diff --git a/run_af2/doc/html/.buildinfo b/run_af2/doc/html/.buildinfo
index 52c6e139f374e1edb6b39fe0b7d9d01901e48613..b87e8934cb1772fb578606a875c67cf6cdfa3480 100644
--- a/run_af2/doc/html/.buildinfo
+++ b/run_af2/doc/html/.buildinfo
@@ -1,4 +1,4 @@
 # 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: c4d4f094057515b594fb8499643853e2
+config: 6325d903612a71b0cf84ff2096c98a7c
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/run_af2/doc/html/.doctrees/environment.pickle b/run_af2/doc/html/.doctrees/environment.pickle
index 021a85ddd1bb193c423f96f619400125cfc73a91..1852f1299a6175e88c48925c70c4a7702bb9a087 100644
Binary files a/run_af2/doc/html/.doctrees/environment.pickle and b/run_af2/doc/html/.doctrees/environment.pickle differ
diff --git a/run_af2/doc/html/.doctrees/index.doctree b/run_af2/doc/html/.doctrees/index.doctree
index db1669a03d038bd70f5152e637a957b06281873b..7ea7a61e31600ac83357fdd58241c5a10e6535c4 100644
Binary files a/run_af2/doc/html/.doctrees/index.doctree and b/run_af2/doc/html/.doctrees/index.doctree differ
diff --git a/run_af2/doc/html/.doctrees/run_singularity.doctree b/run_af2/doc/html/.doctrees/run_singularity.doctree
index cdc966590c682ae644326654ce502be7a1faf93c..e886110d7b2426b00054abe602fe7f7ec8da1b48 100644
Binary files a/run_af2/doc/html/.doctrees/run_singularity.doctree and b/run_af2/doc/html/.doctrees/run_singularity.doctree differ
diff --git a/run_af2/doc/html/_shared.html b/run_af2/doc/html/_shared.html
index 53738c5cd832cfa53b1e6980fc15b2cc911b7288..ea81c0b6f64c6d644c85fd728d44491888743cbe 100644
--- a/run_af2/doc/html/_shared.html
+++ b/run_af2/doc/html/_shared.html
@@ -6,7 +6,7 @@
     <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>_shared &#8212; af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 documentation</title>
+    <title>_shared &#8212; af2@scicore/run_af2 0.0.0 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>
@@ -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 3.1.1.dev0+ge9ef748.d20220330 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 0.0.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">_shared</a></li> 
       </ul>
     </div>  
@@ -67,12 +67,12 @@ creates the version file.</p>
 <span class="sig-prename descclassname"><span class="pre">run_af2._shared.</span></span><span class="sig-name descname"><span class="pre">parse_af2_arguments</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parser</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#run_af2._shared.parse_af2_arguments" title="Permalink to this definition">¶</a></dt>
 <dd><p>AF2 pipeline arguments parsing capabilities.</p>
 <p>Add arguments common for running the AF2 pipeline to an existing
-<a class="reference external" href="https://docs.python.org/3/library/argparse.html#argparse.ArgumentParser" title="(in Python v3.10)"><code class="xref py py-class docutils literal notranslate"><span class="pre">argparse.ArgumentParser</span></code></a> object. Run the parser and return the
+<a class="reference external" href="https://docs.python.org/3/library/argparse.html#argparse.ArgumentParser" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">argparse.ArgumentParser</span></code></a> object. Run the parser and return the
 result. That way tools can implement their own description for the parser
-and run tests on input with the <a class="reference external" href="https://docs.python.org/3/library/argparse.html#argparse.Namespace" title="(in Python v3.10)"><code class="xref py py-class docutils literal notranslate"><span class="pre">argparse.Namespace</span></code></a> object.</p>
+and run tests on input with the <a class="reference external" href="https://docs.python.org/3/library/argparse.html#argparse.Namespace" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">argparse.Namespace</span></code></a> object.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/argparse.html#argparse.Namespace" title="(in Python v3.10)"><code class="xref py py-class docutils literal notranslate"><span class="pre">argparse.Namespace</span></code></a> object from
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/argparse.html#argparse.Namespace" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">argparse.Namespace</span></code></a> object from
 <cite>argparse.ArgumentParser.parse_args</cite>.</p>
 </dd>
 </dl>
@@ -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>
-        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 0.0.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">_shared</a></li> 
       </ul>
     </div>
diff --git a/run_af2/doc/html/_static/documentation_options.js b/run_af2/doc/html/_static/documentation_options.js
index 6b5537d19bd3d7771e38ebeea698d0684219c1df..0dcee420e13d5b49b17c5cf5d5bf529f92daadcc 100644
--- a/run_af2/doc/html/_static/documentation_options.js
