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AbramsGroup · Feb 4, 2024 · 4bcd9c6 · 4bcd9c6
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diff --git a/.buildinfo b/.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: fb7dab2f59a17d08813c9224e28dda3a
+config: 30babaf11b869ae8369a64cf303fb533
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/HTPolyNetPackage.html b/HTPolyNetPackage.html
diff --git a/_modules/HTPolyNet/ambertools.html b/_modules/HTPolyNet/ambertools.html
@@ -4,19 +4,20 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>HTPolyNet.ambertools &#8212; HTPolyNet 1.0.8 documentation</title>
-    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=4f649999" />
-    <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=039e1c02" />
-    <script src="../../_static/documentation_options.js?v=aec50437"></script>
+    <title>HTPolyNet.ambertools &#8212; HTPolyNet 1.0.9 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d1102ebc" />
+    <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=12dfc556" />
+    <script src="../../_static/documentation_options.js?v=0abd802e"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
 
   <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
 
+
+
 
-  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head><body>
 
@@ -177,11 +178,11 @@ <h3 id="searchlabel">Quick search</h3>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2023, Cameron Abrams, Ming Huang.
+      &#169;2024, Cameron Abrams, Ming Huang.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 7.2.6</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.13</a>
+      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 7.2.6</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
 
     </div>
 

diff --git a/_modules/HTPolyNet/analyze.html b/_modules/HTPolyNet/analyze.html
@@ -4,19 +4,20 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>HTPolyNet.analyze &#8212; HTPolyNet 1.0.8 documentation</title>
-    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=4f649999" />
-    <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=039e1c02" />
-    <script src="../../_static/documentation_options.js?v=aec50437"></script>
+    <title>HTPolyNet.analyze &#8212; HTPolyNet 1.0.9 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d1102ebc" />
+    <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=12dfc556" />
+    <script src="../../_static/documentation_options.js?v=0abd802e"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
 
   <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
 
+
+
 
-  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head><body>
 
@@ -365,11 +366,11 @@ <h3 id="searchlabel">Quick search</h3>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2023, Cameron Abrams, Ming Huang.
+      &#169;2024, Cameron Abrams, Ming Huang.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 7.2.6</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.13</a>
+      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 7.2.6</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
 
     </div>
 

diff --git a/_modules/HTPolyNet/banner.html b/_modules/HTPolyNet/banner.html
@@ -4,19 +4,20 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>HTPolyNet.banner &#8212; HTPolyNet 1.0.8 documentation</title>
-    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=4f649999" />
-    <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=039e1c02" />
-    <script src="../../_static/documentation_options.js?v=aec50437"></script>
+    <title>HTPolyNet.banner &#8212; HTPolyNet 1.0.9 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d1102ebc" />
+    <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=12dfc556" />
+    <script src="../../_static/documentation_options.js?v=0abd802e"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
 
   <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
 
+
+
 
-  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head><body>
 
@@ -116,11 +117,11 @@ <h3 id="searchlabel">Quick search</h3>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2023, Cameron Abrams, Ming Huang.
+      &#169;2024, Cameron Abrams, Ming Huang.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 7.2.6</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.13</a>
+      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 7.2.6</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
 
     </div>
 

diff --git a/_modules/HTPolyNet/bondlist.html b/_modules/HTPolyNet/bondlist.html
@@ -4,19 +4,20 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>HTPolyNet.bondlist &#8212; HTPolyNet 1.0.8 documentation</title>
-    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=4f649999" />
-    <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=039e1c02" />
-    <script src="../../_static/documentation_options.js?v=aec50437"></script>
+    <title>HTPolyNet.bondlist &#8212; HTPolyNet 1.0.9 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d1102ebc" />
+    <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=12dfc556" />
+    <script src="../../_static/documentation_options.js?v=0abd802e"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
 
