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GitLab

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<h3>

Nilesh Patra pushed to branch master

at <a href="https://salsa.debian.org/med-team/plip">Debian Med / plip</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/plip/-/commit/e8f1daf1e73b122449b9bb9608417946ac5c1b09">e8f1daf1</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2020-11-10T07:17:33+00:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.1.5+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/plip/-/commit/29d969f22e90980a00a1b477d7b5782e53256c70">29d969f2</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2020-11-10T07:17:33+00:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/plip/-/commit/501ce9a005f80360a8480625860dffa5b635431e">501ce9a0</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2020-11-10T07:17:34+00:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.1.5+dfsg'

Update to upstream version '2.1.5+dfsg'

with Debian dir 845e2e866749f53faec638c88ccd279f85c7f927</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/plip/-/commit/09bfd4f4fbaee9ff3f871de6448769e7cd3a9458">09bfd4f4</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2020-11-10T07:17:35+00:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/plip/-/commit/000720dd89d079d67801efdf168e3a77ad567217">000720dd</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2020-11-10T07:17:44+00:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Add salsa-ci file

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/plip/-/commit/428b943ce2d1d75a003cdd5e05c20f0ade42f00a">428b943c</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2020-11-10T07:17:44+00:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Rules-Requires-Root: no

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/plip/-/commit/dd7cdc2163cf80a7d8d5f612c02005c8ba0ebc3c">dd7cdc21</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2020-11-10T07:17:59+00:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set field Upstream-Contact in debian/copyright.

Changes-By: lintian-brush

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/plip/-/commit/78d8497af2aef0daff02b40a827575548ed78a40">78d8497a</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2020-11-10T07:18:16+00:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.

Changes-By: lintian-brush

Fixes: lintian: upstream-metadata-missing-bug-tracking

See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html

Fixes: lintian: upstream-metadata-missing-repository

See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/plip/-/commit/637b060bf22593125f0f8affa734ff2bba5a49d4">637b060b</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2020-11-10T07:18:16+00:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove obsolete fields Contact, Name from debian/upstream/metadata (already present in machine-readable debian/copyright).

Changes-By: lintian-brush

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/plip/-/commit/43291b9a3cac609068606ad2906c96baf9825fb1">43291b9a</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2020-11-10T07:18:17+00:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable

</pre>

</li>

</ul>

<h4>15 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>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">

debian/copyright

</a>

</li>

<li class="file-stats">

<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">

<span class="new-file">

+

debian/salsa-ci.yml

</span>

</a>

</li>

<li class="file-stats">

<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">

debian/upstream/metadata

</a>

</li>

<li class="file-stats">

<a href="#e0bdfb93722bb0bccd3faf9d5cbf446297ff47c4">

plip/basic/config.py

</a>

</li>

<li class="file-stats">

<a href="#e352319b84deb5f40d3f1a26b4a5cde456ac918d">

plip/exchange/webservices.py

</a>

</li>

<li class="file-stats">

<a href="#7a4c9b79c2f1bb441895d677413efbc1cb536c35">

plip/plipcmd.py

</a>

</li>

<li class="file-stats">

<a href="#b72517a8cd7dbc6709d05fdad49ae468ebf79126">

plip/structure/preparation.py

</a>

</li>

<li class="file-stats">

<a href="#696ac07ae5eed397a25b82f16361e894a7d1b19b">

plip/test/test_basic_functions.py

</a>

</li>

<li class="file-stats">

<a href="#9f67ebbb5ec813295c50bdbd1c02e865215420cd">

plip/test/test_remote_services.py

</a>

</li>

<li class="file-stats">

<a href="#57c07e057e19c12594e381911c4c7605005fcb83">

<span class="new-file">

+

plip/test/test_structure_processing.py

</span>

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="3251d7a8143ce2e789f0468513df8f285f842c3a">

<a href="https://salsa.debian.org/med-team/plip/-/compare/49d9187ccb42a4078ef5c63a7a09b6c13ff93082...43291b9a3cac609068606ad2906c96baf9825fb1#3251d7a8143ce2e789f0468513df8f285f842c3a"><strong>CHANGES.txt</strong></a>

<hr>

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

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

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

1

</td>

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

1

</td>

<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>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

</td>

<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"># 2.2.0</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

</td>

<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">* bug fixes in code and deployment</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5

</td>

<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">* multi-architecture builds on https://hub.docker.com/r/pharmai/plip</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6

</td>

<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">* Docker build for Ubuntu 20.04 LTS</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

</td>

<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"># 2.1.5</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">* option added to handle specific model in NMR structures</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

5

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">* fixes a bug in alt-location handling</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

</td>

<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

</td>

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

<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

</td>

<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

</td>

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

<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"># 2.1.0</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

</td>

<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

</td>

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

<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">* maintainer changed to PharmAI GmbH</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(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="15" style="width: 35px; color: rgba(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">@@ -16,6 +15,9 @@ Changelog</td>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">* adds option to disable non-deterministic protonation of structures (`--nohydro`)</span>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">* protonated structures are now stored to guarantee consistent interaction detection</span>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">* new options to change verbosity levels</span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">* bug fixes in code and deployment</span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">* multi-architecture builds on https://hub.docker.com/r/pharmai/plip</span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">* Docker build for Ubuntu 20.04 LTS</span>