+++ b/run_af2/doc/html/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '3.1.1.dev0+ge9ef748.d20220330',
+    VERSION: '0.0.0',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/run_af2/doc/html/genindex.html b/run_af2/doc/html/genindex.html
index f6bd01e9f758ba44216b72d90ab2de38dba35b06..c0ff8b9a7c05a5de1dc21efc86bf1559501c011d 100644
--- a/run_af2/doc/html/genindex.html
+++ b/run_af2/doc/html/genindex.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Index &#8212; af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 documentation</title>
+    <title>Index &#8212; af2@scicore/run_af2 0.0.0 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>
@@ -24,7 +24,7 @@
         <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 3.1.1.dev0+ge9ef748.d20220330 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 0.0.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Index</a></li> 
       </ul>
     </div>  
@@ -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 3.1.1.dev0+ge9ef748.d20220330 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 0.0.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Index</a></li> 
       </ul>
     </div>
diff --git a/run_af2/doc/html/index.html b/run_af2/doc/html/index.html
index 42e84f8a8a811888e06bfe2c5b6a6d5ac48a6923..c9c032103e516bde9caacfeaebf6f48f5308f543 100644
--- a/run_af2/doc/html/index.html
+++ b/run_af2/doc/html/index.html
@@ -6,7 +6,7 @@
     <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 3.1.1.dev0+ge9ef748.d20220330 documentation</title>
+    <title>Welcome to af2@scicore/run_af2’s documentation! &#8212; af2@scicore/run_af2 0.0.0 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>
@@ -29,7 +29,7 @@
         <li class="right" >
           <a href="_shared.html" title="_shared"
              accesskey="N">next</a> |</li>
-        <li class="nav-item nav-item-0"><a href="#">af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="#">af2@scicore/run_af2 0.0.0 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>
     </div>  
@@ -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 3.1 (release 3.1.1.dev0+ge9ef748.d20220330)
+<p>You are reading the documentation for version 0.0 (release 0.0.0)
 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>
         <li class="right" >
           <a href="_shared.html" title="_shared"
              >next</a> |</li>
-        <li class="nav-item nav-item-0"><a href="#">af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="#">af2@scicore/run_af2 0.0.0 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>
     </div>
diff --git a/run_af2/doc/html/objects.inv b/run_af2/doc/html/objects.inv
index 768871765c0be7c5efe508d3e1cdc9320860418e..066b5f8cbfabb9fdfa123d4dbb710a6495a793ed 100644
Binary files a/run_af2/doc/html/objects.inv and b/run_af2/doc/html/objects.inv differ
diff --git a/run_af2/doc/html/py-modindex.html b/run_af2/doc/html/py-modindex.html
index 599f7a768b12561109399afe832d04725d6a2e16..16a828fb4b2a6c15317bbe47a3795c31570913ec 100644
--- a/run_af2/doc/html/py-modindex.html
+++ b/run_af2/doc/html/py-modindex.html
@@ -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 3.1.1.dev0+ge9ef748.d20220330 documentation</title>
+    <title>Python Module Index &#8212; af2@scicore/run_af2 0.0.0 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>
@@ -27,7 +27,7 @@
         <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 3.1.1.dev0+ge9ef748.d20220330 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 0.0.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Python Module Index</a></li> 
       </ul>
     </div>  
@@ -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 3.1.1.dev0+ge9ef748.d20220330 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 0.0.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Python Module Index</a></li> 
       </ul>
     </div>
diff --git a/run_af2/doc/html/run_singularity.html b/run_af2/doc/html/run_singularity.html
index 4377c70cabfe68caf6492843b5a3093768f59378..1e0f7b29d15f8e4d128f2e2f7e6fde63c5393370 100644
--- a/run_af2/doc/html/run_singularity.html
+++ b/run_af2/doc/html/run_singularity.html
@@ -6,7 +6,7 @@
     <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>run_singularity &#8212; af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 documentation</title>
+    <title>run_singularity &#8212; af2@scicore/run_af2 0.0.0 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>
@@ -29,7 +29,7 @@
         <li class="right" >
           <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 3.1.1.dev0+ge9ef748.d20220330 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 0.0.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">run_singularity</a></li> 
       </ul>
     </div>  
@@ -55,84 +55,84 @@
 
