Upload documentation from latest commit

_static/documentation_options.js

@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.1.dev1+gf9e3c70',
+    VERSION: '0.1.dev1+gbe8c2f2',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

about.html

@@ -17,7 +17,7 @@
 
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=701c80da"></script>
+        <script src="_static/documentation_options.js?v=e9dab49d"></script>
         <script src="_static/doctools.js?v=9a2dae69"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/js/theme.js"></script>

cli.html

@@ -17,7 +17,7 @@
 
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=701c80da"></script>
+        <script src="_static/documentation_options.js?v=e9dab49d"></script>
         <script src="_static/doctools.js?v=9a2dae69"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/js/theme.js"></script>
@@ -97,6 +97,7 @@ <h2>matchmaps<a class="headerlink" href="#matchmaps" title="Link to this heading
 <span class="go">                 [--unmasked-radius UNMASKED_RADIUS] [--verbose]</span>
 <span class="go">                 [--rbr-selections [RBR_SELECTIONS ...]] [--eff EFF]</span>
 <span class="go">                 [--keep-temp-files KEEP_TEMP_FILES] [--script SCRIPT]</span>
+<span class="go">                 [--phenix-version PHENIX_VERSION]</span>
 </pre></div>
 </div>
 <dl class="std option">
@@ -207,6 +208,12 @@ <h2>matchmaps<a class="headerlink" href="#matchmaps" title="Link to this heading
 <dd><p>Name for a file {script}.sh which can be run to repeat this command. By default, this file is called <code class="xref py py-obj docutils literal notranslate"><span class="pre">run_matchmaps.sh</span></code>. Note that this file is written out in the current working directory, NOT the input or output directories</p>
 </dd></dl>
 
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-matchmaps-phenix-version">
+<span class="sig-name descname"><span class="pre">--phenix-version</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;phenix_version&gt;</span></span><a class="headerlink" href="#cmdoption-matchmaps-phenix-version" title="Link to this definition"></a></dt>
+<dd><p>Specify phenix version as a string, e.g. ‘1.20’. If omitted, matchmaps will attempt to automatically detect the version in use by analyzing the output of phenix.version</p>
+</dd></dl>
+
 </section>
 <section id="matchmaps-ncs">
 <h2>matchmaps.ncs<a class="headerlink" href="#matchmaps-ncs" title="Link to this heading"></a></h2>
@@ -217,6 +224,7 @@ <h2>matchmaps.ncs<a class="headerlink" href="#matchmaps-ncs" title="Link to this
 <span class="go">                     [--output-dir OUTPUT_DIR] [--no-bss] [--spacing SPACING]</span>
 <span class="go">                     [--dmin DMIN] [--verbose] [--eff EFF]</span>
 <span class="go">                     [--keep-temp-files KEEP_TEMP_FILES] [--script SCRIPT]</span>
+<span class="go">                     [--phenix-version PHENIX_VERSION]</span>
 </pre></div>
 </div>
 <dl class="std option">
@@ -315,6 +323,12 @@ <h2>matchmaps.ncs<a class="headerlink" href="#matchmaps-ncs" title="Link to this
 <dd><p>Name for a file {script}.sh which can be run to repeat this command. By default, this file is called <code class="xref py py-obj docutils literal notranslate"><span class="pre">run_matchmaps.sh</span></code>. Note that this file is written out in the current working directory, NOT the input or output directories</p>
 </dd></dl>
 
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-matchmaps.ncs-phenix-version">
+<span class="sig-name descname"><span class="pre">--phenix-version</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;phenix_version&gt;</span></span><a class="headerlink" href="#cmdoption-matchmaps.ncs-phenix-version" title="Link to this definition"></a></dt>
+<dd><p>Specify phenix version as a string, e.g. ‘1.20’. If omitted, matchmaps will attempt to automatically detect the version in use by analyzing the output of phenix.version</p>
+</dd></dl>
+
 </section>
 <section id="matchmaps-mr">
 <h2>matchmaps.mr<a class="headerlink" href="#matchmaps-mr" title="Link to this heading"></a></h2>
@@ -327,6 +341,7 @@ <h2>matchmaps.mr<a class="headerlink" href="#matchmaps-mr" title="Link to this h
 <span class="go">                    [--alpha ALPHA] [--verbose]</span>
 <span class="go">                    [--rbr-selections [RBR_SELECTIONS ...]] [--eff EFF]</span>
 <span class="go">                    [--keep-temp-files KEEP_TEMP_FILES] [--script SCRIPT]</span>
+<span class="go">                    [--phenix-version PHENIX_VERSION]</span>
 </pre></div>
 </div>
 <dl class="std option">
@@ -437,6 +452,12 @@ <h2>matchmaps.mr<a class="headerlink" href="#matchmaps-mr" title="Link to this h
 <dd><p>Name for a file {script}.sh which can be run to repeat this command. By default, this file is called <code class="xref py py-obj docutils literal notranslate"><span class="pre">run_matchmaps.sh</span></code>. Note that this file is written out in the current working directory, NOT the input or output directories</p>
 </dd></dl>
 
