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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>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/plip/-/commit/df595f7bced74f598da7e15aeb0a56aaa66758d1">df595f7b</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-05-18T21:13:50+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.2.2+dfsg</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/plip/-/commit/f3ce8260f11314edee96775c5669d846de54317b">f3ce8260</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-05-18T21:13:52+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.2.2+dfsg'
Update to upstream version '2.2.2+dfsg'
with Debian dir c9441adde878ba3e08274035cf401b28239d37d1</pre>
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<strong><a href="https://salsa.debian.org/med-team/plip/-/commit/8c8e67280e95e52c343aca8cf63ec747ad398b8c">8c8e6728</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-05-18T21:15:51+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Interim changelog entry
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<h4>8 changed files:</h4>
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<a href="#3251d7a8143ce2e789f0468513df8f285f842c3a">
CHANGES.txt
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<li class="file-stats">
<a href="#14789896d7d3663d4b2dd496146049d6798d139e">
DOCUMENTATION.md
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#e0bdfb93722bb0bccd3faf9d5cbf446297ff47c4">
plip/basic/config.py
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<li class="file-stats">
<a href="#67d4980fce23584951cb46902ae74ffca7500b93">
plip/exchange/report.py
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<li class="file-stats">
<a href="#7a4c9b79c2f1bb441895d677413efbc1cb536c35">
plip/plipcmd.py
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<li class="file-stats">
<a href="#d209d711b9b399c1e719fb9f3ab88df52dad6612">
plip/test/test_command_line.py
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<h4>Changes:</h4>
<li id="3251d7a8143ce2e789f0468513df8f285f842c3a">
<a href="https://salsa.debian.org/med-team/plip/-/compare/cdf3ace90672432387f5a06aa0b5d0b86b544d03...8c8e67280e95e52c343aca8cf63ec747ad398b8c#3251d7a8143ce2e789f0468513df8f285f842c3a"><strong>CHANGES.txt</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Changelog</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"># 2.2.2</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">* fixes an issue that caused encoding errors to be thrown</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"># 2.2.1</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">* updates citation information to latest paper: https://doi.org/10.1093/nar/gkab294</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="LC9" class="line" lang="plaintext"># 2.2.0</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">* new minor release</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">* increased detail level of report (individual atoms on protein side)</span>
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<li id="14789896d7d3663d4b2dd496146049d6798d139e">
<a href="https://salsa.debian.org/med-team/plip/-/compare/cdf3ace90672432387f5a06aa0b5d0b86b544d03...8c8e67280e95e52c343aca8cf63ec747ad398b8c#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">@@ -99,11 +99,12 @@ $ plip -i 1vsn 1osn 2reg -vx</td>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="markdown">PLIP will create subdirectories for each given structure in the output folder. If in PDB ID mode (<span class="sb" style="color: #d14;">`-i`</span>), the folder structure will be nested and based on the two middle characters of the PDB ID. The structure <span class="sb" style="color: #d14;">`1vsn`</span> in batch processing will have its output files in <span class="sb" style="color: #d14;">`<outputfolder>/vs/1vsn`</span>.</span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Detection of Protein-Peptide Interactions</span></span>
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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="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 class="idiff left right">s</span>`</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> 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 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="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">This option can also be used to analyze interaction between different protein chains or nucleic acid strands and is therefore also available using the synonym <span class="sb" style="color: #d14;">`--inter`</span>.</span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Detection of Intra-Chain Interactions</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="markdown">Intra-protein interactions are important for the stabilization of a structure and can give valuable insights for protein engineering and drug discovery. PLIP supports detection of interactions within one chain. o switch into intra-chain interaction mode, start PLIP with the option <span class="sb" style="color: #d14;">`--intra`</span>, followed by the protein chain of interest, e.g.:</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">@@ -277,6 +278,7 @@ After assigning all target groups to one metal ions, the resulting set of angles</td>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="markdown">| citation_information | How to cite PLIP |</span>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="markdown">| mode | Documents if PLIP was started in default or any special mode (e.g. intra-protein interactions) |</span>
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="markdown">| pdbid | PDB identifier of the input file |</span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="markdown">| model | Number of the model in the PDB file on which analysis was done |</span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="markdown">| pdbfile | Name of the input PDB file |</span>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="markdown">| pdbfixes | Were any fixes applied automatically to the input file? |</span>
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="markdown">| filename | Filename of the processed PDB file |</span>
