diff --git a/run_af2/doc/html/.buildinfo b/run_af2/doc/html/.buildinfo
index 0188c63d450b9e4b24d3263ed9dbd1a912ed77c3..ebb9dbd6d9779142b191f7106bb8070da9e5cb67 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: 28b0c8014ab9635fcc7ca0d345e21e72
+config: b9aa92d5a319ad1e85a69d45f2e2182e
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/run_af2/doc/html/.doctrees/environment.pickle b/run_af2/doc/html/.doctrees/environment.pickle
index 29618e21d500520e21cde2d341ec78fa1ea08388..0ab7c93465f369e593c3f4008f58728fdd40010b 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 f18bbddd0b33b1548bf5ccc30de4860f4b815f6d..9be3072355c3435e7b2742cf7c304d7f7b7dbee6 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 36345007756ce69ce2e2f4e78bdab6947dffca26..9e8f20dbc40187cec609c8762bd9f3475da00d55 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 ad58f5fd18f718883abb0c59d7db16a330fb61f4..e60eaf48c74f0d8bb63ebba47a4f9dd2075e7e9e 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 1.0.5 documentation</title>
+    <title>_shared &#8212; af2@scicore/run_af2 2.0.0 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 1.0.5 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 2.0.0 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 v3.9)"><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 v3.10)"><code class="xref py py-class docutils literal notranslate"><span class="pre">argparse.ArgumentParser</span></code></a> object. Run the parser and return the
 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 v3.9)"><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 v3.10)"><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 v3.9)"><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 v3.10)"><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 1.0.5 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 2.0.0 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 8314691c50802cb9363e60730703f13e377607fd..5a94801b9847dc0839b12a42aa9838a892fbd744 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: '1.0.5',
+    VERSION: '2.0.0',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/run_af2/doc/html/genindex.html b/run_af2/doc/html/genindex.html
index 1c31e0b278f45e584abcca4a219a1b0429b239fe..222a75a1163c6cf895daef12943b0da7d6bcf76e 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 1.0.5 documentation</title>
+    <title>Index &#8212; af2@scicore/run_af2 2.0.0 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 1.0.5 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 2.0.0 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 1.0.5 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 2.0.0 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 5a1cc3f042e8e0d0832ffe5e111bd43fdb158d6d..8ac8ff7d6a17edc65077ee968b39aaf4d5059982 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 1.0.5 documentation</title>
+    <title>Welcome to af2@scicore/run_af2’s documentation! &#8212; af2@scicore/run_af2 2.0.0 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 1.0.5 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="#">af2@scicore/run_af2 2.0.0 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 1.0 (release 1.0.5)
+<p>You are reading the documentation for version 2.0 (release 2.0.0)
 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 1.0.5 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="#">af2@scicore/run_af2 2.0.0 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 37bbfe224f11814373b24bf601f56e10a5b304b6..5b4c013dcd8a1851b59411f0c2899c8bbc8bb4a8 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 ff9d638d2e77e5394ff4cd5fac5bf92c0964dedf..0ef51e8ffc938bb8e632f908051e5505f2451f33 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 1.0.5 documentation</title>
+    <title>Python Module Index &#8212; af2@scicore/run_af2 2.0.0 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 1.0.5 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 2.0.0 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 1.0.5 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 2.0.0 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 a8bb9bcb0b19d64356695e8358818ee1ff00a437..cc8fb90c63fe917e9b666edae75e2f08ebcb1b0e 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 1.0.5 documentation</title>
+    <title>run_singularity &#8212; af2@scicore/run_af2 2.0.0 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 1.0.5 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 2.0.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">run_singularity</a></li> 
       </ul>
     </div>  
@@ -55,61 +55,72 @@
 
 <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">model_names</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">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">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/data/managed/AF2params/frozen_210805T171956/'</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">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">template_mmcif_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'/scicore/data/managed/PDB/latest/data/structures/all/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/data/managed/PDB/latest/data/status/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">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 v3.9)"><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 v3.10)"><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 v3.9)"><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 v3.9)"><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 v3.10)"><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
 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 v3.9)"><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 v3.10)"><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
 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 v3.9)"><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 v3.10)"><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>model_names</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><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 v3.9)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – model_names parameter of AF2. DL models to use for
-modelling.</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 v3.9)"><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>preset</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Model configuration - no ensembling and smaller genetic
-databases (reduced_dbs), no ensembling and full genetic
-databases configuration (full_dbs). Corresponds to the preset
+<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
+(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
 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 v3.9)"><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>is_prokaryote_list</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> like needed by AF2, e.g.
+“true,false,true”) – For the multimer model, mark sequences as
+prokaryotic. Corresponds to the
+is_prokaryote_list 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>
-<li><p><strong>af2_image_dir</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><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 v3.10)"><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 v3.9)"><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 v3.9)"><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 v3.10)"><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>data_dir</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><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 v3.10)"><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 v3.9)"><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 v3.10)"><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 v3.9)"><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 v3.10)"><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 v3.9)"><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 v3.10)"><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 v3.9)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Small BFD database path, used with
-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 v3.9)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Uniclust30 database prefix. Corresponds to
+<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
+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>pdb70_database_path</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><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.</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 v3.9)"><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>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
+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
+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
+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
 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 v3.9)"><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 v3.10)"><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>
@@ -118,7 +129,7 @@ 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 v3.9)"><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 v3.10)"><code class="xref py py-class docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> if the Singularity/ AF2 call fails.</p>
 </dd>
 </dl>
 </dd></dl>
@@ -168,7 +179,7 @@ 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 1.0.5 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 2.0.0 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 d2de903eccf7583cfffc8aefa17408cc26ee5239..d28f9bf427b559d11ab115cc26c4adc3512d3808 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 1.0.5 documentation</title>
+    <title>Search &#8212; af2@scicore/run_af2 2.0.0 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 1.0.5 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 2.0.0 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 1.0.5 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 2.0.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Search</a></li> 
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diff --git a/run_af2/doc/html/searchindex.js b/run_af2/doc/html/searchindex.js
index 533d9fd76debe477591ed06972e73c2d728a9a39..256a420d36ade47aed24ab001d1031510de2f5ca 100644
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+++ b/run_af2/doc/html/searchindex.js
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