 <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">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>
+<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">uniref30_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/uniref30/UniRef30_2021_03'</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
+<p>If the Singularity container fails, a <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#RuntimeError" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> will be
 raised.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>fasta_files</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> of <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>) – A list of target FASTA files. Every sequence is a
+<li><p><strong>fasta_files</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – A list of target FASTA files. Every sequence is a
 separate target. Only one sequence per file. Basenames
 must be unique, AF2 uses them as names for the
 result-directories.</p></li>
-<li><p><strong>output_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>) – Path to the output directory which will hold all the
+<li><p><strong>output_dir</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the output directory which will hold all the
 result directories for the targets.</p></li>
-<li><p><strong>max_template_date</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>) – max_template_date parameter of AF2. Templates
+<li><p><strong>max_template_date</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – max_template_date parameter of AF2. Templates
 released by PDB after this date are not
 considered.If None, set to tomorrow so all
 templates are included.</p></li>
-<li><p><strong>use_gpu</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 the AF2 pipeline using GPUs or not.</p></li>
-<li><p><strong>db_preset</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>) – Database configuration - smaller genetic databases
+<li><p><strong>use_gpu</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Run the AF2 pipeline using GPUs or not.</p></li>
+<li><p><strong>db_preset</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Database configuration - smaller genetic databases
 (reduced_dbs) and full genetic databases configuration
 (full_dbs). Corresponds to the db_preset parameter in AF2.</p></li>
-<li><p><strong>model_preset</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>) – Model configuration - corresponds to the model_preset
+<li><p><strong>model_preset</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Model configuration - corresponds to the model_preset
 parameter in AF2.</p></li>
-<li><p><strong>use_precomputed_msas</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>) – Use existing MSAs from cwd. Corresponds to the
+<li><p><strong>use_precomputed_msas</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Use existing MSAs from cwd. Corresponds to the
 use_precomputed_msas parameter in AF2.</p></li>
-<li><p><strong>no_run_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>) – Disable relaxation at the end of modelling.
+<li><p><strong>no_run_relax</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Disable relaxation at the end of modelling.
 Corresponds to AF2’s no_run_relax parameter but works
 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
+<li><p><strong>use_gpu_relax</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.11)"><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
+<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 v3.11)"><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
+<li><p><strong>af2_image_file</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><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>
-<li><p><strong>af2_image_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>) – Declare from which directory the Singularity image
+<li><p><strong>af2_image_dir</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Declare from which directory the Singularity image
 should be used. Image file names need to be of form
 alphafold-&lt;YYYY-MM-DD&gt;.sif. By default, the latest
 image will be used. This parameter has no effect if
 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
+<li><p><strong>snglrty_bin</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><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 v3.11)"><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
+<li><p><strong>extra_arg_list</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.11)"><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.
+<li><p><strong>data_dir</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><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.
+<li><p><strong>uniref90_database_path</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Holds the UniRef90 database path.
