</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="n" style="color: #333;">stack</span><span class="p">.</span><span class="n" style="color: #333;">reschain_l</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;">protein_atom_ids</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;">stack</span><span class="p">.</span><span class="n" style="color: #333;">distance</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="s" style="color: #d14;">'%.2f'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">stack</span><span class="p">.</span><span class="n" style="color: #333;">angle</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;">stack</span><span class="p">.</span><span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="n" style="color: #333;">stack</span><span class="p">.</span><span class="nb" style="color: #0086b3;">type</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <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_atom_ids</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python"> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">stack</span><span class="p">.</span><span class="n" style="color: #333;">ligandring</span><span class="p">.</span><span class="n" style="color: #333;">center</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">stack</span><span class="p">.</span><span class="n" style="color: #333;">proteinring</span><span class="p">.</span><span class="n" style="color: #333;">center</span><span class="p">)))</span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">##########################</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -231,24 +242,28 @@ class BindingSiteReport:</td>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">##########################</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pication_features</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="python"> <span class="s" style="color: #d14;">'RESNR'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESTYPE'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESCHAIN'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESNR_LIG'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESTYPE_LIG'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESCHAIN_LIG'</span><span class="p">,</span> <span class="s" style="color: #d14;">'DIST'</span><span class="p">,</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">'OFFSET'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'PROTCHARGED'</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">LIG_GROUP</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="python"> <span class="s" style="color: #d14;">'LIG_IDX_LIST'</span><span class="p">,</span> <span class="s" style="color: #d14;">'LIGCOO'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PROTCOO'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="s" style="color: #d14;">'RESNR'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESTYPE'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESCHAIN'</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left">'PROT_IDX_LIST'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">'RESNR_LIG'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESTYPE_LIG'</span><span class="p">,</span> <span class="s" style="color: #d14;">'RESCHAIN_LIG'</span><span class="p">,</span> <span class="s" style="color: #d14;">'DIST'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">OFFSET</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left">'PROTCHARGED'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'LIG_GROUP'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">'LIG_IDX_LIST'</span><span class="p">,</span> <span class="s" style="color: #d14;">'LIGCOO'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PROTCOO'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pication_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">picat</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">complex</span><span class="p">.</span><span class="n" style="color: #333;">pication_laro</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">complex</span><span class="p">.</span><span class="n" style="color: #333;">pication_paro</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">protcharged</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">str</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;">picat</span><span class="p">.</span><span class="n" style="color: #333;">ring</span><span class="p">.</span><span class="n" style="color: #333;">atoms_orig_idx</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="n" style="color: #333;">ligand_atom_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">str</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;">picat</span><span class="p">.</span><span class="n" style="color: #333;">ring</span><span class="p">.</span><span class="n" style="color: #333;">atoms_orig_idx</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="n" style="color: #333;">protein_atom_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">str</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;">picat</span><span class="p">.</span><span class="n" style="color: #333;">charge</span><span class="p">.</span><span class="n" style="color: #333;">atoms_orig_idx</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="python"> <span class="n" style="color: #333;">group</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Aromatic'</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pication_info</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 class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">reschain</span><span class="p">,</span> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pication_info</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 class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">reschain</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;">protein_atom_ids</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python"> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">reschain_l</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;">picat</span><span class="p">.</span><span class="n" style="color: #333;">distance</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python"> <span class="s" style="color: #d14;">'%.2f'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">protcharged</span><span class="p">,</span> <span class="n" style="color: #333;">group</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;">ids</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"> <span class="s" style="color: #d14;">'%.2f'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">protcharged</span><span class="p">,</span> <span class="n" style="color: #333;">group</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;"><span class="idiff left right">ligand_atom_</span>ids</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="python"> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">ring</span><span class="p">.</span><span class="n" style="color: #333;">center</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">charge</span><span class="p">.</span><span class="n" style="color: #333;">center</span><span class="p">)))</span></span>