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

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"># 1.4.5</span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">* Updates contact info</span>

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</li>

<li id="14789896d7d3663d4b2dd496146049d6798d139e">

<a href="https://salsa.debian.org/med-team/plip/-/compare/49d9187ccb42a4078ef5c63a7a09b6c13ff93082...43291b9a3cac609068606ad2906c96baf9825fb1#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">@@ -102,7 +102,7 @@ PLIP will create subdirectories for each given structure in the output folder. I</td>

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="markdown">For the detection of ligands, PLIP relies on the separation of <span class="sb" style="color: #d14;">`ATOM`</span> and <span class="sb" style="color: #d14;">`HETATM`</span> entries in the PDB file. The latter are searched for suitable ligands when running in normal mode. Peptide ligands, however, are usually deposited as <span class="sb" style="color: #d14;">`ATOM`</span> entries in a separate chain. PLIP can not detect these entities automatically. To switch into protein-peptide interaction mode, start PLIP with the option <span class="sb" style="color: #d14;">`--peptide`</span>, followed by the peptide chain of interest, e.g.:</span>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="markdown"><span class="nv" style="color: #008080;">$ </span>plip <span class="nt" style="color: #000080;">-i</span> 5hi4 <span class="nt" style="color: #000080;">--peptide<span class="idiff left right">s</span></span> I <span class="nt" style="color: #000080;">-vx</span></span>

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="markdown"><span class="nv" style="color: #008080;">$ </span>plip <span class="nt" style="color: #000080;">-i</span> 5hi4 <span class="nt" style="color: #000080;">--peptide</span> I <span class="nt" style="color: #000080;">-vx</span></span>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="markdown"><span class="p">```</span></span>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Detection of Intra-Chain Interactions</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="142" style="width: 35px; color: rgba(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="142" style="width: 35px; color: rgba(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">@@ -142,6 +142,7 @@ PLIP offers further command line options which enables you to switch advanced se</td>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="markdown"><span class="p">-</span> Turn off automatic fixing of errors in PDB files (<span class="sb" style="color: #d14;">`--nofix`</span>)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="markdown"><span class="p">-</span> Keep modified residues as ligands (<span class="sb" style="color: #d14;">`--keepmod`</span>)</span>

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="markdown"><span class="p">-</span> Do not protonate structures with non-deterministic OpenBabel routines (<span class="sb" style="color: #d14;">`--nohydro`</span>)</span>

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="markdown"><span class="p">-</span> Select a specific model from an ensemble structure (<span class="sb" style="color: #d14;">`--model`</span>)</span>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="markdown"></span>

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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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="147" style="width: 35px; color: rgba(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="LC148" class="line" lang="markdown">A web service for analysis of protein-ligand complexes using PLIP is available at</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="376" style="width: 35px; color: rgba(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="377" style="width: 35px; color: rgba(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">@@ -376,4 +377,4 @@ metal_complex | coordination | Metal coordination number |</td>

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<pre style="margin: 0;"> <span id="LC377" class="line" lang="markdown">metal_complex | location | Location of the target group |</span>

</pre>

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<pre style="margin: 0;"> <span id="LC378" class="line" lang="markdown">metal_complex | rms | RMS of the geometry fit |</span>

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<pre style="margin: 0;"> <span id="LC379" class="line" lang="markdown">metal_complex | geometry | Metal coordination type |</span>

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<pre style="margin: 0;">-<span id="LC379" class="line" lang="markdown">metal_complex | complexnum | Continous numbering for the metal complex |</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="LC380" class="line" lang="markdown">metal_complex | complexnum | Continous numbering for the metal complex |</span></pre>

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</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/plip/-/compare/49d9187ccb42a4078ef5c63a7a09b6c13ff93082...43291b9a3cac609068606ad2906c96baf9825fb1#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

<hr>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,11 +13,13 @@ Analyze noncovalent protein-ligand interactions in 3D structures with ease.</td>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown">| Use Case                                                                  | <span class="p">[</span><span class="nv" style="color: #008080;">Web Server</span><span class="p">](</span><span class="sx" style="color: #d14;">https://projects.biotec.tu-dresden.de/plip-web/plip</span><span class="p">)</span>         | Docker             | Singularity        | Python Module       |</span>

</pre>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown">|---------------------------------------------------------------------------|--------------------|--------------------|--------------------|--------------------|</span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown">| "I want to analyze my protein-ligand complex!"                            | :heavy_check_mark: | :<span class="idiff left right">yellow_circle:   </span> | :yellow_circle:    | :x:                |</span>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="markdown">| "I want to analyze <span class="ge" style="font-style: italic;">*a billion*</span> protein-ligand complexes!"                 <span class="idiff left right">  </span>| :x:                | :yellow_circle:    | :heavy_check_mark: | :yellow_circle:    |</span>

