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Updated documentation

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# Sphinx build info version 1
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config: 80029e49350607596e13800ac8a707b6
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run_af2/doc/html/.doctrees/environment.pickle
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run_af2/doc/html/_shared.html
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<meta charset="utf-8" />
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<title>_shared &#8212; af2@scicore/run_af2 3.0.0 documentation</title>
<title>_shared &#8212; af2@scicore/run_af2 3.0.1.dev0+g6a14f8a.d20220324 documentation</title>
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......@@ -33,7 +33,7 @@
<li class="right" >
<a href="index.html" title="Welcome to af2@scicore/run_af2’s documentation!"
accesskey="P">previous</a> |</li>
<li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 3.0.0 documentation</a> &#187;</li>
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<li class="nav-item nav-item-this"><a href="">_shared</a></li>
</ul>
</div>
......@@ -129,7 +129,7 @@ and run tests on input with the <a class="reference external" href="https://docs
<li class="right" >
<a href="index.html" title="Welcome to af2@scicore/run_af2’s documentation!"
>previous</a> |</li>
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......
run_af2/doc/html/_static/documentation_options.js
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var DOCUMENTATION_OPTIONS = {
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run_af2/doc/html/genindex.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Index &#8212; af2@scicore/run_af2 3.0.0 documentation</title>
<title>Index &#8212; af2@scicore/run_af2 3.0.1.dev0+g6a14f8a.d20220324 documentation</title>
<link rel="stylesheet" type="text/css" href="_static/pygments.css" />
<link rel="stylesheet" type="text/css" href="_static/sphinxdoc.css" />
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
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<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 3.0.0 documentation</a> &#187;</li>
<li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 3.0.1.dev0+g6a14f8a.d20220324 documentation</a> &#187;</li>
<li class="nav-item nav-item-this"><a href="">Index</a></li>
</ul>
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......@@ -132,7 +132,7 @@
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 3.0.0 documentation</a> &#187;</li>
<li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 3.0.1.dev0+g6a14f8a.d20220324 documentation</a> &#187;</li>
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run_af2/doc/html/index.html
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<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
<title>Welcome to af2@scicore/run_af2’s documentation! &#8212; af2@scicore/run_af2 3.0.0 documentation</title>
<title>Welcome to af2@scicore/run_af2’s documentation! &#8212; af2@scicore/run_af2 3.0.1.dev0+g6a14f8a.d20220324 documentation</title>
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......@@ -29,7 +29,7 @@
<li class="right" >
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accesskey="N">next</a> |</li>
<li class="nav-item nav-item-0"><a href="#">af2@scicore/run_af2 3.0.0 documentation</a> &#187;</li>
<li class="nav-item nav-item-0"><a href="#">af2@scicore/run_af2 3.0.1.dev0+g6a14f8a.d20220324 documentation</a> &#187;</li>
<li class="nav-item nav-item-this"><a href="">Welcome to af2&#64;scicore/run_af2’s documentation!</a></li>
</ul>
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......@@ -41,7 +41,7 @@
<section id="welcome-to-af2-scicore-run-af2-s-documentation">
<h1>Welcome to af2&#64;scicore/run_af2’s documentation!<a class="headerlink" href="#welcome-to-af2-scicore-run-af2-s-documentation" title="Permalink to this headline"></a></h1>
<p>You are reading the documentation for version 3.0 (release 3.0.0)
<p>You are reading the documentation for version 3.0 (release 3.0.1.dev0+g6a14f8a.d20220324)
of <strong>run_af2</strong>.</p>
<p><strong>run_af2</strong> is a Python package to run the <a class="reference external" href="https://github.com/deepmind/alphafold">AlphaFold 2 (AF2) pipeline</a> on the sciCORE cluster.</p>
<p>The package comes with two major parts: userland commands to just execute the
......@@ -114,7 +114,7 @@ Python modules is here:</p>
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<li class="nav-item nav-item-this"><a href="">Welcome to af2&#64;scicore/run_af2’s documentation!</a></li>
</ul>
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run_af2/doc/html/py-modindex.html
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......@@ -5,7 +5,7 @@
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Python Module Index &#8212; af2@scicore/run_af2 3.0.0 documentation</title>
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<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
......@@ -27,7 +27,7 @@
<li class="right" >
<a href="#" title="Python Module Index"
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<li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 3.0.0 documentation</a> &#187;</li>
<li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 3.0.1.dev0+g6a14f8a.d20220324 documentation</a> &#187;</li>
<li class="nav-item nav-item-this"><a href="">Python Module Index</a></li>
</ul>
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......@@ -96,7 +96,7 @@
<li class="right" >
<a href="#" title="Python Module Index"
>modules</a> |</li>
<li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 3.0.0 documentation</a> &#187;</li>
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run_af2/doc/html/run_singularity.html
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......@@ -6,7 +6,7 @@
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<meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
<title>run_singularity &#8212; af2@scicore/run_af2 3.0.0 documentation</title>
<title>run_singularity &#8212; af2@scicore/run_af2 3.0.1.dev0+g6a14f8a.d20220324 documentation</title>
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......@@ -29,7 +29,7 @@
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<a href="_shared.html" title="_shared"
accesskey="P">previous</a> |</li>
<li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 3.0.0 documentation</a> &#187;</li>
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<li class="nav-item nav-item-this"><a href="">run_singularity</a></li>
</ul>
</div>
......@@ -55,7 +55,7 @@
<dl class="py function">
<dt class="sig sig-object py" id="run_af2.run_singularity.run_af2_singularity_image">