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<a href="https://salsa.debian.org/med-team/plip/-/compare/cdf3ace90672432387f5a06aa0b5d0b86b544d03...8c8e67280e95e52c343aca8cf63ec747ad398b8c#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,7 +11,7 @@ Analyze noncovalent protein-ligand interactions in 3D structures with ease.</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"><span class="nt" style="color: #000080;"><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"pliplogo.png"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"PLIP Logo"</span> <span class="na" style="color: #008080;">height=</span><span class="s" style="color: #d14;">"100"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"></span>
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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://p<span class="idiff left">rojects</span>.biotec.tu-dresden.de<span class="idiff right">/plip-web/plip</span></span><span class="p">)</span> | Docker | Singularity | Python Module |</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://p<span class="idiff left right">lip-tool</span>.biotec.tu-dresden.de</span><span class="p">)</span> | Docker | Singularity | Python Module |</span>
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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: | :heavy_check_mark: | :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!" | :x: | :yellow_circle: | :heavy_check_mark: | :yellow_circle: |</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">@@ -22,6 +22,7 @@ Analyze noncovalent protein-ligand interactions in 3D structures with ease.</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Quickstart</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Docker</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown">If you have Docker installed, you can run a PLIP analysis for the structure <span class="sb" style="color: #d14;">`1vsn`</span> with the following shell command:</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown">On Linux / MacOS:</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">@@ -30,7 +31,7 @@ $ docker run --rm \</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"> <span class="nt" style="color: #000080;">-v</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PWD</span><span class="k" style="font-weight: 600;">}</span>:/results <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"> <span class="nt" style="color: #000080;">-w</span> /results <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"> <span class="nt" style="color: #000080;">-u</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">id</span> <span class="nt" style="color: #000080;">-u</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">USER</span><span class="k" style="font-weight: 600;">}</span><span class="si" style="color: #d14;">)</span>:<span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">id</span> <span class="nt" style="color: #000080;">-g</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">USER</span><span class="k" style="font-weight: 600;">}</span><span class="si" style="color: #d14;">)</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="markdown"> pharmai/plip:latest <span class="nt" style="color: #000080;">-i</span> 1<span class="idiff left right">s3v</span> <span class="nt" style="color: #000080;">-yv</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"> pharmai/plip:latest <span class="nt" style="color: #000080;">-i</span> 1<span class="idiff left right">vsn</span> <span class="nt" style="color: #000080;">-yv</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown">On Windows:</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -39,8 +40,9 @@ $ docker run --rm \</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown"> <span class="nt" style="color: #000080;">-v</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PWD</span><span class="k" style="font-weight: 600;">}</span>:/results <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown"> <span class="nt" style="color: #000080;">-w</span> /results <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="markdown"> <span class="nt" style="color: #000080;">-u</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">id</span> <span class="nt" style="color: #000080;">-u</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">USER</span><span class="k" style="font-weight: 600;">}</span><span class="si" style="color: #d14;">)</span>:<span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">id</span> <span class="nt" style="color: #000080;">-g</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">USER</span><span class="k" style="font-weight: 600;">}</span><span class="si" style="color: #d14;">)</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="markdown"> pharmai/plip:latest <span class="nt" style="color: #000080;">-i</span> 1<span class="idiff left right">s3v</span> <span class="nt" style="color: #000080;">-yv</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown"> pharmai/plip:latest <span class="nt" style="color: #000080;">-i</span> 1<span class="idiff left right">vsn</span> <span class="nt" style="color: #000080;">-yv</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Singularity</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="markdown">The equivalent command for our pre-built <span class="p">[</span><span class="nv" style="color: #008080;">Singularity</span><span class="p">](</span><span class="sx" style="color: #d14;">https://singularity.lbl.gov/</span><span class="p">)</span> image for Linux (available under <span class="p">[</span><span class="nv" style="color: #008080;">Releases</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/pharmai/plip/releases</span><span class="p">)</span>) is as follows:</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="markdown"></span>