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<pre style="margin: 0;"> <span id="LC259" 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="LC247" class="line" lang="python"> <span class="n" style="color: #333;">ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">str</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;">picat</span><span class="p">.</span><span class="n" style="color: #333;">charge</span><span class="p">.</span><span class="n" style="color: #333;">atoms_orig_idx</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"> <span class="n" style="color: #333;">ligand_atom_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">str</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;">picat</span><span class="p">.</span><span class="n" style="color: #333;">charge</span><span class="p">.</span><span class="n" style="color: #333;">atoms_orig_idx</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"> <span class="n" style="color: #333;">protein_atom_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">str</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;">picat</span><span class="p">.</span><span class="n" style="color: #333;">ring</span><span class="p">.</span><span class="n" style="color: #333;">atoms_orig_idx</span><span class="p">]</span></span>
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="python"> <span class="n" style="color: #333;">group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">charge</span><span class="p">.</span><span class="n" style="color: #333;">fgroup</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pication_info</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 class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">reschain</span><span class="p">,</span> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pication_info</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 class="n" style="color: #333;">resnr</span><span class="p">,</span> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">restype</span><span class="p">,</span> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">reschain</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;">protein_atom_ids</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="python"> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">resnr_l</span><span class="p">,</span> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">restype_l</span><span class="p">,</span></span>
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python"> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">reschain_l</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;">picat</span><span class="p">.</span><span class="n" style="color: #333;">distance</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="python"> <span class="s" style="color: #d14;">'%.2f'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">protcharged</span><span class="p">,</span> <span class="n" style="color: #333;">group</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;">ids</span><span class="p">),</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"> <span class="s" style="color: #d14;">'%.2f'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">protcharged</span><span class="p">,</span> <span class="n" style="color: #333;">group</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;"><span class="idiff left right">ligand_atom_</span>ids</span><span class="p">),</span></span>
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python"> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">charge</span><span class="p">.</span><span class="n" style="color: #333;">center</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">picat</span><span class="p">.</span><span class="n" style="color: #333;">ring</span><span class="p">.</span><span class="n" style="color: #333;">center</span><span class="p">)))</span></span>
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#################</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -451,9 +466,15 @@ class BindingSiteReport:</td>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="python"> <span class="n" style="color: #333;">new_contact</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">et</span><span class="p">.</span><span class="n" style="color: #333;">SubElement</span><span class="p">(</span><span class="n" style="color: #333;">interaction</span><span class="p">,</span> <span class="n" style="color: #333;">element_name</span><span class="p">[:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">j</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="LC467" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">feature</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">single_contact</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Just assign the value unless it's an atom list, use subelements in this case</span></span>
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<pre style="margin: 0;">-<span id="LC454" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">features</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'LIG_IDX_LIST'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">features</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'LIG_IDX_LIST'</span><span class="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">features</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'PROT_IDX_LIST'</span></span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="python"> <span class="n" style="color: #333;">feat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">et</span><span class="p">.</span><span class="n" style="color: #333;">SubElement</span><span class="p">(</span><span class="n" style="color: #333;">new_contact</span><span class="p">,</span> <span class="n" style="color: #333;">features</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">lower</span><span class="p">())</span></span>
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<pre style="margin: 0;">-<span id="LC456" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">atm_idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">feature</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">','</span><span class="p">)):</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="python"> <span class="n" style="color: #333;">split</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># check whether multiple atoms are contained in the atom group</span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">feature</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="python"> <span class="n" style="color: #333;">split</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">feature</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">','</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC475" 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="LC476" class="line" lang="python"> <span class="n" style="color: #333;">split</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">feature</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">atm_idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">split</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="python"> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">et</span><span class="p">.</span><span class="n" style="color: #333;">SubElement</span><span class="p">(</span><span class="n" style="color: #333;">feat</span><span class="p">,</span> <span class="s" style="color: #d14;">'idx'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">k</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="LC479" class="line" lang="python"> <span class="n" style="color: #333;">idx</span><span class="p">.</span><span class="n" style="color: #333;">text</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">atm_idx</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">features</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'COO'</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/plip/-/commit/0cc446a02dd7fc78ac0e1f3aad38788bf24a98ce#65da37aabb52e08df77545976cc2684a5df1de5f"><strong>plip/exchange/xml.