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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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="16" 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="LC16" class="line" lang="markdown">| "I want to analyze my protein-ligand complex!"                            | :heavy_check_mark: | :<span class="idiff left right">heavy_check_mark:</span> | :yellow_circle:    | :x:                |</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown">| "I want to analyze <span class="ge" style="font-style: italic;">*a billion*</span> protein-ligand complexes!"                 | :x:                | :yellow_circle:    | :heavy_check_mark: | :yellow_circle:    |</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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:    <span class="idiff left right">            </span>| :heavy_check_mark: | :heavy_check_mark: | :yellow_circle:    |</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(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="LC20" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"><span class="p">---</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Quickstart</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="59" style="width: 35px; color: rgba(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="61" style="width: 35px; color: rgba(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">@@ -59,7 +61,7 @@ For more details, see the [Documentation](DOCUMENTATION.md).</td>

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<td class="diff-line-num old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="61" style="width: 35px; color: rgba(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="LC61" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="markdown">Open a new system terminal and clone this repository using</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="63" style="width: 35px; color: rgba(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="LC63" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="markdown"><span class="nv" style="color: #008080;">$ </span>git clone https://github.com/<span class="idiff left right">ssalentin/plip.git ~/pliptool</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown"><span class="nv" style="color: #008080;">$ </span>git clone https://github.com/<span class="idiff left right">pharmai/plip.git</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="65" style="width: 35px; color: rgba(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="LC65" class="line" lang="markdown"><span class="p">```</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

66

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

<pre style="margin: 0;"> <span id="LC66" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="67" style="width: 35px; color: rgba(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="LC67" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### 2. Install PLIP</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -169,6 +171,10 @@ Due to the non-deterministic nature on how hydrogen atoms can be added to the in</td>

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169

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171

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="markdown"><span class="p">-</span> protonate the input structure once with PLIP or your tool of preference</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

170

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<td class="diff-line-num new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

172

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="markdown"><span class="p">-</span> run PLIP with <span class="sb" style="color: #d14;">`--nohydro`</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

171

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173

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<pre style="margin: 0;"> <span id="LC173" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

174

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="markdown"><span class="gt" style="color: #a00;">> How does PLIP handle NMR structures?</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

175

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="markdown"><span class="gt" style="color: #a00;">></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="markdown">By default PLIP uses the first model it sees in a PDB file. You can change this behavior with the flag <span class="sb" style="color: #d14;">`--model`</span>.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="177" 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">

177

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

172

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Contact / Maintainer</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

173

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<td class="diff-line-num new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

179

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="markdown">As of April 2020 PLIP is now officially maintained by <span class="p">[</span><span class="nv" style="color: #008080;">PharmAI GmbH</span><span class="p">](</span><span class="sx" style="color: #d14;">https://pharm.ai</span><span class="p">)</span>. Do you have feature requests, found a bug or want to use  PLIP in your project? Commercial support is available upon request.</span>

</pre>

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174

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<td class="diff-line-num new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

180

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="markdown"></span>

</pre>

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</table>

<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/plip/-/compare/49d9187ccb42a4078ef5c63a7a09b6c13ff93082...43291b9a3cac609068606ad2906c96baf9825fb1#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

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

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

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">plip (2.1.5+dfsg-1) unstable; urgency=medium</span>

</pre>

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

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

2

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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="LC2" class="line" lang="plaintext"></span>

</pre>

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

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

3

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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">  * Team upload.</span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

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

</pre>

</td>

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

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

5

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  * debhelper-compat 13 (routine-update)</span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">  * Add salsa-ci file (routine-update)</span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">  * Rules-Requires-Root: no (routine-update)</span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="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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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com>  Tue, 10 Nov 2020 07:18:16 +0000</span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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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="LC10" class="line" lang="plaintext"></span>

</pre>

</td>

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

1

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">plip (2.1.4+dfsg-2) unstable; urgency=medium</span>

</pre>

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2

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>

</pre>

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3

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">  * No change, source-only upload to allow testing migration.</span>

</pre>

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<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/plip/-/compare/49d9187ccb42a4078ef5c63a7a09b6c13ff93082...43291b9a3cac609068606ad2906c96baf9825fb1#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>

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3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Alexandre Mestiashvili <mestia@debian.org></span>

</pre>

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4

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

</pre>

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

5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6

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<td class="diff-line-num new_line old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>

</pre>

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7

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">               help2man,</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">               python3-all,</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(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="16" style="width: 35px; color: rgba(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">@@ -16,6 +16,7 @@ Standards-Version: 4.5.0</td>

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16

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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(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="LC16" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/plip</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/plip.git</span>

</pre>

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<td class="diff-line-num old_line" 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">

18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Homepage: https://projects.biotec.tu-dresden.de/plip-web/plip/</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Rules-Requires-Root: no</span>

</pre>

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19

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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(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="LC20" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Architecture: all</span>

</pre>

</td>

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<br>

</li>

<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">

<a href="https://salsa.debian.org/med-team/plip/-/compare/49d9187ccb42a4078ef5c63a7a09b6c13ff93082...43291b9a3cac609068606ad2906c96baf9825fb1#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,6 +10,7 @@ Files-Excluded:</td>