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-matchmaps.mr-phenix-version">
+<span class="sig-name descname"><span class="pre">--phenix-version</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;phenix_version&gt;</span></span><a class="headerlink" href="#cmdoption-matchmaps.mr-phenix-version" title="Link to this definition"></a></dt>
+<dd><p>Specify phenix version as a string, e.g. ‘1.20’. If omitted, matchmaps will attempt to automatically detect the version in use by analyzing the output of phenix.version</p>
+</dd></dl>
+
 </section>
 </section>
 

genindex.html

@@ -16,7 +16,7 @@
 
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=701c80da"></script>
+        <script src="_static/documentation_options.js?v=e9dab49d"></script>
         <script src="_static/doctools.js?v=9a2dae69"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/js/theme.js"></script>
@@ -255,6 +255,19 @@ <h2 id="Symbols">Symbols</h2>
 </li>
       </ul></li>
       <li>
+    --phenix-version
+
+      <ul>
+        <li><a href="cli.html#cmdoption-matchmaps-phenix-version">matchmaps command line option</a>
+</li>
+        <li><a href="cli.html#cmdoption-matchmaps.mr-phenix-version">matchmaps.mr command line option</a>
+</li>
+        <li><a href="cli.html#cmdoption-matchmaps.ncs-phenix-version">matchmaps.ncs command line option</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li>
     --rbr-selections
 
       <ul>
@@ -263,8 +276,6 @@ <h2 id="Symbols">Symbols</h2>
         <li><a href="cli.html#cmdoption-matchmaps.mr-rbr-selections">matchmaps.mr command line option</a>
 </li>
       </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li>
     --script
 
@@ -466,6 +477,8 @@ <h2 id="M">M</h2>
         <li><a href="cli.html#cmdoption-matchmaps-output-dir">--output-dir</a>
 </li>
         <li><a href="cli.html#cmdoption-matchmaps-pdboff">--pdboff</a>
+</li>
+        <li><a href="cli.html#cmdoption-matchmaps-phenix-version">--phenix-version</a>
 </li>
         <li><a href="cli.html#cmdoption-matchmaps-rbr-selections">--rbr-selections</a>
 </li>
@@ -529,6 +542,8 @@ <h2 id="M">M</h2>
         <li><a href="cli.html#cmdoption-matchmaps.mr-output-dir">--output-dir</a>
 </li>
         <li><a href="cli.html#cmdoption-matchmaps.mr-pdboff">--pdboff</a>
+</li>
+        <li><a href="cli.html#cmdoption-matchmaps.mr-phenix-version">--phenix-version</a>
 </li>
         <li><a href="cli.html#cmdoption-matchmaps.mr-rbr-selections">--rbr-selections</a>
 </li>
@@ -594,6 +609,8 @@ <h2 id="M">M</h2>
         <li><a href="cli.html#cmdoption-matchmaps.ncs-pdb">--pdb</a>
 </li>
         <li><a href="cli.html#cmdoption-matchmaps.ncs-phases">--phases</a>
+</li>
+        <li><a href="cli.html#cmdoption-matchmaps.ncs-phenix-version">--phenix-version</a>
 </li>
         <li><a href="cli.html#cmdoption-matchmaps.ncs-script">--script</a>
 </li>

index.html

@@ -17,7 +17,7 @@
 
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=701c80da"></script>
+        <script src="_static/documentation_options.js?v=e9dab49d"></script>
         <script src="_static/doctools.js?v=9a2dae69"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
         <script>window.MathJax = {"options": {"processHtmlClass": "tex2jax_process|mathjax_process|math|output_area"}}</script>

quickstart.html

@@ -17,7 +17,7 @@
 
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=701c80da"></script>
+        <script src="_static/documentation_options.js?v=e9dab49d"></script>
         <script src="_static/doctools.js?v=9a2dae69"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/js/theme.js"></script>

search.html

@@ -17,7 +17,7 @@
 
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=701c80da"></script>
+        <script src="_static/documentation_options.js?v=e9dab49d"></script>
         <script src="_static/doctools.js?v=9a2dae69"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/js/theme.js"></script>

troubleshooting.html

@@ -17,7 +17,7 @@
 
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=701c80da"></script>
+        <script src="_static/documentation_options.js?v=e9dab49d"></script>
         <script src="_static/doctools.js?v=9a2dae69"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
         <script>window.MathJax = {"options": {"processHtmlClass": "tex2jax_process|mathjax_process|math|output_area"}}</script>

visualization.html

@@ -17,7 +17,7 @@
 
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=701c80da"></script>
+        <script src="_static/documentation_options.js?v=e9dab49d"></script>
         <script src="_static/doctools.js?v=9a2dae69"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/js/theme.js"></script>