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<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">@@ -50,31 +52,41 @@ $ ./plip.simg -i 1vsn -yv</td>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="markdown">Singularity allows to use PLIP with ease in HPC environments. Note that you need to have Singularity installed on your base system.</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Usage</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown">This README provides instructions for setup and using basic functions of PLIP.</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="markdown">For more details, see the <span class="p">[</span><span class="nv" style="color: #008080;">Documentation</span><span class="p">](</span><span class="sx" style="color: #d14;">DOCUMENTATION.md</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### 1. (optional) Clone the repository</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="markdown">Open a new system terminal and clone this repository using</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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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/pharmai/plip.git</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### 2. Install PLIP</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### 1. Install PLIP</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Containerized Image (recommended)</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="markdown">:exclamation: We ship PLIP as <span class="idiff left right">a </span>pre-built containers for multiple architectures (amd64/ARM), available on the <span class="p">[</span><span class="nv" style="color: #008080;">Docker Hub</span><span class="p">](</span><span class="sx" style="color: #d14;">https://hub.docker.com/r/pharmai/plip</span><span class="p">)</span> or as pre-built Singularity image under <span class="p">[</span><span class="nv" style="color: #008080;">Releases</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/pharmai/plip/releases</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown">:exclamation: We ship PLIP as pre-built containers for multiple architectures (amd64/ARM), available on the <span class="p">[</span><span class="nv" style="color: #008080;">Docker Hub</span><span class="p">](</span><span class="sx" style="color: #d14;">https://hub.docker.com/r/pharmai/plip</span><span class="p">)</span> or as pre-built Singularity image under <span class="p">[</span><span class="nv" style="color: #008080;">Releases</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/pharmai/plip/releases</span><span class="p">)</span>.<span class="idiff left right"> See the quickstart section above for usage instructions.</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### <span class="idiff left right">From Source</span></span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### <span class="idiff left right">Dependencies</span></span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="markdown">If you cannot use the containerized bundle or want to use PLIP sources, make sure you have the following requirements installed:</span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="markdown"><span class="p">-</span> Python >= 3.6.9</span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="markdown"><span class="p">-</span> OpenBabel<span class="idiff left right"> >= 3.0.0</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="markdown"><span class="p">-</span> <span class="p"><span class="idiff left">[</span></span><span class="nv" style="color: #008080;">OpenBabel</span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">#Installing-OpenBabel</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> >= 3.0.0 with </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">Python bindings</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://open-babel.readthedocs.io/en/latest/UseTheLibrary/PythonInstall.html</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="markdown"><span class="p">-</span> PyMOL >= 2.3.0 with Python bindings (optional, for visualization only)</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="markdown"><span class="p">-</span> ImageMagick >= 6.9 (optional)</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="markdown">Set your <span class="sb" style="color: #d14;">`PYTHONPATH`</span> environment variable to the root directory of this repository.</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Python:**</span> If you are on a system where Python 3 is executed using <span class="sb" style="color: #d14;">`python3`</span> instead of just <span class="sb" style="color: #d14;">`python`</span>, replace the <span class="sb" style="color: #d14;">`python`</span> and <span class="sb" style="color: #d14;">`pip`</span> commands in the following steps with <span class="sb" style="color: #d14;">`python3`</span> and <span class="sb" style="color: #d14;">`pip3`</span> accordingly.</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**OpenBabel:**</span> Many users have trouble setting up OpenBabel with Python bindings correctly. We therefore provide some <span class="p">[</span><span class="nv" style="color: #008080;">installation help for OpenBabel</span><span class="p">](</span><span class="sx" style="color: #d14;">#Installing-OpenBabel</span><span class="p">)</span> below.</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### From Source</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="markdown">Open a terminal and clone this repository using</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="markdown"><span class="nv" style="color: #008080;">$ </span>git clone https://github.com/pharmai/plip.git</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="markdown">Either set your <span class="sb" style="color: #d14;">`PYTHONPATH`</span> environment variable to the root directory of your PLIP repository or run the following command in it</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="markdown"><span class="nv" style="color: #008080;">$ </span>python setup.py <span class="nb" style="color: #0086b3;">install</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Via PyPi</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="markdown">We deploy the PLIP package to <span class="p">[</span><span class="nv" style="color: #008080;">PyPi</span><span class="p">](</span><span class="sx" style="color: #d14;">https://pypi.org/project/plip/</span><span class="p">)</span>. You can install PLIP as Python module with:</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">@@ -83,9 +95,9 @@ We deploy the PLIP package to [PyPi](https://pypi.org/project/plip/). You can in</td>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="markdown"><span class="nv" style="color: #008080;">$ </span>pip <span class="nb" style="color: #0086b3;">install </span>plip</span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Note:**</span> Be aware that you still have to install <span class="idiff left right">all other</span> dependencies and link them correctly.</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Note:**</span> Be aware that you still have to install <span class="idiff left right">the above mentioned</span> dependencies and link them correctly.</span>
