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Updated documentation

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# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: b9aa92d5a319ad1e85a69d45f2e2182e
config: 171d4b693e6557a2ce6f741e7bf24c8f
tags: 645f666f9bcd5a90fca523b33c5a78b7
run_af2/doc/html/.doctrees/environment.pickle
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<meta charset="utf-8" />
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......@@ -129,7 +129,7 @@ and run tests on input with the <a class="reference external" href="https://docs
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var DOCUMENTATION_OPTIONS = {
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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 2.0.0 documentation</title>
<title>Index &#8212; af2@scicore/run_af2 2.1.0 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 2.0.0 documentation</a> &#187;</li>
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<li class="nav-item nav-item-this"><a href="">Index</a></li>
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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 2.0.0 documentation</a> &#187;</li>
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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 2.0.0 documentation</title>
<title>Welcome to af2@scicore/run_af2’s documentation! &#8212; af2@scicore/run_af2 2.1.0 documentation</title>
<link rel="stylesheet" type="text/css" href="_static/pygments.css" />
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</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 2.0 (release 2.0.0)
<p>You are reading the documentation for version 2.1 (release 2.1.0)
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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<head>
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<li class="nav-item nav-item-this"><a href="">Python Module Index</a></li>
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......@@ -96,7 +96,7 @@
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<meta charset="utf-8" />
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<title>run_singularity &#8212; af2@scicore/run_af2 2.0.0 documentation</title>
<title>run_singularity &#8212; af2@scicore/run_af2 2.1.0 documentation</title>
<link rel="stylesheet" type="text/css" href="_static/pygments.css" />
<link rel="stylesheet" type="text/css" href="_static/sphinxdoc.css" />
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accesskey="P">previous</a> |</li>
<li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 2.0.0 documentation</a> &#187;</li>
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<li class="nav-item nav-item-this"><a href="">run_singularity</a></li>
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......@@ -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">is_prokaryote_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">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">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">is_prokaryote_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">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
......@@ -94,6 +94,9 @@ af2_image_file is not None.</p></li>
<li><p><strong>snglrty_bin</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>) – Path to the singularity binary.</p></li>
<li><p><strong>tmpdir_var</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>) – An environment variable defining tmp space, that is not
necessarily “/tmp” on some systems.</p></li>
<li><p><strong>extra_arg_list</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.10)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of extra arguments appended to the Singularity
call. That is for adding extra arguments in a
modified version of run_alphafold.py.</p></li>
<li><p><strong>data_dir</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>) – Holds the params sub directory with model parameters.
Corresponds to DOWNLOAD_DIR in AF2.</p></li>
<li><p><strong>uniref90_database_path</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>) – Holds the UniRef90 database path.
......@@ -179,7 +182,7 @@ in AF2.</p></li>
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