 Corresponds to uniref90_database_path in AF2.</p></li>
-<li><p><strong>mgnify_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 MGnify database path. Corresponds to
+<li><p><strong>mgnify_database_path</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Holds the MGnify database path. Corresponds to
 mgnify_database_path in AF2.</p></li>
-<li><p><strong>bfd_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>) – BFD database prefix. Corresponds to
+<li><p><strong>bfd_database_path</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – BFD database prefix. Corresponds to
 bfd_database_path in AF2.</p></li>
-<li><p><strong>small_bfd_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>) – Small BFD database path, used with
+<li><p><strong>small_bfd_database_path</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Small BFD database path, used with
 db_preset=”reduced_dbs”, not a HHblits
 prefix as for the large BFD database.
 Corresponds to small_bfd_database_path in
 AF2.</p></li>
-<li><p><strong>uniclust30_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>) – Uniclust30 database prefix. Corresponds to
-uniclust30_database_path in AF2.</p></li>
-<li><p><strong>uniprot_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>) – UniProt sequence file. Corresponds to
+<li><p><strong>uniref30_database_path</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – UniRef30 database prefix. Corresponds to
+uniref30_database_path in AF2.</p></li>
+<li><p><strong>uniprot_database_path</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – UniProt sequence file. Corresponds to
 uniprot_database_path in AF2. Needed for
 model_preset == multimer.</p></li>
-<li><p><strong>pdb70_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>) – PDB70 database prefix. Corresponds to
+<li><p><strong>pdb70_database_path</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – PDB70 database prefix. Corresponds to
 pdb70_database_path in AF2. Will be disabled if
 model_preset == multimer.</p></li>
-<li><p><strong>pdb_seqres_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>) – PDB seqres file. Corresponds to
+<li><p><strong>pdb_seqres_database_path</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – PDB seqres file. Corresponds to
 pdb_seqres_database_path in AF2. Needed for
 model_preset == multimer.</p></li>
-<li><p><strong>template_mmcif_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>) – Path to the template structures. Corresponds to
+<li><p><strong>template_mmcif_dir</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the template structures. Corresponds to
 template_mmcif_dir in AF2.</p></li>
-<li><p><strong>obsolete_pdbs_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>) – Mapping file of obsoleted PDB entries and
+<li><p><strong>obsolete_pdbs_path</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Mapping file of obsoleted PDB entries and
 replacements. Corresponds to obsolete_pdbs_path
 in AF2.</p></li>
 </ul>
@@ -141,7 +141,7 @@ in AF2.</p></li>
 <dd class="field-even"><p>Nothing.</p>
 </dd>
 <dt class="field-odd">Raises</dt>
-<dd class="field-odd"><p><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> if the Singularity/ AF2 call fails.</p>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#RuntimeError" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> if the Singularity/ AF2 call fails.</p>