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;">from</span> <span class="nn" style="color: #555;">lxml</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">etree</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">urllib.request</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">urlopen</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="LC3" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC4" 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="LC5" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="109" style="width: 35px; color: rgba(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">@@ -109,6 +107,8 @@ class SaltBridge(Interaction):</td>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">lig_group</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">getdata</span><span class="p">(</span><span class="n" style="color: #333;">sbridge_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'lig_group'</span><span class="p">,</span> <span class="n" style="color: #333;">force_string</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">lig_idx_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">tagpart</span><span class="p">.</span><span class="n" style="color: #333;">text</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tagpart</span> <span class="ow" style="font-weight: 600;">in</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">sbridge_part</span><span class="p">.</span><span class="n" style="color: #333;">xpath</span><span class="p">(</span><span class="s" style="color: #d14;">'lig_idx_list/idx'</span><span class="p">)]</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prot_idx_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">tagpart</span><span class="p">.</span><span class="n" style="color: #333;">text</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tagpart</span> <span class="ow" style="font-weight: 600;">in</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">sbridge_part</span><span class="p">.</span><span class="n" style="color: #333;">xpath</span><span class="p">(</span><span class="s" style="color: #d14;">'prot_idx_list/idx'</span><span class="p">)]</span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PiStacking</span><span class="p">(</span><span class="n" style="color: #333;">Interaction</span><span class="p">):</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -123,6 +123,8 @@ class PiStacking(Interaction):</td>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">type</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;">getdata</span><span class="p">(</span><span class="n" style="color: #333;">pistack_part</span><span class="p">,</span> <span class="s" style="color: #d14;">'type'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">lig_idx_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">tagpart</span><span class="p">.</span><span class="n" style="color: #333;">text</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tagpart</span> <span class="ow" style="font-weight: 600;">in</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">pistack_part</span><span class="p">.</span><span class="n" style="color: #333;">xpath</span><span class="p">(</span><span class="s" style="color: #d14;">'lig_idx_list/idx'</span><span class="p">)]</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prot_idx_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">tagpart</span><span class="p">.</span><span class="n" style="color: #333;">text</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tagpart</span> <span class="ow" style="font-weight: 600;">in</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">pistack_part</span><span class="p">.</span><span class="n" style="color: #333;">xpath</span><span class="p">(</span><span class="s" style="color: #d14;">'prot_idx_list/idx'</span><span class="p">)]</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PiCation</span><span class="p">(</span><span class="n" style="color: #333;">Interaction</span><span class="p">):</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -233,7 +235,7 @@ class BSite(XMLStorage):</td>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">halogens</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">HalogenBond</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">interactions</span><span class="p">.</span><span class="n" style="color: #333;">xpath</span><span class="p">(</span><span class="s" style="color: #d14;">'halogen_bonds/halogen_bond'</span><span class="p">)]</span></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">metal_complexes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">MetalComplex</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">interactions</span><span class="p">.</span><span class="n" style="color: #333;">xpath</span><span class="p">(</span><span class="s" style="color: #d14;">'metal_complexes/metal_complex'</span><span class="p">)]</span></span>
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237
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">num_contacts</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hydrophobics</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hbonds</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">wbridges</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sbridges</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> \</span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="python"> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pi_stacks</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pi_cations</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">halogens</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">metal_complexes</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"><span class="idiff left right"> </span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pi_stacks</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pi_cations</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">halogens</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">metal_complexes</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">has_interactions</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;">num_contacts</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span></span>
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238
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240
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python"></span>
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239
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">get_atom_mapping</span><span class="p">()</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="260" style="width: 35px; color: rgba(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="262" style="width: 35px; color: rgba(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">@@ -260,7 +262,8 @@ class BSite(XMLStorage):</td>
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="python"> <span class="s" style="color: #d14;">'pications'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pi_cations</span><span class="p">),</span> <span class="s" style="color: #d14;">'halogens'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">halogens</span><span class="p">),</span> <span class="s" style="color: #d14;">'metal'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">metal_complexes</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="python"> <span class="s" style="color: #d14;">'hbond_back'</span><span class="p">:</span> <span class="n" style="color: #333;">hbondsback</span><span class="p">,</span> <span class="s" style="color: #d14;">'hbond_nonback'</span><span class="p">:</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hbonds</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">hbondsback</span><span class="p">)}</span></span>