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10

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10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">  Dockerfile*</span>

</pre>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">  plip/__pycache__</span>

</pre>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">  build_multi.sh</span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Upstream-Contact: Sebastian Salentin <sebastian.salentin@biotec.tu-dresden.de></span>

</pre>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Files: *</span>

</pre>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Copyright: 2016 Sebastian Salentin <sebastian.salentin@biotec.tu-dresden.de></span>

</pre>

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<br>

</li>

<li id="b1dbf22e88351ec0d5d1d1a7f53295504b480e61">

<a href="https://salsa.debian.org/med-team/plip/-/compare/49d9187ccb42a4078ef5c63a7a09b6c13ff93082...43291b9a3cac609068606ad2906c96baf9825fb1#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="nn" style="color: #555;">---</span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml</span></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml</span></span></pre>

</td>

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</table>

<br>

</li>

<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">

<a href="https://salsa.debian.org/med-team/plip/-/compare/49d9187ccb42a4078ef5c63a7a09b6c13ff93082...43291b9a3cac609068606ad2906c96baf9825fb1#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">Contact: Sebastian Salentin <sebastian.salentin@biotec.tu-dresden.de></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"><span class="idiff left right">Name: plip</span></span>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">Bug-Database: https://github.com/ssalentin/plip/issues</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"><span class="idiff left right">Bug-Submit: https://github.com/ssalentin/plip/issues/new</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Cite-As: "Salentin, S. et al. PLIP: fully automated protein-ligand \</span>

</pre>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> interaction profiler. Nucl. Acids Res. first published online April 14, \</span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> 2015 doi:10.1093/nar/gkv315"</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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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">@@ -25,3 +25,5 @@ Registry:</td>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">   Entry: plip</span>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> - Name: conda:bioconda</span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">   Entry: NA</span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Repository: https://github.com/ssalentin/plip.git</span>

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Repository-Browse: https://github.com/ssalentin/plip</span></pre>

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<br>

</li>

<li id="e0bdfb93722bb0bccd3faf9d5cbf446297ff47c4">

<a href="https://salsa.debian.org/med-team/plip/-/compare/49d9187ccb42a4078ef5c63a7a09b6c13ff93082...43291b9a3cac609068606ad2906c96baf9825fb1#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;">'2.1.<span class="idiff left right">4</span>'</span></span>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'2.1.<span class="idiff left right">5</span>'</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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>

</pre>

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,6 +28,7 @@ DNARECEPTOR = False</td>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"><span class="n" style="color: #333;">OUTPUTFILENAME</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"report"</span>  <span class="c1" style="color: #998; font-style: italic;"># Naming for the TXT and XML report files</span></span>

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<td class="diff-line-num new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="n" style="color: #333;">NOPDBCANMAP</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span>  <span class="c1" style="color: #998; font-style: italic;"># Skip calculation of mapping canonical atom order: PDB atom order</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="n" style="color: #333;">NOHYDRO</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span>  <span class="c1" style="color: #998; font-style: italic;"># Do not add hydrogen bonds (in case already present in the structure)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="n" style="color: #333;">MODEL</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span>  <span class="c1" style="color: #998; font-style: italic;"># The model to be selected for multi-model structures (default = 1).</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Configuration file for Protein-Ligand Interaction Profiler (PLIP)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Set thresholds for detection of interactions</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="e352319b84deb5f40d3f1a26b4a5cde456ac918d">

<a href="https://salsa.debian.org/med-team/plip/-/compare/49d9187ccb42a4078ef5c63a7a09b6c13ff93082...43291b9a3cac609068606ad2906c96baf9825fb1#e352319b84deb5f40d3f1a26b4a5cde456ac918d"><strong>plip/exchange/webservices.py</strong></a>

<hr>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,19 +28,20 @@ def fetch_pdb(pdbid):</td>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python">    <span class="s" style="color: #d14;">"""Get the newest entry from the RCSB server for the given PDB ID. Exits with '1' if PDB ID is invalid."""</span></span>

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<pre style="margin: 0;"> <span id="LC29" 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;">pdbid</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python">    <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">f'checking status of PDB-ID </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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python">    <span class="n" style="color: #333;">state</span><span class="p">,</span> <span class="n" style="color: #333;">current_entry</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">check_pdb_status</span><span class="p">(</span><span class="n" style="color: #333;">pdbid</span><span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;"># Get state and current PDB ID</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'OBSOLETE'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python">        <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">f'entry is obsolete, getting </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">current_entry</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> instead'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python">    <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'CURRENT'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python">        <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'entry is up-to-date'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python">    <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'UNKNOWN'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python">        <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">'invalid PDB-ID (entry does not exist on PDB server)'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># @todo re-implement state check with ew RCSB API, see https://www.rcsb.org/news?year=2020&article=5eb18ccfd62245129947212a&feature=true</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># state, current_entry = check_pdb_status(pdbid)  # Get state and current PDB ID</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="33" 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="LC33" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="34" 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="LC34" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># if state == 'OBSOLETE':</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="35" 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="LC35" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#     logger.info(f'entry is obsolete, getting {current_entry} instead')</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="36" 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="LC36" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># elif state == 'CURRENT':</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="37" 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="LC37" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#     logger.info('entry is up-to-date')</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="38" 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="LC38" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># elif state == 'UNKNOWN':</span></span>