<span class="sig-prename descclassname"><span class="pre">run_af2.run_singularity.</span></span><span class="sig-name descname"><span class="pre">run_af2_singularity_image</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fasta_files</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_dir</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_template_date</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_gpu</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">db_preset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'full_dbs'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model_preset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'monomer'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_precomputed_msas</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_run_relax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_gpu_relax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">af2_image_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">af2_image_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/home/schwede/GROUP/alphafold_data/'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">snglrty_bin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/usr/bin/singularity'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tmpdir_var</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'TMPDIR'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extra_arg_list</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/home/schwede/GROUP/alphafold_data/'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uniref90_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/UniProt/latest/uniref/uniref90/uniref90.fasta'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mgnify_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/MGnify/frozen_210805T103002/mgy_clusters_2018_12.fa'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bfd_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/BFD/frozen_210805T085238/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">small_bfd_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/BFD_small/frozen_210812T135116/bfd-first_non_consensus_sequences.fasta'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uniclust30_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/Uniclust/frozen_181015T170110/uniclust30_2018_08/uniclust30_2018_08'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uniprot_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/home/schwede/GROUP/alphafold_data/uniprot/uniprot.fasta'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pdb70_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/PDB70/frozen_210805T142857/pdb70'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pdb_seqres_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/home/schwede/GROUP/alphafold_data/pdb_seqres/pdb_seqres.txt'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">template_mmcif_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/home/schwede/GROUP/alphafold_data/pdb_mmcif/mmcif_files/'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">obsolete_pdbs_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/home/schwede/GROUP/alphafold_data/pdb_mmcif/obsolete.dat'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#run_af2.run_singularity.run_af2_singularity_image" title="Permalink to this definition"></a></dt>
<span class="sig-prename descclassname"><span class="pre">run_af2.run_singularity.</span></span><span class="sig-name descname"><span class="pre">run_af2_singularity_image</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fasta_files</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_dir</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_template_date</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_gpu</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">db_preset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'full_dbs'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model_preset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'monomer'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_precomputed_msas</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_run_relax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_gpu_relax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_multimer_predictions_per_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">af2_image_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">af2_image_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/home/schwede/GROUP/alphafold_data/'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">snglrty_bin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/usr/bin/singularity'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tmpdir_var</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'TMPDIR'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extra_arg_list</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/home/schwede/GROUP/alphafold_data/'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uniref90_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/UniProt/latest/uniref/uniref90/uniref90.fasta'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mgnify_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/MGnify/frozen_210805T103002/mgy_clusters_2018_12.fa'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bfd_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/BFD/frozen_210805T085238/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">small_bfd_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/BFD_small/frozen_210812T135116/bfd-first_non_consensus_sequences.fasta'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uniclust30_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/Uniclust/frozen_181015T170110/uniclust30_2018_08/uniclust30_2018_08'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uniprot_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/home/schwede/GROUP/alphafold_data/uniprot/uniprot.fasta'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pdb70_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/PDB70/frozen_210805T142857/pdb70'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pdb_seqres_database_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/home/schwede/GROUP/alphafold_data/pdb_seqres/pdb_seqres.txt'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">template_mmcif_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/home/schwede/GROUP/alphafold_data/pdb_mmcif/mmcif_files/'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">obsolete_pdbs_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/home/schwede/GROUP/alphafold_data/pdb_mmcif/obsolete.dat'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#run_af2.run_singularity.run_af2_singularity_image" title="Permalink to this definition"></a></dt>
<dd><p>Run the AlphaFold 2 Singularity image on host.</p>
<p>The keyword arguments all come with defaults to run on the sciCORE cluster.</p>
<p>If the Singularity container fails, a <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#RuntimeError" title="(in Python v3.10)"><code class="xref py py-class docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> will be
......@@ -87,6 +87,11 @@ oppositely, True means no relaxation, False means
relaxation.</p></li>
<li><p><strong>use_gpu_relax</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.10)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Run relaxation on GPU. Corresponds to the
use_gpu_relax parameter in AF2.</p></li>
<li><p><strong>num_multimer_predictions_per_model</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.10)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – In multimer mode, no. of
predictions per model.
Corresponds to the
num_multimer_predictions_per_model
parameter in AF2.</p></li>
<li><p><strong>af2_image_file</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.10)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Declare a Singularity image to run the AF2 pipeline
from. If None, an image from af2_image_dir will be
used.</p></li>
......@@ -186,7 +191,7 @@ in AF2.</p></li>
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