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python"> <span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="s" style="color: #d14;">'total'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="s" style="color: #d14;">'hydrophobics'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="s" style="color: #d14;">'hbonds'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="s" style="color: #d14;">'wbridges'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> \</span>
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="python"> <span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="s" style="color: #d14;">'sbridges'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="s" style="color: #d14;">'pistacks'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="s" style="color: #d14;">'pications'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="s" style="color: #d14;">'halogens'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="s" style="color: #d14;">'metal'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python"> <span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="s" style="color: #d14;">'sbridges'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="s" style="color: #d14;">'pistacks'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="s" style="color: #d14;">'pications'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="s" style="color: #d14;">'halogens'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">counts</span><span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"> <span class="s" style="color: #d14;">'metal'</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">counts</span></span>
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python"></span>
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269
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<pre style="margin: 0;"> <span id="LC269" 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">@@ -284,4 +287,4 @@ class PlipXML(XMLStorage):</td>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">load_data</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">xmlfile</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="python"> <span class="s" style="color: #d14;">"""Loads/parses an XML file and saves it as a tree if successful."""</span></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">doc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">etree</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">xmlfile</span><span class="p">)</span></span></pre>
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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">\ No newline at end of file</td>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">doc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">etree</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">xmlfile</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/plip/-/commit/0cc446a02dd7fc78ac0e1f3aad38788bf24a98ce#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">@@ -210,7 +210,7 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Turns off calculation of mapping between canonical and PDB atom order for ligands."</span><span class="p">,</span></span>
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211
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<pre style="margin: 0;"> <span id="LC211" 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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212
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<pre style="margin: 0;"> <span id="LC212" 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;">"--dnareceptor"</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"dnareceptor"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC213" 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;">"<span class="idiff left">Uses the DNA instead of the protein as a receptor for</span> inte<span class="idiff right">ractions</span>."</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"<span class="idiff left">Treat nucleic acids as part of the receptor structure (together with any present protein)</span> in<span class="idiff">s</span>te<span class="idiff right">ad of as a ligand</span>."</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">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="LC215" 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;">"--name"</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"outputfilename"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"report"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Set a filename for the report TXT and XML files. Will only work when processing single structures."</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/plip/-/commit/0cc446a02dd7fc78ac0e1f3aad38788bf24a98ce#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">@@ -86,6 +86,7 @@ class PDBParser:</td>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">corrected_pdb</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">model_dict</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">corrected_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model_dict</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">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;">1</span></span>
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">'invalid model number specified, using first model instead'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC91" 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="LC92" class="line" lang="python"> <span class="n" style="color: #333;">corrected_pdb</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;">pdbpath</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">@@ -1407,7 +1408,9 @@ class PDBComplex:</td>
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1408
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<pre style="margin: 0;"> <span id="LC1408" class="line" lang="python"></span>
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1409
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<pre style="margin: 0;"> <span id="LC1409" 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;">DNARECEPTOR</span><span class="p">:</span></span>
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1410
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<pre style="margin: 0;"> <span id="LC1410" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">resis</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">obres</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;">pybel</span><span class="p">.</span><span class="n" style="color: #333;">ob</span><span class="p">.</span><span class="n" style="color: #333;">OBResidueIter</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC1410" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">protcomplex</span><span class="p">.</span><span class="n" style="color: #333;">OBMol</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">obres</span><span class="p">.</span><span class="n" style="color: #333;">GetName</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">DNA</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">RNA</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC1411" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">protcomplex</span><span class="p">.</span><span class="n" style="color: #333;">OBMol</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">obres</span><span class="p">.</span><span class="n" style="color: #333;">GetName</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">DNA</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">RNA</span></span>