 </dd>
 </dl>
 </dd></dl>
@@ -191,7 +191,7 @@ in AF2.</p></li>
         <li class="right" >
           <a href="_shared.html" title="_shared"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 0.0.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">run_singularity</a></li> 
       </ul>
     </div>
diff --git a/run_af2/doc/html/search.html b/run_af2/doc/html/search.html
index 9314d37a397c9c608813f5d3b56f471006ddc7fb..230e8df92b1517dd3748892ab320a6c0426e6e53 100644
--- a/run_af2/doc/html/search.html
+++ b/run_af2/doc/html/search.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Search &#8212; af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 documentation</title>
+    <title>Search &#8212; af2@scicore/run_af2 0.0.0 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/sphinxdoc.css" />
     
@@ -30,7 +30,7 @@
         <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 3.1.1.dev0+ge9ef748.d20220330 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 0.0.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Search</a></li> 
       </ul>
     </div>  
@@ -89,7 +89,7 @@
         <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 3.1.1.dev0+ge9ef748.d20220330 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 0.0.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Search</a></li> 
       </ul>
     </div>
diff --git a/run_af2/doc/html/searchindex.js b/run_af2/doc/html/searchindex.js
index 1cbbdaa1331dec46e59915c685a4b3307c814ff6..3636090a9207c9b323896f52f1abc9396809c5e6 100644
--- a/run_af2/doc/html/searchindex.js
+++ b/run_af2/doc/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({docnames:["_shared","index","run_singularity"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":4,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":3,"sphinx.domains.rst":2,"sphinx.domains.std":2,"sphinx.ext.intersphinx":1,sphinx:56},filenames:["_shared.rst","index.rst","run_singularity.rst"],objects:{"run_af2._shared":{get_version:[0,1,1,""],parse_af2_arguments:[0,1,1,""]},"run_af2.run_singularity":{main:[2,1,1,""],run_af2_singularity_image:[2,1,1,""]},run_af2:{_shared:[0,0,0,"-"],run_singularity:[2,0,0,"-"]}},objnames:{"0":["py","module","Python module"],"1":["py","function","Python function"]},objtypes:{"0":"py:module","1":"py:function"},terms:{"0":[],"1":1,"2":[1,2],"3":1,"4":[],"5":2,"case":0,"default":2,"export":[],"function":0,"import":0,"int":2,"return":[0,2],"true":2,A:[0,2],By:2,For:[],If:[0,2],In:2,Not:[],That:[0,2],The:[1,2],There:2,Will:2,_share:1,access:1,ad:2,add:0,af2:[0,2],af2_image_dir:2,af2_image_fil:2,af2param:[],after:[0,2],all:2,alphafold2:2,alphafold:[1,2],alphafold_data:2,an:[0,2],append:2,ar:[1,2],argpars:0,argument:[0,2],argumentpars:0,avail:2,basenam:2,bfd:2,bfd_database_path:2,bfd_metaclust_clu_complete_id30_c90_final_seq:2,bfd_small:2,bin:2,binari:2,bool:2,build:0,call:2,can:[0,1],capabl:0,cfg:0,cluster:[1,2],come:[1,2],command:1,common:0,configur:2,consid:2,contain:2,correspond:2,creat:0,cwd:2,d20220128:[],d20220324:[],d20220330:1,dat:2,data:2,data_dir:2,databas:2,date:2,db_preset:2,dd:2,declar:2,defin:2,deliv:0,descript:0,dev0:1,did:0,directori:[0,2],disabl:2,dl:[],download_dir:2,e:[],effect:2,end:2,ensembl:[],entri:2,environ:2,everi:2,execut:[1,2],exist:[0,2],extern:0,