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### <span class="idiff left right">3</span>. Run PLIP</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### <span class="idiff left right">2</span>. Run PLIP</span></span>
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Command Line Tool</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="94" style="width: 35px; color: rgba(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="106" style="width: 35px; color: rgba(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">@@ -94,8 +106,10 @@ Run the `plipcmd.py` script inside the PLIP folder to detect, report, and visual</td>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Note:**</span> If you have installed PLIP with <span class="sb" style="color: #d14;">`python setup.py install`</span> or PyPi, you will not have to set an alias for the <span class="sb" style="color: #d14;">`plip`</span> command.</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="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="markdown"><span class="nv" style="color: #008080;">$ </span><span class="nb" style="color: #0086b3;">alias </span><span class="nv" style="color: #008080;">plip</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'python ~/pliptool/plip/plipcmd.py'</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"># Set an alias to make your life easier and create and enter /tmp/1vsn</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="markdown"><span class="nv" style="color: #008080;">$ </span><span class="nb" style="color: #0086b3;">alias </span><span class="nv" style="color: #008080;">plip</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'python ~/plip/plip/plipcmd.py'</span></span>
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98
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="markdown"><span class="nv" style="color: #008080;">$ </span><span class="nb" style="color: #0086b3;">mkdir</span> /tmp/1vsn <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> /tmp/1vsn</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"># Run PLIP for 1vsn and open the resulting visualization in PyMOL</span></span>
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="markdown"><span class="nv" style="color: #008080;">$ </span>plip <span class="nt" style="color: #000080;">-i</span> 1vsn <span class="nt" style="color: #000080;">-yv</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="markdown"><span class="nv" style="color: #008080;">$ </span>pymol 1VSN_NFT_A_283.pse</span>
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="124" style="width: 35px; color: rgba(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="138" style="width: 35px; color: rgba(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">@@ -124,7 +138,7 @@ my_interactions = my_mol.interaction_sets[my_bsid] # Contains all interaction da</td>
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124
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="markdown"><span class="k" style="font-weight: 600;">print</span><span class="p">([</span><span class="n" style="color: #333;">pistack</span><span class="p">.</span><span class="n" style="color: #333;">resnr</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pistack</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">my_interactions</span><span class="p">.</span><span class="n" style="color: #333;">pistacking</span><span class="p">])</span> <span class="c1" style="color: #998; font-style: italic;"># Prints [84, 129]</span></span>
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125
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="markdown"><span class="p">```</span></span>
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="markdown"></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### <span class="idiff left right">4</span>. Investigate the Results</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### <span class="idiff left right">3</span>. Investigate the Results</span></span>
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128
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="markdown">PLIP offers various output formats, ranging from renderes images and PyMOL session files to human-readable text files and XML files. By default, all files are deposited in the working directory unless and output path is provided. For a full documentation of running options and output formats, please refer to the <span class="p">[</span><span class="nv" style="color: #008080;">Documentation</span><span class="p">](</span><span class="sx" style="color: #d14;">DOCUMENTATION.md</span><span class="p">)</span>.</span>
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129
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="markdown"></span>
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130
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Versions and Branches</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="137" style="width: 35px; color: rgba(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="151" style="width: 35px; color: rgba(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">@@ -137,9 +151,10 @@ For production environments, you should use the latest tagged commit from the `m</td>
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="markdown"><span class="p">-</span> Alexandre Mestiashvili | <span class="p">[</span><span class="nv" style="color: #008080;">github.com/mestia</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/mestia</span><span class="p">)</span></span>
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138
