deploy: 877eeb4

HTPolyNetPackage.html

@@ -4021,11 +4021,6 @@ <h1>HTPolyNet package<a class="headerlink" href="#htpolynet-package" title="Link
 <dd class="field-odd"><p><strong>Enum</strong> (<em>class</em>) – inherits from Enum class</p>
 </dd>
 </dl>
-<dl class="py attribute">
-<dt class="sig sig-object py" id="HTPolyNet.topocoord.BTRC.failed_bondcycle">
-<span class="sig-name descname"><span class="pre">failed_bondcycle</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">3</span></em><a class="headerlink" href="#HTPolyNet.topocoord.BTRC.failed_bondcycle" title="Link to this definition">¶</a></dt>
-<dd></dd></dl>
-
 <dl class="py attribute">
 <dt class="sig sig-object py" id="HTPolyNet.topocoord.BTRC.failed_pierced_ring">
 <span class="sig-name descname"><span class="pre">failed_pierced_ring</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">1</span></em><a class="headerlink" href="#HTPolyNet.topocoord.BTRC.failed_pierced_ring" title="Link to this definition">¶</a></dt>
@@ -4196,11 +4191,11 @@ <h1>HTPolyNet package<a class="headerlink" href="#htpolynet-package" title="Link
 <dt class="sig sig-object py" id="HTPolyNet.topocoord.TopoCoord.bondcycle_collective">
 <span class="sig-name descname"><span class="pre">bondcycle_collective</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">bdf</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">DataFrame</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/HTPolyNet/topocoord.html#TopoCoord.bondcycle_collective"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#HTPolyNet.topocoord.TopoCoord.bondcycle_collective" title="Link to this definition">¶</a></dt>
 <dd><p>bondcycle_collective Check to see if, when considered as a collective, this
-set of bondrecs leads to one or more cyclic bondchain; if so, longest bonds that
+set of bondrecs leads to one or more cyclic bondchains; if so, longest bonds that
 break bondcycles are removed from bondrecs list and resulting list is returned</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><p><strong>bdf</strong> (<em>pandas.DataFrame</em>) – bonds data frame</p>
+<dd class="field-odd"><p><strong>bdf</strong> (<em>pandas.DataFrame</em>) – bonds data frame, sorted in ascending order by bondlength</p>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>
 <dd class="field-even"><p>list of bond records that results in no new bondcycles</p>
@@ -4706,26 +4701,6 @@ <h1>HTPolyNet package<a class="headerlink" href="#htpolynet-package" title="Link
 </dl>
 </dd></dl>
 
-<dl class="py method">
-<dt class="sig sig-object py" id="HTPolyNet.topocoord.TopoCoord.makes_bondcycle">
-<span class="sig-name descname"><span class="pre">makes_bondcycle</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">aidx</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bidx</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/HTPolyNet/topocoord.html#TopoCoord.makes_bondcycle"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#HTPolyNet.topocoord.TopoCoord.makes_bondcycle" title="Link to this definition">¶</a></dt>
-<dd><p>makes_bondcycle checks the current ‘bondchain’ index lists to see if a bond between aidx and bidx (global atom indices) would generate a C-C’ bondcycle, which they do if they have the same ‘bondchain’ attribute, shorter than the minimum allowable bondcycle length, if this is not -1</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>aidx</strong> (<em>int</em>) – global index of an atom</p></li>
-<li><p><strong>bidx</strong> (<em>int</em>) – global index of another atom</p></li>
-</ul>
-</dd>
-<dt class="field-even">Returns<span class="colon">:</span></dt>
-<dd class="field-even"><p>True if a bond betwen aidx and bidx would form a C-C’ bondcycle</p>
-</dd>
-<dt class="field-odd">Return type<span class="colon">:</span></dt>
-<dd class="field-odd"><p>bool</p>
-</dd>
-</dl>
-</dd></dl>
-
 <dl class="py method">
 <dt class="sig sig-object py" id="HTPolyNet.topocoord.TopoCoord.makes_shortcircuit">
 <span class="sig-name descname"><span class="pre">makes_shortcircuit</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">i</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">j</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/HTPolyNet/topocoord.html#TopoCoord.makes_shortcircuit"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#HTPolyNet.topocoord.TopoCoord.makes_shortcircuit" title="Link to this definition">¶</a></dt>

_modules/HTPolyNet/molecule.html

@@ -167,7 +167,7 @@ <h1>Source code for HTPolyNet.molecule</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">bond_templates</span><span class="p">:</span><span class="n">BondTemplateList</span><span class="o">=</span><span class="p">[]</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">symmetry_relateds</span><span class="o">=</span><span class="p">[]</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">stereocenters</span><span class="o">=</span><span class="p">[]</span> <span class="c1"># list of atomnames</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">stereoisomers</span><span class="p">:</span><span class="nb">dict</span><span class="p">(</span><span class="nb">str</span><span class="p">,</span><span class="n">Molecule</span><span class="p">)</span><span class="o">=</span><span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">stereoisomers</span><span class="o">=</span><span class="p">{}</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">nconformers</span><span class="o">=</span><span class="mi">0</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">conformers_dict</span><span class="o">=</span><span class="p">{}</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">conformers</span><span class="o">=</span><span class="p">[]</span> <span class="c1"># just a list of gro file basenames</span>
@@ -1013,7 +1013,7 @@ <h1>Source code for HTPolyNet.molecule</h1><div class="highlight"><pre>
         <span class="n">overall_maximum</span><span class="o">=</span><span class="p">(</span><span class="o">-</span><span class="mf">1.e9</span><span class="p">,</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span>
         <span class="n">coord_trials</span><span class="o">=</span><span class="p">{}</span>
         <span class="k">for</span> <span class="n">myH</span><span class="p">,</span><span class="n">myHnm</span> <span class="ow">in</span> <span class="n">myHpartners</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>  <span class="c1"># keys are globalIdx&#39;s, values are names</span>
-            <span class="n">coord_trials</span><span class="p">[</span><span class="n">myH</span><span class="p">]:</span><span class="nb">dict</span><span class="p">[</span><span class="n">TopoCoord</span><span class="p">]</span><span class="o">=</span><span class="p">{}</span>
+            <span class="n">coord_trials</span><span class="p">[</span><span class="n">myH</span><span class="p">]</span><span class="o">=</span><span class="p">{}</span>
             <span class="n">Rh</span><span class="o">=</span><span class="n">TC</span><span class="o">.</span><span class="n">get_R</span><span class="p">(</span><span class="n">myH</span><span class="p">)</span>
             <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;  Rh </span><span class="si">{</span><span class="n">myH</span><span class="si">}</span><span class="s1"> </span><span class="si">{</span><span class="n">Rh</span><span class="si">}</span><span class="s1"> </span><span class="si">{</span><span class="n">Rh</span><span class="o">.</span><span class="n">dtype</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
             <span class="n">Rih</span><span class="o">=</span><span class="n">Ri</span><span class="o">-</span><span class="n">Rh</span>

_modules/HTPolyNet/software.html

@@ -42,7 +42,6 @@ <h1>Source code for HTPolyNet.software</h1><div class="highlight"><pre>
 <span class="kn">import</span> <span class="nn">logging</span>
 <span class="kn">import</span> <span class="nn">os</span>
 <span class="kn">from</span> <span class="nn">HTPolyNet.stringthings</span> <span class="kn">import</span> <span class="n">my_logger</span>
-<span class="c1"># from GPUtil import getGPUs</span>
 <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>
 
 <div class="viewcode-block" id="Software">