extra:2,extra_arg_list:2,fa:2,fail:2,fals:2,fasta:2,fasta_fil:2,file:[0,2],first:[],first_non_consensus_sequ:2,form:2,found:1,from:[0,1,2],frozen_181015t170110:2,frozen_210805t085238:2,frozen_210805t103002:2,frozen_210805t142857:2,frozen_210805t171956:[],frozen_210812t135116:2,full:2,full_db:2,g6a14f8a:[],g:[],ge9ef748:1,genet:2,get_vers:0,gf71d760:[],gitlab:1,gpu:2,group:2,ha:2,happen:0,here:1,hhblit:2,hold:2,home:2,host:2,imag:2,implement:0,includ:2,index:1,input:0,is_prokaryote_list:[],itself:0,just:[1,2],keyword:2,larg:2,latest:2,like:[],list:2,load:0,m:0,main:2,major:1,manag:2,map:2,mark:[],max_template_d:2,mean:2,mgnifi:2,mgnify_database_path:2,mgy_clusters_2018_12:2,mm:2,mmcif_fil:2,mode:2,model:2,model_nam:[],model_preset:2,modifi:2,modul:[0,1,2],monom:2,msa:2,multim:2,must:2,name:2,namespac:0,necessarili:2,need:[0,2],no_run_relax:2,none:2,noth:2,num_multimer_predictions_per_model:2,object:0,obsolet:2,obsolete_pdbs_path:2,onc:0,one:2,onli:[0,2],opposit:2,other:0,output:2,output_dir:2,outsid:0,own:[0,1],packag:[0,1],page:1,param:2,paramet:2,pars:0,parse_af2_argu:0,parse_arg:0,parser:0,part:1,path:2,pdb70:2,pdb70_database_path:2,pdb:2,pdb_mmcif:2,pdb_seqr:2,pdb_seqres_database_path:2,per:2,pipelin:[0,1,2],predict:2,prefix:2,preset:[],programmat:1,prokaryot:[],proper:0,py:2,python:[0,1,2],rais:2,read:1,reduced_db:2,relax:2,releas:[1,2],replac:2,repositori:1,request:0,result:[0,2],run:[0,1,2],run_af2:[0,2],run_af2_singularity_imag:2,run_alphafold:2,run_singular:1,runtimeerror:2,s:2,same:0,schwede:2,scicor:2,script:[1,2],search:1,separ:2,seqr:2,sequenc:2,set:2,setup:0,share:0,should:[0,2],sif:2,sinc:0,singular:2,small:2,small_bfd_database_path:2,smaller:2,snglrty_bin:2,so:2,soft:[],some:[0,2],sorted_opt:2,space:2,statu:[],str:2,string:0,structur:2,sub:2,system:2,target:2,templat:2,template_mmcif_dir:2,test:0,them:2,thi:[0,2],tmp:2,tmpdir:2,tmpdir_var:2,tomorrow:2,tool:0,two:[1,2],txt:2,uniclust30:2,uniclust30_2018_08:2,uniclust30_database_path:2,uniclust:2,uniprot:2,uniprot_database_path:2,uniqu:2,uniref90:2,uniref90_database_path:2,uniref:2,upon:0,us:[0,2],use_gpu:2,use_gpu_relax:2,use_precomputed_msa:2,userland:1,usr:2,variabl:2,version:[0,1,2],wai:0,we:0,which:2,work:2,x:0,you:[0,1],your:1,yyyi:2},titles:["_shared","Welcome to af2&#64;scicore/run_af2\u2019s documentation!","run_singularity"],titleterms:{_share:0,af2:1,document:1,indic:1,run_af2:1,run_singular:2,s:1,scicor:1,tabl:1,welcom:1}})
\ No newline at end of file
+Search.setIndex({docnames:["_shared","index","run_singularity"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":4,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":3,"sphinx.domains.rst":2,"sphinx.domains.std":2,"sphinx.ext.intersphinx":1,sphinx:56},filenames:["_shared.rst","index.rst","run_singularity.rst"],objects:{"run_af2._shared":{get_version:[0,1,1,""],parse_af2_arguments:[0,1,1,""]},"run_af2.run_singularity":{main:[2,1,1,""],run_af2_singularity_image:[2,1,1,""]},run_af2:{_shared:[0,0,0,"-"],run_singularity:[2,0,0,"-"]}},objnames:{"0":["py","module","Python module"],"1":["py","function","Python