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="markdown"><span class="p">-</span> Christoph Leberecht | <span class="p">[</span><span class="nv" style="color: #008080;">github.com/cleberecht</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/cleberecht</span><span class="p">)</span></span>
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="markdown"><span class="p">-</span> Florian Kaiser | <span class="p">[</span><span class="nv" style="color: #008080;">github.com/fkaiserbio</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/fkaiserbio</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="markdown"><span class="p">-</span> Katja Linnemann | <span class="p">[</span><span class="nv" style="color: #008080;">github.com/kalinni</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/kalinni</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## PLIP Web Server</span></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="markdown">Visit our PLIP Web Server on <span class="p">[</span><span class="nv" style="color: #008080;">plip.biotec.tu-dresden.de<span class="idiff left">/plip-web</span></span><span class="p">](</span><span class="sx" style="color: #d14;">https://plip.biotec.tu-dresden.de<span class="idiff right">/plip-web</span></span><span class="p">)</span>.</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="markdown">Visit our PLIP Web Server on <span class="p">[</span><span class="nv" style="color: #008080;">plip<span class="idiff left">-tool</span>.biotec.tu-dresden.de</span><span class="p">](</span><span class="sx" style="color: #d14;">https://plip<span class="idiff right">-tool</span>.biotec.tu-dresden.de</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## License Information</span></span>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="markdown">PLIP is published under the GNU GPLv2. For more information, please read the <span class="sb" style="color: #d14;">`LICENSE.txt`</span> file.</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="162" style="width: 35px; color: rgba(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">@@ -147,6 +162,11 @@ Using PLIP in your commercial or non-commercial project is generally possible wh</td>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Citation Information</span></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="markdown">If you are using PLIP in your work, please cite</span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="markdown"><span class="gt" style="color: #a00;">> Adasme,M. et al. PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA.</span></span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="markdown"><span class="gt" style="color: #a00;">> Nucl. Acids Res. (05 May 2021), gkab294. doi: 10.1093/nar/gkab294</span></span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="markdown"> </span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="markdown">or</span>
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="markdown"><span class="gt" style="color: #a00;">> Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler.</span></span>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="markdown"><span class="gt" style="color: #a00;">> Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315</span></span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="175" style="width: 35px; color: rgba(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">@@ -155,8 +175,8 @@ If you are using PLIP in your work, please cite</td>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="markdown"><span class="gt" style="color: #a00;">> ValueError: [...] is not a recognised Open Babel descriptor type</span></span>
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="markdown"><span class="gt" style="color: #a00;">></span></span>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="markdown">Make sure OpenBabel is correctly installed. This error can occur if the installed Python bindings don't match the OpenBabel version on your machine.</span>
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="markdown">We don't offer technical support for installation of third-party packages.</span>
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="markdown"><span class="idiff left right">For an instruction how to install Open Babel, please</span> refer to their <span class="p">[</span><span class="nv" style="color: #008080;">website</span><span class="p">](</span><span class="sx" style="color: #d14;">https://openbabel.org/docs/dev/Installation/install.html</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="markdown">We don't offer technical support for installation of third-party packages<span class="idiff left"> but added some </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">installation help for OpenBabel</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">#Installing-OpenBabel</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> below</span>.</span>
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="markdown"><span class="idiff left right">Alternatively you can</span> refer to their <span class="p">[</span><span class="nv" style="color: #008080;">website</span><span class="p">](</span><span class="sx" style="color: #d14;">https://openbabel.org/docs/dev/Installation/install.html</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="markdown"><span class="gt" style="color: #a00;">> I'm unsure on how to run PLIP and don't have much Linux experience.</span></span>
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="markdown"><span class="gt" style="color: #a00;">></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">@@ -173,9 +193,56 @@ Due to the non-deterministic nature on how hydrogen atoms can be added to the in</td>
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="markdown"><span class="gt" style="color: #a00;">></span></span>
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<pre style="margin: 0;"> <span id="LC194" 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>
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Installing OpenBabel</span></span>