   <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
 
+
+
 
-  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head><body>
 
@@ -317,11 +318,11 @@ <h3 id="searchlabel">Quick search</h3>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2023, Cameron Abrams, Ming Huang.
+      &#169;2024, Cameron Abrams, Ming Huang.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 7.2.6</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.13</a>
+      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 7.2.6</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
 
     </div>
 

diff --git a/_modules/HTPolyNet/bondtemplate.html b/_modules/HTPolyNet/bondtemplate.html
@@ -4,19 +4,20 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>HTPolyNet.bondtemplate &#8212; HTPolyNet 1.0.8 documentation</title>
-    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=4f649999" />
-    <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=039e1c02" />
-    <script src="../../_static/documentation_options.js?v=aec50437"></script>
+    <title>HTPolyNet.bondtemplate &#8212; HTPolyNet 1.0.9 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d1102ebc" />
+    <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=12dfc556" />
+    <script src="../../_static/documentation_options.js?v=0abd802e"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
 
   <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
 
+
+
 
-  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head><body>
 
@@ -206,11 +207,11 @@ <h3 id="searchlabel">Quick search</h3>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2023, Cameron Abrams, Ming Huang.
+      &#169;2024, Cameron Abrams, Ming Huang.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 7.2.6</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.13</a>
+      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 7.2.6</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
 
     </div>
 

diff --git a/_modules/HTPolyNet/checkpoint.html b/_modules/HTPolyNet/checkpoint.html
@@ -4,19 +4,20 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>HTPolyNet.checkpoint &#8212; HTPolyNet 1.0.8 documentation</title>
-    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=4f649999" />
-    <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=039e1c02" />
-    <script src="../../_static/documentation_options.js?v=aec50437"></script>
+    <title>HTPolyNet.checkpoint &#8212; HTPolyNet 1.0.9 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d1102ebc" />
+    <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=12dfc556" />
+    <script src="../../_static/documentation_options.js?v=0abd802e"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
 
   <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
 
+
+
 
-  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head><body>
 
@@ -183,11 +184,11 @@ <h3 id="searchlabel">Quick search</h3>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2023, Cameron Abrams, Ming Huang.
+      &#169;2024, Cameron Abrams, Ming Huang.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 7.2.6</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.13</a>
+      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 7.2.6</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
 
     </div>
 

diff --git a/_modules/HTPolyNet/command.html b/_modules/HTPolyNet/command.html
@@ -4,19 +4,20 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>HTPolyNet.command &#8212; HTPolyNet 1.0.8 documentation</title>
-    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=4f649999" />
-    <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=039e1c02" />
-    <script src="../../_static/documentation_options.js?v=aec50437"></script>
+    <title>HTPolyNet.command &#8212; HTPolyNet 1.0.9 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d1102ebc" />
+    <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=12dfc556" />
+    <script src="../../_static/documentation_options.js?v=0abd802e"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
 
   <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
 
+
+
 
-  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head><body>
 
@@ -128,11 +129,11 @@ <h3 id="searchlabel">Quick search</h3>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2023, Cameron Abrams, Ming Huang.
+      &#169;2024, Cameron Abrams, Ming Huang.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 7.2.6</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.13</a>
+      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 7.2.6</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
 
     </div>
 

diff --git a/_modules/HTPolyNet/configuration.html b/_modules/HTPolyNet/configuration.html
@@ -4,19 +4,20 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>HTPolyNet.configuration &#8212; HTPolyNet 1.0.8 documentation</title>
-    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=4f649999" />
-    <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=039e1c02" />
-    <script src="../../_static/documentation_options.js?v=aec50437"></script>
+    <title>HTPolyNet.configuration &#8212; HTPolyNet 1.0.9 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d1102ebc" />
+    <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=12dfc556" />
+    <script src="../../_static/documentation_options.js?v=0abd802e"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
 
   <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
 
+
+
 
-  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head><body>
 
@@ -335,11 +336,11 @@ <h3 id="searchlabel">Quick search</h3>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2023, Cameron Abrams, Ming Huang.
+      &#169;2024, Cameron Abrams, Ming Huang.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 7.2.6</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.13</a>
+      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 7.2.6</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
 