function"]},objtypes:{"0":"py:module","1":"py:function"},terms:{"0":1,"1":[],"2":[1,2],"3":[],"4":[],"5":2,"case":0,"default":2,"export":[],"function":0,"import":0,"int":2,"return":[0,2],"true":2,A:[0,2],By:2,For:[],If:[0,2],In:2,Not:[],That:[0,2],The:[1,2],There:2,Will:2,_share:1,access:1,ad:2,add:0,af2:[0,2],af2_image_dir:2,af2_image_fil:2,af2param:[],after:[0,2],all:2,alphafold2:2,alphafold:[1,2],alphafold_data:2,an:[0,2],append:2,ar:[1,2],argpars:0,argument:[0,2],argumentpars:0,avail:2,basenam:2,bfd:2,bfd_database_path:2,bfd_metaclust_clu_complete_id30_c90_final_seq:2,bfd_small:2,bin:2,binari:2,bool:2,build:0,call:2,can:[0,1],capabl:0,cfg:0,cluster:[1,2],come:[1,2],command:1,common:0,configur:2,consid:2,contain:2,correspond:2,creat:0,cwd:2,d20220128:[],d20220324:[],d20220330:[],dat:2,data:2,data_dir:2,databas:2,date:2,db_preset:2,dd:2,declar:2,defin:2,deliv:0,descript:0,dev0:[],did:0,directori:[0,2],disabl:2,dl:[],download_dir:2,e:[],effect:2,end:2,ensembl:[],entri:2,environ:2,everi:2,execut:[1,2],exist:[0,2],extern:0,extra:2,extra_arg_list:2,fa:2,fail:2,fals:2,fasta:2,fasta_fil:2,file:[0,2],first:[],first_non_consensus_sequ:2,form:2,found:1,from:[0,1,2],frozen_181015t170110:[],frozen_210805t085238:2,frozen_210805t103002:2,frozen_210805t142857:2,frozen_210805t171956:[],frozen_210812t135116:2,full:2,full_db:2,g6a14f8a:[],g:[],ge9ef748:[],genet:2,get_vers:0,gf71d760:[],gitlab:1,gpu:2,group:2,ha:2,happen:0,here:1,hhblit:2,hold:2,home:2,host:2,imag:2,implement:0,includ:2,index:1,input:0,is_prokaryote_list:[],itself:0,just:[1,2],keyword:2,larg:2,latest:2,like:[],list:2,load:0,m:0,main:2,major:1,manag:2,map:2,mark:[],max_template_d:2,mean:2,mgnifi:2,mgnify_database_path:2,mgy_clusters_2018_12:2,mm:2,mmcif_fil:2,mode:2,model:2,model_nam:[],model_preset:2,modifi:2,modul:[0,1,2],monom:2,msa:2,multim:2,must:2,name:2,namespac:0,necessarili:2,need:[0,2],no_run_relax:2,none:2,noth:2,num_multimer_predictions_per_model:2,object:0,obsolet:2,obsolete_pdbs_path:2,onc:0,one:2,onli:[0,2],opposit:2,other:0,output:2,output_dir:2,outsid:0,own:[0,1],packag:[0,1],page:1,param:2,paramet:2,pars:0,parse_af2_argu:0,parse_arg:0,parser:0,part:1,path:2,pdb70:2,pdb70_database_path:2,pdb:2,pdb_mmcif:2,pdb_seqr:2,pdb_seqres_database_path:2,per:2,pipelin:[0,1,2],predict:2,prefix:2,preset:[],programmat:1,prokaryot:[],proper:0,py:2,python:[0,1,2],rais:2,read:1,reduced_db:2,relax:2,releas:[1,2],replac:2,repositori:1,request:0,result:[0,2],run:[0,1,2],run_af2:[0,2],run_af2_singularity_imag:2,run_alphafold:2,run_singular:1,runtimeerror:2,s:2,same:0,schwede:2,scicor:2,script:[1,2],search:1,separ:2,seqr:2,sequenc:2,set:2,setup:0,share:0,should:[0,2],sif:2,sinc:0,singular:2,small:2,small_bfd_database_path:2,smaller:2,snglrty_bin:2,so:2,soft:[],some:[0,2],sorted_opt:2,space:2,statu:[],str:2,string:0,structur:2,sub:2,system:2,target:2,templat:2,template_mmcif_dir:2,test:0,them:2,thi:[0,2],tmp:2,tmpdir:2,tmpdir_var:2,tomorrow:2,tool:0,two:[1,2],txt:2,uniclust30:[],uniclust30_2018_08:[],uniclust30_database_path:[],uniclust:[],uniprot:2,uniprot_database_path:2,uniqu:2,uniref30:2,uniref30_2021_03:2,uniref30_database_path:2,uniref90:2,uniref90_database_path:2,uniref:2,upon:0,us:[0,2],use_gpu:2,use_gpu_relax:2,use_precomputed_msa:2,userland:1,usr:2,variabl:2,version:[0,1,2],wai:0,we:0,which:2,work:2,x:0,you:[0,1],your:1,yyyi:2},titles:["_shared","Welcome to af2&#64;scicore/run_af2\u2019s documentation!","run_singularity"],titleterms:{_share:0,af2:1,document:1,indic:1,run_af2:1,run_singular:2,s:1,scicor:1,tabl:1,welcom:1}})
\ No newline at end of file