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<td class="diff-line-num new new_line" data-linenumber="39" 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="LC39" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#     logger.error('invalid PDB-ID (entry does not exist on PDB server)')</span></span>

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<td class="diff-line-num new new_line" data-linenumber="40" 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="LC40" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#     sys.exit(1)</span></span>

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<td class="diff-line-num old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="41" style="width: 35px; color: rgba(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="LC41" class="line" lang="python">    <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'downloading file from PDB'</span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(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="LC42" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># get URL for current entry</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="43" style="width: 35px; color: rgba(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="LC43" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># @todo needs update to react properly on response codes of RCSB servers</span></span>

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<td class="diff-line-num new_line old" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python">    <span class="n" style="color: #333;">pdburl</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">f'http://www.rcsb.org/pdb/files/</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;"><span class="idiff left right">current_entry</span></span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">.pdb'</span></span>

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<td class="diff-line-num new old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="44" 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="LC44" class="line" lang="python">    <span class="n" style="color: #333;">pdburl</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">f'http://www.rcsb.org/pdb/files/</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;"><span class="idiff left right">pdbid</span></span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">.pdb'</span></span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC46" 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;">urlopen</span><span class="p">(</span><span class="n" style="color: #333;">pdburl</span><span class="p">).</span><span class="n" style="color: #333;">read</span><span class="p">().</span><span class="n" style="color: #333;">decode</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># If no PDB file is available, a text is now shown with "We're sorry, but ..."</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -51,4 +52,4 @@ def fetch_pdb(pdbid):</td>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">HTTPError</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python">        <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">'no file in PDB format available from wwPDB for the given PDB ID'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">pdbfile</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">current_entry</span></span><span class="p">]</span></span></pre>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">pdbfile</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">pdbid</span></span><span class="p">]</span></span></pre>

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<br>

</li>

<li id="7a4c9b79c2f1bb441895d677413efbc1cb536c35">

<a href="https://salsa.debian.org/med-team/plip/-/compare/49d9187ccb42a4078ef5c63a7a09b6c13ff93082...43291b9a3cac609068606ad2906c96baf9825fb1#7a4c9b79c2f1bb441895d677413efbc1cb536c35"><strong>plip/plipcmd.py</strong></a>

<hr>

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

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="225" style="width: 35px; color: rgba(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">@@ -225,6 +225,9 @@ def main():</td>

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<pre style="margin: 0;"> <span id="LC225" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--nohydro"</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"nohydro"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python">                        <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Do not add polar hydrogens in case your structure already contains hydrogens."</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python">                        <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--model"</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"model"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python">                        <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Model number to be used for multi-model structures."</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python">                        <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Optional threshold arguments, not shown in help</span></span>

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python">    <span class="n" style="color: #333;">thr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">namedtuple</span><span class="p">(</span><span class="s" style="color: #d14;">'threshold'</span><span class="p">,</span> <span class="s" style="color: #d14;">'name type'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python">    <span class="n" style="color: #333;">thresholds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">thr</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'aromatic_planarity'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'angle'</span><span class="p">),</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -275,6 +278,7 @@ def main():</td>

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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python">    <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">DNARECEPTOR</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arguments</span><span class="p">.</span><span class="n" style="color: #333;">dnareceptor</span></span>

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<pre style="margin: 0;"> <span id="LC279" class="line" lang="python">    <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">OUTPUTFILENAME</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arguments</span><span class="p">.</span><span class="n" style="color: #333;">outputfilename</span></span>

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<pre style="margin: 0;"> <span id="LC280" class="line" lang="python">    <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">NOHYDRO</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arguments</span><span class="p">.</span><span class="n" style="color: #333;">nohydro</span></span>

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<pre style="margin: 0;">+<span id="LC281" 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="n" style="color: #333;">arguments</span><span class="p">.</span><span class="n" style="color: #333;">model</span></span>

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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Make sure we have pymol with --pics and --pymol</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">PICS</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">PYMOL</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC284" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<br>

</li>

<li id="b72517a8cd7dbc6709d05fdad49ae468ebf79126">

<a href="https://salsa.debian.org/med-team/plip/-/compare/49d9187ccb42a4078ef5c63a7a09b6c13ff93082...43291b9a3cac609068606ad2906c96baf9825fb1#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">@@ -51,25 +51,39 @@ class PDBParser:</td>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python">        <span class="n" style="color: #333;">alt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python">        <span class="n" style="color: #333;">previous_ter</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python">        <span class="n" style="color: #333;">model_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">1</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">()}</span></span>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Standard without fixing</span></span>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">NOFIX</span><span class="p">:</span></span>

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<td class="diff-line-num new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">PLUGIN_MODE</span><span class="p">:</span></span>