     </div>
 

diff --git a/_modules/HTPolyNet/coordinates.html b/_modules/HTPolyNet/coordinates.html
@@ -4,19 +4,20 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>HTPolyNet.coordinates &#8212; HTPolyNet 1.0.8 documentation</title>
-    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=4f649999" />
-    <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=039e1c02" />
-    <script src="../../_static/documentation_options.js?v=aec50437"></script>
+    <title>HTPolyNet.coordinates &#8212; HTPolyNet 1.0.9 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d1102ebc" />
+    <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=12dfc556" />
+    <script src="../../_static/documentation_options.js?v=0abd802e"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
 
   <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
 
+
+
 
-  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head><body>
 
@@ -53,15 +54,15 @@ <h1>Source code for HTPolyNet.coordinates</h1><div class="highlight"><pre>
 
 <span class="n">logger</span><span class="o">=</span><span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>
 
-<span class="n">GRX_ATTRIBUTES</span>     <span class="o">=</span><span class="p">[</span>  <span class="s1">&#39;z&#39;</span><span class="p">,</span><span class="s1">&#39;nreactions&#39;</span><span class="p">,</span><span class="s1">&#39;reactantName&#39;</span><span class="p">,</span><span class="s1">&#39;sea_idx&#39;</span><span class="p">,</span><span class="s1">&#39;chain&#39;</span><span class="p">,</span><span class="s1">&#39;chain_idx&#39;</span><span class="p">,</span><span class="s1">&#39;molecule&#39;</span><span class="p">,</span><span class="s1">&#39;molecule_name&#39;</span><span class="p">]</span>
+<span class="n">GRX_ATTRIBUTES</span>     <span class="o">=</span><span class="p">[</span>  <span class="s1">&#39;z&#39;</span><span class="p">,</span><span class="s1">&#39;nreactions&#39;</span><span class="p">,</span><span class="s1">&#39;reactantName&#39;</span><span class="p">,</span><span class="s1">&#39;sea_idx&#39;</span><span class="p">,</span><span class="s1">&#39;bondchain&#39;</span><span class="p">,</span><span class="s1">&#39;bondchain_idx&#39;</span><span class="p">,</span><span class="s1">&#39;molecule&#39;</span><span class="p">,</span><span class="s1">&#39;molecule_name&#39;</span><span class="p">]</span>
 <span class="sd">&quot;&quot;&quot;Extended atom attributes</span>
 
 <span class="sd">    - &#39;z&#39; number of sacrificial H&#39;s on atom </span>
 <span class="sd">    - &#39;nreactions&#39; number of H&#39;s sacrificed so far to form bonds</span>
 <span class="sd">    - &#39;reactantName&#39; name of most recent reactant to which atom belonged</span>
 <span class="sd">    - &#39;sea_idx&#39; index of the group of symmetry-related atoms this atom belongs to (atoms with the same sea_idx in the same resid are considered symmetry-equivalent)</span>
-<span class="sd">    - &#39;chain&#39; index of the unique chain this atom belongs to</span>
-<span class="sd">    - &#39;chain_idx&#39; index of this atom within this chain</span>
+<span class="sd">    - &#39;bondchain&#39; index of the unique bondchain this atom belongs to; a bondchain is a continuous linear chain of C-C bonds</span>
+<span class="sd">    - &#39;bondchain_idx&#39; index of this atom within this chain</span>
 <span class="sd">    - &#39;molecule&#39; index of the unique molecule this atom belongs to</span>
 <span class="sd">    - &#39;molecule_name&#39; name of that molecule</span>
 <span class="sd">&quot;&quot;&quot;</span>
@@ -1324,11 +1325,11 @@ <h3 id="searchlabel">Quick search</h3>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2023, Cameron Abrams, Ming Huang.
+      &#169;2024, Cameron Abrams, Ming Huang.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 7.2.6</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.13</a>
+      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 7.2.6</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
 
     </div>