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="markdown">As many users encounter problems with installing the required OpenBabel tools, we want to provide some help here. However, we cannot offer technical support. Comprehensive information about the installation of OpenBabel for Windows, Linux, and macOS can be found in the <span class="p">[</span><span class="nv" style="color: #008080;">OpenBabel wiki</span><span class="p">](</span><span class="sx" style="color: #d14;">http://openbabel.org/wiki/Category:Installation</span><span class="p">)</span> and the <span class="p">[</span><span class="nv" style="color: #008080;">OpenBabel Docs</span><span class="p">](</span><span class="sx" style="color: #d14;">https://open-babel.readthedocs.io/en/latest/Installation/install.html</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="markdown">Information about the installation of <span class="p">[</span><span class="nv" style="color: #008080;">OpenBabel Python bindings</span><span class="p">](</span><span class="sx" style="color: #d14;">https://open-babel.readthedocs.io/en/latest/UseTheLibrary/PythonInstall.html</span><span class="p">)</span> can also be found there.</span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Using Conda, HomeBrew or the binary Windows Installer</span></span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="markdown">Install OpenBabel using the <span class="p">[</span><span class="nv" style="color: #008080;">binary from GitHub</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/openbabel/openbabel/releases/latest</span><span class="p">)</span> or with</span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"># For Conda users</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="markdown"><span class="nv" style="color: #008080;">$ </span>conda <span class="nb" style="color: #0086b3;">install </span>openbabel <span class="nt" style="color: #000080;">-c</span> conda-forge</span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"># On macOS</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="markdown"><span class="nv" style="color: #008080;">$ </span>brew <span class="nb" style="color: #0086b3;">install </span>open-babel</span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="markdown">Install the Python bindings with</span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="markdown"><span class="nv" style="color: #008080;">$ </span>pip <span class="nb" style="color: #0086b3;">install </span>openbabel</span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Note:**</span> If you have trouble, make sure the OpenBabel version matches the one for the python bindings!</span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Using your Package Manager (Example for Ubuntu 20.04)</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="markdown"><span class="nv" style="color: #008080;">$ </span>apt-get update <span class="o" style="font-weight: 600;">&&</span> apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-y</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="markdown"> libopenbabel-dev <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="markdown"> libopenbabel6 <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="markdown"> python3-openbabel <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="markdown"> openbabel</span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### From Source (Example for Ubuntu 18.04)</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="markdown">Clone the OpenBabel repository into the /src directory</span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="markdown"><span class="nv" style="color: #008080;">$ </span>git clone <span class="nt" style="color: #000080;">-b</span> openbabel-3-0-0 <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="markdown">https://github.com/openbabel/openbabel.git</span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="markdown">Within /src/openbabel create end enter a directory /build and configure the build using</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="markdown"><span class="nv" style="color: #008080;">$ </span>cmake .. <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="markdown"><span class="nt" style="color: #000080;">-DPYTHON_EXECUTABLE</span><span class="o" style="font-weight: 600;">=</span>/usr/bin/python3.6 <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="markdown"><span class="nt" style="color: #000080;">-DPYTHON_BINDINGS</span><span class="o" style="font-weight: 600;">=</span>ON <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="markdown"><span class="nt" style="color: #000080;">-DCMAKE_INSTALL_PREFIX</span><span class="o" style="font-weight: 600;">=</span>/usr/local <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="markdown"><span class="nt" style="color: #000080;">-DRUN_SWIG</span><span class="o" style="font-weight: 600;">=</span>ON</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="markdown">From within the same directory (/src/openbabel/build) compile and install using</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="markdown"><span class="nv" style="color: #008080;">$ </span>make <span class="nt" style="color: #000080;">-j</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">nproc</span> <span class="nt" style="color: #000080;">--all</span><span class="si" style="color: #d14;">)</span> <span class="nb" style="color: #0086b3;">install</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Contact / Maintainer</span></span>
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<pre style="margin: 0;"> <span id="LC244" 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>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="markdown"> !<span class="p">[](</span><span class="sx" style="color: #d14;">https://www.pharm.ai/wp-content/uploads/2020/04/PharmAI_logo_color_no_slogan_500px.png</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="markdown"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="markdown"> Please get in touch: <span class="sb" style="color: #d14;">`hello@pharm.ai`</span></span></pre>