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<td class="diff-line-num new_line" data-linenumber="59" style="width: 35px; color: rgba(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="LC59" class="line" lang="python">                <span class="n" style="color: #333;">lastnum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span>  <span class="c1" style="color: #998; font-style: italic;"># Atom numbering (has to be consecutive)</span></span>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python">                <span class="n" style="color: #333;">other_models</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python">                <span class="n" style="color: #333;">current_model</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fil</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">other_models</span><span class="p">:</span>  <span class="c1" style="color: #998; font-style: italic;"># Only consider the first model in an NRM structure</span></span>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python">                        <span class="n" style="color: #333;">corrected_line</span><span class="p">,</span> <span class="n" style="color: #333;">newnum</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fix_pdbline</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">lastnum</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">corrected_line</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python">                            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">corrected_line</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'MODEL'</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python">                                <span class="k" style="font-weight: 600;">try</span><span class="p">:</span>  <span class="c1" style="color: #998; font-style: italic;"># Get number of MODEL (1,2,3)</span></span>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python">                                    <span class="n" style="color: #333;">model_num</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">corrected_line</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">:</span><span class="mi" style="color: #099;">14</span><span class="p">])</span></span>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python">                                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">model_num</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span>  <span class="c1" style="color: #998; font-style: italic;"># MODEL 2,3,4 etc.</span></span>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python">                                        <span class="n" style="color: #333;">other_models</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python">                                <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python">                                    <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">f'ignoring invalid MODEL entry: </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">corrected_line</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python">                            <span class="n" style="color: #333;">corrected_lines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">corrected_line</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python">                            <span class="n" style="color: #333;">lastnum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newnum</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC72" 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;">corrected_lines</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python">                    <span class="n" style="color: #333;">corrected_line</span><span class="p">,</span> <span class="n" style="color: #333;">newnum</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fix_pdbline</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">lastnum</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="64" 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="LC64" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">corrected_line</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">corrected_line</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'MODEL'</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python">                            <span class="k" style="font-weight: 600;">try</span><span class="p">:</span>  <span class="c1" style="color: #998; font-style: italic;"># Get number of MODEL (1,2,3)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python">                                <span class="n" style="color: #333;">model_num</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">corrected_line</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">:</span><span class="mi" style="color: #099;">14</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="68" 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="LC68" class="line" lang="python">                                <span class="c1" style="color: #998; font-style: italic;"># initialize storage for new model</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="69" 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="LC69" class="line" lang="python">                                <span class="n" style="color: #333;">model_dict</span><span class="p">[</span><span class="n" style="color: #333;">model_num</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="70" 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="LC70" class="line" lang="python">                                <span class="n" style="color: #333;">current_model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model_num</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="71" 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="LC71" class="line" lang="python">                                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">model_num</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span>  <span class="c1" style="color: #998; font-style: italic;"># MODEL 2,3,4 etc.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python">                                    <span class="n" style="color: #333;">other_models</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python">                            <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python">                                <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">f'ignoring invalid MODEL entry: </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">corrected_line</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python">                        <span class="n" style="color: #333;">lastnum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newnum</span></span>

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<td class="diff-line-num new new_line" data-linenumber="76" 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="LC76" class="line" lang="python">                        <span class="n" style="color: #333;">model_dict</span><span class="p">[</span><span class="n" style="color: #333;">current_model</span><span class="p">].</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">corrected_line</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="77" 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="LC77" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># select model</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python">                <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="79" 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="LC79" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">other_models</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python">                        <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">f'selecting 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;"> for analysis'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="81" 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="LC81" 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="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">MODEL</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="82" 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="LC82" 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="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">MODEL</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC83" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC84" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="85" 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="LC85" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC86" 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>

</pre>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC88" 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>

</pre>

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<pre style="margin: 0;"> <span id="LC89" 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;">fil</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">@@ -295,15 +309,16 @@ class LigandFinder:</td>

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<pre style="margin: 0;"> <span id="LC309" class="line" lang="python">            <span class="n" style="color: #333;">cur_hetatoms</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">obatom</span><span class="p">.</span><span class="n" style="color: #333;">GetIdx</span><span class="p">():</span> <span class="n" style="color: #333;">obatom</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">obatom</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">pybel</span><span class="p">.</span><span class="n" style="color: #333;">ob</span><span class="p">.</span><span class="n" style="color: #333;">OBResidueAtomIter</span><span class="p">(</span><span class="n" style="color: #333;">obresidue</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span></span>

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<pre style="margin: 0;"> <span id="LC310" class="line" lang="python">                            <span class="n" style="color: #333;">obatom</span><span class="p">.</span><span class="n" style="color: #333;">GetAtomicNum</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">ALTLOC</span><span class="p">:</span></span>

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<td class="diff-line-num old old_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC298" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># <span class="idiff left right">R</span>emove alternative conformations (standard -> True)</span></span>

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<pre style="margin: 0;">-<span id="LC299" class="line" lang="python">                <span class="n" style="color: #333;">ids_to_remove</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">atom_id</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">atom_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">hetatoms</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">()</span> <span class="k" style="font-weight: 600;">if</span></span>