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<pre style="margin: 0;">+<span id="LC1412" class="line" lang="python"> <span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="n" style="color: #333;">obres</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;">pybel</span><span class="p">.</span><span class="n" style="color: #333;">ob</span><span class="p">.</span><span class="n" style="color: #333;">OBResidueIter</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC1413" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">protcomplex</span><span class="p">.</span><span class="n" style="color: #333;">OBMol</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</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>
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1411
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1414
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<pre style="margin: 0;"> <span id="LC1414" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1415
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<pre style="margin: 0;"> <span id="LC1415" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">resis</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">obres</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;">pybel</span><span class="p">.</span><span class="n" style="color: #333;">ob</span><span class="p">.</span><span class="n" style="color: #333;">OBResidueIter</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC1416" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">protcomplex</span><span class="p">.</span><span class="n" style="color: #333;">OBMol</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</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>
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<a href="https://salsa.debian.org/med-team/plip/-/commit/0cc446a02dd7fc78ac0e1f3aad38788bf24a98ce#b624eb6adf41991d65d443e842dbcef853777899"><strong>plip/test/test_intra.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;">unittest</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC3" 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="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.exchange.report</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">StructureReport</span></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.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="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">IntraTest</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="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;">test_4day</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">PEPTIDES</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'C'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC12" 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="LC13" 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="s" style="color: #d14;">'./pdb/4day.pdb'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC14" 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="LC15" 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="LC16" class="line" lang="python"> <span class="n" style="color: #333;">structure_report</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StructureReport</span><span class="p">(</span><span class="n" style="color: #333;">pdb_complex</span><span class="p">,</span> <span class="n" style="color: #333;">outputprefix</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"test_"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">structure_report</span><span class="p">.</span><span class="n" style="color: #333;">write_xml</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;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">PEPTIDES</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span></pre>
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<li id="2525073c8fbdbd4c496cc540b74b251789f6c700">
<a href="https://salsa.debian.org/med-team/plip/-/commit/0cc446a02dd7fc78ac0e1f3aad38788bf24a98ce#2525073c8fbdbd4c496cc540b74b251789f6c700"><strong>plip/test/test_literature_validated.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">@@ -6,6 +6,7 @@ test_literature_validated.py - Unit Tests for literature-validated cases.</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC8" 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="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC10" 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="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/plip/-/commit/0cc446a02dd7fc78ac0e1f3aad38788bf24a98ce#7af7ba0f20f7cc7cc84eaf2bb6be9042e9aeca25"><strong>plip/test/test_metal_coordination.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">@@ -6,6 +6,7 @@ test_metal_coordination.py - Unit Tests for Metal Coordination.</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC8" 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="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC10" 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="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>
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<li id="9f67ebbb5ec813295c50bdbd1c02e865215420cd">
<a href="https://salsa.debian.org/med-team/plip/-/commit/0cc446a02dd7fc78ac0e1f3aad38788bf24a98ce#9f67ebbb5ec813295c50bdbd1c02e865215420cd"><strong>plip/test/test_remote_services.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">@@ -6,6 +6,7 @@ test_remote_services.py - Unit Tests for remote services.</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC8" 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="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.exchange.webservices</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">check_pdb_status</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/plip/-/commit/0cc446a02dd7fc78ac0e1f3aad38788bf24a98ce#39a55f5514122e772e551dfe1a697052fe0d8bab"><strong>plip/test/test_xml_parser.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,6 +6,7 @@ test_xml_parser.py - Unit Tests for XML Parser.</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC8" 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="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.exchange.xml</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">PlipXML</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/plip/-/commit/0cc446a02dd7fc78ac0e1f3aad38788bf24a98ce#e380c6d288ff4e672ad4665145e8773ede9205d0"><strong>plip/test/test_xml_writer.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;">unittest</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.exchange.report</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">StructureReport</span></span>
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<pre style="margin: 0;">+<span id="LC4" 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="LC5" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">XMLWriterTest</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="LC8" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_pi_stacking</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC9" 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="LC10" 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="s" style="color: #d14;">'./pdb/4dst_protonated.pdb'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC11" 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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12