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<a href="https://salsa.debian.org/med-team/plip/-/compare/cdf3ace90672432387f5a06aa0b5d0b86b544d03...8c8e67280e95e52c343aca8cf63ec747ad398b8c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">plip (2.2.<span class="idiff left right">0</span>+dfsg-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">plip (2.2.<span class="idiff left right">2</span>+dfsg-1) 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"> * New upstream version 2.2.<span class="idiff left right">0</span>+dfsg</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version 2.2.<span class="idiff left right">2</span>+dfsg</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"> -- Nilesh Patra <nilesh@debian.org> Mon, 19 Apr 2021 17:10:53 +0530</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/plip/-/compare/cdf3ace90672432387f5a06aa0b5d0b86b544d03...8c8e67280e95e52c343aca8cf63ec747ad398b8c#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;">'2.2.<span class="idiff left right">0</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;">'2.2.<span class="idiff left right">2</span>'</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="n" style="color: #333;">__maintainer__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'PharmAI GmbH (2020-2021) - www.pharm.ai - hello@pharm.ai'</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">__citation_information__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Adasme,M. et al. PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA. "</span> \</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"> <span class="s" style="color: #d14;">"Nucl. Acids Res. (05 May 2021), gkab294. doi: 10.1093/nar/gkab294"</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<li id="67d4980fce23584951cb46902ae74ffca7500b93">
<a href="https://salsa.debian.org/med-team/plip/-/compare/cdf3ace90672432387f5a06aa0b5d0b86b544d03...8c8e67280e95e52c343aca8cf63ec747ad398b8c#67d4980fce23584951cb46902ae74ffca7500b93"><strong>plip/exchange/report.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,8 +28,7 @@ class StructureReport:</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">date_of_creation</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">et</span><span class="p">.</span><span class="n" style="color: #333;">SubElement</span><span class="p">(</span><span class="n" style="color: #333;">report</span><span class="p">,</span> <span class="s" style="color: #d14;">'date_of_creation'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">date_of_creation</span><span class="p">.</span><span class="n" style="color: #333;">text</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">strftime</span><span class="p">(</span><span class="s" style="color: #d14;">"%Y/%m/%d"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">citation_information</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">et</span><span class="p">.</span><span class="n" style="color: #333;">SubElement</span><span class="p">(</span><span class="n" style="color: #333;">report</span><span class="p">,</span> <span class="s" style="color: #d14;">'citation_information'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">citation_information</span><span class="p">.</span><span class="n" style="color: #333;">text</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler. "</span> \</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="s" style="color: #d14;">"Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315"</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">citation_information</span><span class="p">.</span><span class="n" style="color: #333;">text</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">__citation_information__</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="n" style="color: #333;">maintainer_information</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">et</span><span class="p">.</span><span class="n" style="color: #333;">SubElement</span><span class="p">(</span><span class="n" style="color: #333;">report</span><span class="p">,</span> <span class="s" style="color: #d14;">'maintainer_information'</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;">maintainer_information</span><span class="p">.</span><span class="n" style="color: #333;">text</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">__maintainer__</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">@@ -69,8 +68,7 @@ class StructureReport:</td>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">textlines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"="</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">textlines</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]))</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">textlines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">'Created on %s using PLIP v%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">strftime</span><span class="p">(</span><span class="s" style="color: #d14;">"%Y/%m/%d"</span><span class="p">),</span> <span class="n" style="color: #333;">__version__</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;">textlines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">'If you are using PLIP in your work, please cite:'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">textlines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">'Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">textlines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">'Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">textlines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">__citation_information__</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">excluded</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">textlines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">'Excluded molecules as ligands: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span> <span class="o" style="font-weight: 600;">%</span> <span class="s" style="color: #d14;">','</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">lig</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">lig</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">excluded</span><span class="p">]))</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">DNARECEPTOR</span><span class="p">:</span></span>
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<li id="7a4c9b79c2f1bb441895d677413efbc1cb536c35">
<a href="https://salsa.debian.org/med-team/plip/-/compare/cdf3ace90672432387f5a06aa0b5d0b86b544d03...8c8e67280e95e52c343aca8cf63ec747ad398b8c#7a4c9b79c2f1bb441895d677413efbc1cb536c35"><strong>plip/plipcmd.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -25,11 +25,10 @@ from plip.exchange.webservices import fetch_pdb</td>