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<td class="diff-line-num new new_line" data-linenumber="312" 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="LC312" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># <span class="idiff left right">r</span>emove alternative conformations (standard -> True)</span></span>

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<pre style="margin: 0;">+<span id="LC313" class="line" lang="python">                <span class="n" style="color: #333;">ids_to_remove</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">atom_id</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">atom_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left right">cur_</span>hetatoms</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">()</span> <span class="k" style="font-weight: 600;">if</span></span>

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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python">                                 <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mapper</span><span class="p">.</span><span class="n" style="color: #333;">mapid</span><span class="p">(</span><span class="n" style="color: #333;">atom_id</span><span class="p">,</span> <span class="n" style="color: #333;">mtype</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'protein'</span><span class="p">,</span> <span class="n" style="color: #333;">to</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'internal'</span><span class="p">)</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;">altconformations</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC315" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">atom_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ids_to_remove</span><span class="p">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="316" style="width: 35px; color: rgba(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="LC316" class="line" lang="python">                    <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">cur_hetatoms</span><span class="p">[</span><span class="n" style="color: #333;">atom_id</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC317" class="line" lang="python">            <span class="n" style="color: #333;">hetatoms</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">cur_hetatoms</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python">        <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">f'hetero atoms determined (n=</span><span class="si" style="color: #d14;">{</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">hetatoms</span><span class="p">)</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">)'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC306" class="line" lang="python">        <span class="n" style="color: #333;">lig</span> <span class="o" style="font-weight: 600;">=</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;">OBMol</span><span class="p">()</span>  <span class="c1" style="color: #998; font-style: italic;"># new ligand mol</span></span>

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<td class="diff-line-num new old_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC320" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># create a new ligand molecule representing any k-mer linked structures</span></span>

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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python">        <span class="n" style="color: #333;">lig</span> <span class="o" style="font-weight: 600;">=</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;">OBMol</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC322" class="line" lang="python">        <span class="n" style="color: #333;">neighbours</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC323" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">obatom</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">hetatoms</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">():</span>  <span class="c1" style="color: #998; font-style: italic;"># iterate over atom objects</span></span>

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<pre style="margin: 0;"> <span id="LC324" 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;">obatom</span><span class="p">.</span><span class="n" style="color: #333;">GetIdx</span><span class="p">()</span></span>

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<br>

</li>

<li id="696ac07ae5eed397a25b82f16361e894a7d1b19b">

<a href="https://salsa.debian.org/med-team/plip/-/compare/49d9187ccb42a4078ef5c63a7a09b6c13ff93082...43291b9a3cac609068606ad2906c96baf9825fb1#696ac07ae5eed397a25b82f16361e894a7d1b19b"><strong>plip/test/test_basic_functions.py</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,15 +4,16 @@ Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand inter</td>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;">test_basic_functions.py - Unit Tests for basic functionality.</span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">random</span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Python Standard Library</span></span>

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<pre style="margin: 0;"> <span id="LC9" 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="LC10" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span></span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">random</span></span>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Own modules</span></span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.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="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.basic.supplemental</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">euclidean3d</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="p">,</span> <span class="n" style="color: #333;">vecangle</span><span class="p">,</span> <span class="n" style="color: #333;">projection</span></span>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.basic.supplemental</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">normalize_vector</span><span class="p">,</span> <span class="n" style="color: #333;">cluster_doubles</span><span class="p">,</span> <span class="n" style="color: #333;">centroid</span></span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Own modules</span></span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plip.structure.preparation</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">PDBComplex</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestLigandSupport</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,6 +30,13 @@ class TestLigandSupport(unittest.TestCase):</td>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># DNA only contains four bases</span></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">ligset</span><span class="p">,</span> <span class="p">{</span><span class="s" style="color: #d14;">'DG'</span><span class="p">,</span> <span class="s" style="color: #d14;">'DC'</span><span class="p">,</span> <span class="s" style="color: #d14;">'DA'</span><span class="p">,</span> <span class="s" style="color: #d14;">'DT'</span><span class="p">})</span></span>

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

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_composite_ligand_alternate_locations</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="LC34" 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="LC35" 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/4gql.pdb'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC36" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="37" 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="LC37" 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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="38" 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="LC38" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">pdb_complex</span><span class="p">.</span><span class="n" style="color: #333;">ligands</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">can_to_pdb</span><span class="p">),</span> <span class="mi" style="color: #099;">53</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestMapping</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>

</pre>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python">    <span class="s" style="color: #d14;">"""Test"""</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="73" style="width: 35px; color: rgba(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="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -73,7 +81,7 @@ class GeometryTest(unittest.TestCase):</td>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

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<td class="diff-line-num old_line" data-linenumber="75" style="width: 35px; color: rgba(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="LC83" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">vector_magnitude</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">):</span></span>

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<td class="diff-line-num old old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">sqrt</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">2</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">v</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="85" style="width: 35px; color: rgba(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="LC85" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="86" style="width: 35px; color: rgba(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="LC86" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># noinspection PyUnusedLocal</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<br>