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<pre style="margin: 0;">+<span id="LC12" 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="s" style="color: #d14;">'GCP:A:202'</span><span class="p">:</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="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="LC14" class="line" lang="python"> <span class="n" style="color: #333;">structure_report</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StructureReport</span><span class="p">(</span><span class="n" style="color: #333;">pdb_complex</span><span class="p">,</span> <span class="n" style="color: #333;">outputprefix</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"test_"</span><span class="p">)</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">structure_report</span><span class="p">.</span><span class="n" style="color: #333;">write_xml</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;">True</span><span class="p">)</span></span>
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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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_pication</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC18" 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="LC19" 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="s" style="color: #d14;">'./pdb/6nhb.pdb'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">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="LC21" 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="s" style="color: #d14;">'H4B:A:802'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">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="LC23" class="line" lang="python"> <span class="n" style="color: #333;">structure_report</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StructureReport</span><span class="p">(</span><span class="n" style="color: #333;">pdb_complex</span><span class="p">,</span> <span class="n" style="color: #333;">outputprefix</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"test_"</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;">structure_report</span><span class="p">.</span><span class="n" style="color: #333;">write_xml</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;">True</span><span class="p">)</span></span></pre>
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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">@@ -5,6 +5,8 @@ from time import sleep</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></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;">pymol</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">cmd</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></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.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="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;">PyMOLVisualizer</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -340,10 +342,11 @@ class PyMOLVisualizer:</td>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">viewport</span><span class="p">(</span><span class="n" style="color: #333;">width</span><span class="p">,</span> <span class="n" style="color: #333;">height</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">zoom</span><span class="p">(</span><span class="s" style="color: #d14;">'visible'</span><span class="p">,</span> <span class="mf" style="color: #099;">1.5</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># Adapt the zoom to the viewport</span></span>
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<pre style="margin: 0;"> <span id="LC344" 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;">'ray_trace_frames'</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># Frames are raytraced before saving an image.</span></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">mpng</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># Use batch png mode with 1 frame only</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">mpng</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">config</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">MODEL</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">config</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">MODEL</span></span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># Use batch png mode with 1 frame only</span></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">mplay</span><span class="p">()</span> <span class="c1" style="color: #998; font-style: italic;"># cmd.mpng needs the animation to 'run'</span></span>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">refresh</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="python"> <span class="n" style="color: #333;">originalfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">filepath</span><span class="p">,</span> <span class="s" style="color: #d14;">'0001.png'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="python"> <span class="n" style="color: #333;">originalfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="python"> <span class="p">[</span><span class="n" style="color: #333;">filepath</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">MODEL</span><span class="p">)))</span> <span class="o" style="font-weight: 600;">*</span> <span class="s" style="color: #d14;">'0'</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">MODEL</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.png'</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="python"> <span class="n" style="color: #333;">newfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">filepath</span><span class="p">,</span> <span class="s" style="color: #d14;">'.png'</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#################################################</span></span>
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<a href="https://salsa.debian.org/med-team/plip/-/commit/0cc446a02dd7fc78ac0e1f3aad38788bf24a98ce#814e5fbe237dcc3e3aabaee96b3a65b231d08b1c"><strong>plip/visualization/visualize.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="38" style="width: 35px; color: rgba(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="38" style="width: 35px; color: rgba(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">@@ -38,6 +38,7 @@ def visualize_in_pymol(plcomplex):</td>
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">vis</span><span class="p">.</span><span class="n" style="color: #333;">set_initial_representations</span><span class="p">()</span></span>
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39
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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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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">frame</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">MODEL</span><span class="p">)</span></span>
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41
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42
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<pre style="margin: 0;"> <span id="LC42" 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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42
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"></span>
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43
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44
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<pre style="margin: 0;"> <span id="LC44" 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="sa">f</span><span class="s" style="color: #d14;">'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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