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<pre style="margin: 0;"> <span id="LC25" 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;">create_folder_if_not_exists</span><span class="p">,</span> <span class="n" style="color: #333;">extract_pdbid</span></span>
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<pre style="margin: 0;"> <span id="LC26" 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;">tilde_expansion</span><span class="p">,</span> <span class="n" style="color: #333;">PDBComplex</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"><span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">f</span><span class="s" style="color: #d14;">"The Protein-Ligand Interaction Profiler (PLIP) </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">__version__</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span> \</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">f</span><span class="s" style="color: #d14;">"The Protein-Ligand Interaction Profiler (PLIP) <span class="idiff left">Version </span></span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">__version__</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"><span class="idiff right"> </span>"</span> \</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="s" style="color: #d14;">"is a command-line based tool to analyze interactions in a protein-ligand complex. "</span> \</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="s" style="color: #d14;">"If you are using PLIP in your work, please cite: "</span> \</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="s" style="color: #d14;">"Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler. "</span> \</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="s" style="color: #d14;">"Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi:10.1093/nar/gkv315"</span> \</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="sa">f</span><span class="s" style="color: #d14;">"</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;">__citation_information__</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> "</span> \</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"> <span class="sa">f</span><span class="s" style="color: #d14;">"Supported and maintained by: </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;">__maintainer__</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -124,7 +123,7 @@ def run_analysis(inputstructs, inputpdbids):</td>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Print title and version</span></span>
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<pre style="margin: 0;"> <span id="LC124" 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="sa">f</span><span class="s" style="color: #d14;">'Protein-Ligand Interaction Profiler (PLIP) </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">__version__</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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126
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125
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<pre style="margin: 0;"> <span id="LC125" 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="sa">f</span><span class="s" style="color: #d14;">'brought to you by: </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;">__maintainer__</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="LC127" 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="sa">f</span><span class="s" style="color: #d14;">'please cite: <span class="idiff left right">https://www.doi.org/10.1093/nar/gkv315</span>'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC126" 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="sa">f</span><span class="s" style="color: #d14;">'please cite: </span><span class="si" style="color: #d14;"><span class="idiff left">{</span></span><span class="n" style="color: #333;"><span class="idiff">config</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">__citation_information__</span></span><span class="si" style="color: #d14;"><span class="idiff right">}</span></span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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128
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">output_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">OUTPUTFILENAME</span></span>
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129
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"></span>
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130
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">inputstructs</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 class="c1" style="color: #998; font-style: italic;"># Process PDB file(s)</span></span>
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<a href="https://salsa.debian.org/med-team/plip/-/compare/cdf3ace90672432387f5a06aa0b5d0b86b544d03...8c8e67280e95e52c343aca8cf63ec747ad398b8c#d209d711b9b399c1e719fb9f3ab88df52dad6612"><strong>plip/test/test_command_line.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -57,3 +57,8 @@ class CommandLineTest(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">exitcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">executable</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> ../plipcmd.py -t -f ./pdb/1eve.pdb -O'</span><span class="p">,</span> <span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC58" 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;">exitcode</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_help</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="LC61" class="line" lang="python"> <span class="s" style="color: #d14;">"""A PDB ID with no valid PDB record is provided."""</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">exitcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">executable</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> ../plipcmd.py -h'</span><span class="p">,</span> <span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" 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;">exitcode</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"></span></pre>
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