</li>

<li id="9f67ebbb5ec813295c50bdbd1c02e865215420cd">

<a href="https://salsa.debian.org/med-team/plip/-/compare/49d9187ccb42a4078ef5c63a7a09b6c13ff93082...43291b9a3cac609068606ad2906c96baf9825fb1#9f67ebbb5ec813295c50bdbd1c02e865215420cd"><strong>plip/test/test_remote_services.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,6 +12,7 @@ from plip.exchange.webservices import check_pdb_status</td>

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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestPDB</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>

</pre>

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python">    <span class="s" style="color: #d14;">"""Test PDB Web Service methods"""</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">unittest</span><span class="p">.</span><span class="n" style="color: #333;">skip</span><span class="p">(</span><span class="s" style="color: #d14;">"needs re-implementation to new RCSB API standards"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(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="LC16" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_pdb_entry_status</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># 1a0v is an obsolete entry and is replaced by 1y46</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" 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="python">        <span class="n" style="color: #333;">status</span><span class="p">,</span> <span class="n" style="color: #333;">current_pdbid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">check_pdb_status</span><span class="p">(</span><span class="s" style="color: #d14;">'1a0v'</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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<br>

</li>

<li id="57c07e057e19c12594e381911c4c7605005fcb83">

<a href="https://salsa.debian.org/med-team/plip/-/compare/49d9187ccb42a4078ef5c63a7a09b6c13ff93082...43291b9a3cac609068606ad2906c96baf9825fb1#57c07e057e19c12594e381911c4c7605005fcb83"><strong>plip/test/test_structure_processing.py</strong></a>

<hr>

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</td>

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

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">unittest</span></span>

</pre>

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

</td>

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

2

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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="LC2" class="line" lang="python"></span>

</pre>

</td>

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

</td>

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

3

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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="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>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<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 class="p">,</span> <span class="n" style="color: #333;">PLInteraction</span></span>

</pre>

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

</td>

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

5

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">characterize_complex</span><span class="p">(</span><span class="n" style="color: #333;">pdb_file</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">binding_site_id</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">PLInteraction</span><span class="p">:</span></span>

</pre>

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

</td>

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

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="python">    <span class="n" style="color: #333;">pdb_complex</span><span class="p">.</span><span class="n" style="color: #333;">load_pdb</span><span class="p">(</span><span class="n" style="color: #333;">pdb_file</span><span class="p">)</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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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="LC10" 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>

</pre>

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

</td>

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

11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">':'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">ligand</span><span class="p">.</span><span class="n" style="color: #333;">hetid</span><span class="p">,</span> <span class="n" style="color: #333;">ligand</span><span class="p">.</span><span class="n" style="color: #333;">chain</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">ligand</span><span class="p">.</span><span class="n" style="color: #333;">position</span><span class="p">)])</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">binding_site_id</span><span class="p">:</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="12" 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">

12

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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="LC12" 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>

</pre>

</td>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="13" 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">

13

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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="LC13" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pdb_complex</span><span class="p">.</span><span class="n" style="color: #333;">interaction_sets</span><span class="p">[</span><span class="n" style="color: #333;">binding_site_id</span><span class="p">]</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>

</pre>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

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

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<td class="diff-line-num new new_line" data-linenumber="16" 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">

16

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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="LC16" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">StructureProcessingTestCase</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>

</pre>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<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_nmr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python">        <span class="n" style="color: #333;">all_hydrogen_bonds</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="20" 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">

20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python">            <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">MODEL</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python">            <span class="n" style="color: #333;">interactions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">characterize_complex</span><span class="p">(</span><span class="s" style="color: #d14;">'./pdb/2ndo.pdb'</span><span class="p">,</span> <span class="s" style="color: #d14;">'SFQ:A:201'</span><span class="p">)</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python">            <span class="n" style="color: #333;">all_hbonds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">interactions</span><span class="p">.</span><span class="n" style="color: #333;">hbonds_ldon</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">interactions</span><span class="p">.</span><span class="n" style="color: #333;">hbonds_pdon</span></span>

</pre>

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</td>

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

23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python">            <span class="n" style="color: #333;">all_hydrogen_bonds</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">all_hbonds</span><span class="p">))</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="24" 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="LC24" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># models contain from 0-2 hydrogen bonds</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEquals</span><span class="p">(</span><span class="n" style="color: #333;">all_hydrogen_bonds</span><span class="p">,</span> <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">})</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_nmr_invalid_model</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="28" 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="LC28" class="line" lang="python">        <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">MODEL</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">11</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="29" 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="LC29" class="line" lang="python">        <span class="n" style="color: #333;">interactions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">characterize_complex</span><span class="p">(</span><span class="s" style="color: #d14;">'./pdb/2ndo.pdb'</span><span class="p">,</span> <span class="s" style="color: #d14;">'SFQ:A:201'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="30" 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="LC30" class="line" lang="python">        <span class="n" style="color: #333;">all_hbonds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">interactions</span><span class="p">.</span><span class="n" style="color: #333;">hbonds_ldon</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">interactions</span><span class="p">.</span><span class="n" style="color: #333;">hbonds_pdon</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEquals</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">all_hbonds</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span></pre>

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