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<h3>
Andrius Merkys pushed to branch master
at <a href="https://salsa.debian.org/med-team/pdb2pqr">Debian Med / pdb2pqr</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pdb2pqr/commit/b05b5ddccf28719035fd3d7e9da8d35c38aefcb0">b05b5ddc</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2019-03-09T10:54:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixing autopkgtest 'installation-test' by substituting non-existent PDB file with an existing one.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pdb2pqr/commit/a7d90a7e8b2f321da440af4845644e927b901d7f">a7d90a7e</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2019-03-09T11:09:06Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removing autopkgtest 'ligands-test' as it depended on files that are not shipped by the upstream anymore.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pdb2pqr/commit/2c2679128f1ebae0b5f7a482b5085d72c29165f2">2c267912</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2019-03-09T11:13:23Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removing 'ligands-test' from debian/tests/control.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pdb2pqr/commit/3b3c1168828880de2a5ab73b7422d0f5b3707c13">3b3c1168</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2019-03-09T11:17:33Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating debian/changelog.
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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<li class="file-stats">
<a href="#17d8869115f55e024a85a6d17443302815985358">
debian/tests/installation-test
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<a href="#cd65208f02a4d33033d120afa8c31f8a814a8894">
<span class="deleted-file">
−
debian/tests/ligands-test
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/pdb2pqr/compare/c417245a2589ef09845c5f4ebbe6f485f8764555...3b3c1168828880de2a5ab73b7422d0f5b3707c13#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">pdb2pqr (2.1.1+dfsg-5) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Build-Depends: dh-python</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 18 Jul 2018 09:59:58 +0200</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> [ Andrius Merkys ]</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Fixing autopkgtest 'installation-test' by substituting non-existent PDB</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> file with an existing one. Removing autopkgtest 'ligands-test' as it</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> depended on files that are not shipped by the upstream anymore.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> (Closes: #903759)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> -- Andrius Merkys <andrius.merkys@gmail.com> Sat, 09 Mar 2019 06:16:19 -0500</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">pdb2pqr (2.1.1+dfsg-4) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/pdb2pqr/compare/c417245a2589ef09845c5f4ebbe6f485f8764555...3b3c1168828880de2a5ab73b7422d0f5b3707c13#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</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">@@ -2,10 +2,6 @@ Tests: installation-test</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Depends: pdb2pqr</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">Tests: ligands-test</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Depends: @</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Restrictions: allow-stderr</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Tests: pdb2pka-test</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Depends: @, python-networkx</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/pdb2pqr/compare/c417245a2589ef09845c5f4ebbe6f485f8764555...3b3c1168828880de2a5ab73b7422d0f5b3707c13#17d8869115f55e024a85a6d17443302815985358"><strong>debian/tests/installation-test</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 +4,6 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: navy;">-e</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"><span class="nv" style="color: teal;">pkg</span><span class="o" style="font-weight: 600;">=</span>pdb2pqr</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$ADTTMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">ADTTMP</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: navy;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: navy;">-test</span>.XXXXXX<span class="k" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: teal;">$ADTTMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$ADTTMP</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Run pdb2pqr..."</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell">pdb2pqr <span class="nt" style="color: navy;">--ff</span><span class="o" style="font-weight: 600;">=</span>amber <span class="s2" style="color: #d14;"><span class="idiff left">"1FAS"</span></span><span class="idiff right"> </span>output.txt</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> output.txt <span class="o" style="font-weight: 600;">]</span></span></pre>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell">pdb2pqr <span class="nt" style="color: navy;">--ff</span><span class="o" style="font-weight: 600;">=</span>amber <span class="idiff left">examples/1a1p/1a1p.pdb </span><span class="k" style="font-weight: 600;"><span class="idiff">${</span></span><span class="nv" style="color: teal;"><span class="idiff">AUTOPKGTEST_TMP</span></span><span class="k" style="font-weight: 600;"><span class="idiff">}</span></span><span class="idiff right">/</span>output.txt</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> <span class="k" style="font-weight: 600;"><span class="idiff left">${</span></span><span class="nv" style="color: teal;"><span class="idiff">AUTOPKGTEST_TMP</span></span><span class="k" style="font-weight: 600;"><span class="idiff">}</span></span><span class="idiff right">/</span>output.txt <span class="o" style="font-weight: 600;">]</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pdb2pqr/compare/c417245a2589ef09845c5f4ebbe6f485f8764555...3b3c1168828880de2a5ab73b7422d0f5b3707c13#cd65208f02a4d33033d120afa8c31f8a814a8894"><strong>debian/tests/ligands-test</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># autopkgtest check: build and run with default test data</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Author: Tatiana Malygina <merlettaia@gmail.com></span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: navy;">-e</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"><span class="nv" style="color: teal;">pkg</span><span class="o" style="font-weight: 600;">=</span>pdb2pqr</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"><span class="nv" style="color: teal;">example_pkg</span><span class="o" style="font-weight: 600;">=</span>pdb2pqr</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$ADTTMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">ADTTMP</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: navy;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: navy;">-test</span>.XXXXXX<span class="k" style="font-weight: 600;">)</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: teal;">$ADTTMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$ADTTMP</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: navy;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">example_pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">.</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell">find <span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: navy;">-type</span> f <span class="nt" style="color: navy;">-name</span> <span class="s2" style="color: #d14;">"*.gz"</span> <span class="nt" style="color: navy;">-exec</span> <span class="nb" style="color: #0086b3;">gunzip</span> <span class="se" style="color: #d14;">\{\}</span> <span class="se" style="color: #d14;">\;</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>lnk <span class="k" style="font-weight: 600;">in</span> <span class="sb" style="color: #d14;">`</span>find <span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: navy;">-type</span> l <span class="nt" style="color: navy;">-name</span> <span class="s2" style="color: #d14;">"*.gz"</span><span class="sb" style="color: #d14;">`</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: navy;">-s</span> <span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">basename</span> <span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">readlink</span> <span class="nv" style="color: teal;">$lnk</span><span class="k" style="font-weight: 600;">)</span> .gz<span class="sb" style="color: #d14;">`</span> <span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$lnk</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/\.gz$//'</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nv" style="color: teal;">$lnk</span></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Run pdb2pqr..."</span></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># following sample call was adopted from fabfile.py, </span></span>
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<td class="diff-line-num old old_line" data-linenumber="27" 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">
27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># method "linux_bin_cross_platform_test":</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>pdb <span class="k" style="font-weight: 600;">in </span>1ABF 1HPV 1HPX 1QBS 1XL5<span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"******** </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pdb</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> starting"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="shell"> pdb2pqr <span class="nt" style="color: navy;">--ff</span><span class="o" style="font-weight: 600;">=</span>parse <span class="nt" style="color: navy;">--verbose</span> <span class="nt" style="color: navy;">--ligand</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"ligands/LIG_</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pdb</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">.mol2"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pdb</span><span class="k" style="font-weight: 600;">}</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pdb</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">.pqr"</span></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="shell"> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pdb</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">.pqr"</span> <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"******** </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pdb</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> done"</span></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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