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kfir4444 committed Jul 4, 2024
1 parent 8c188fd commit b877c30
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58 changes: 35 additions & 23 deletions _modules/arc/main.html
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9 changes: 6 additions & 3 deletions _modules/arc/reaction.html
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Expand Up @@ -394,9 +394,11 @@ <h1>Source code for arc.reaction</h1><div class="highlight"><pre>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">reaction_dict</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
<span class="n">reaction_dict</span><span class="p">[</span><span class="s1">&#39;label&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">label</span>
<span class="n">reaction_dict</span><span class="p">[</span><span class="s1">&#39;index&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">index</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">index</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">reaction_dict</span><span class="p">[</span><span class="s1">&#39;index&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">index</span>
<span class="n">reaction_dict</span><span class="p">[</span><span class="s1">&#39;multiplicity&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">multiplicity</span>
<span class="n">reaction_dict</span><span class="p">[</span><span class="s1">&#39;charge&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">charge</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">charge</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">reaction_dict</span><span class="p">[</span><span class="s1">&#39;charge&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">charge</span>
<span class="n">reaction_dict</span><span class="p">[</span><span class="s1">&#39;reactants&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">reactants</span>
<span class="n">reaction_dict</span><span class="p">[</span><span class="s1">&#39;products&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">products</span>
<span class="n">reaction_dict</span><span class="p">[</span><span class="s1">&#39;r_species&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">spc</span><span class="o">.</span><span class="n">as_dict</span><span class="p">(</span><span class="n">reset_atom_ids</span><span class="o">=</span><span class="n">reset_atom_ids</span><span class="p">)</span> <span class="k">for</span> <span class="n">spc</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">r_species</span><span class="p">]</span>
Expand All @@ -420,7 +422,8 @@ <h1>Source code for arc.reaction</h1><div class="highlight"><pre>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ts_xyz_guess</span><span class="p">):</span>
<span class="n">reaction_dict</span><span class="p">[</span><span class="s1">&#39;ts_xyz_guess&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ts_xyz_guess</span>
<span class="n">reaction_dict</span><span class="p">[</span><span class="s1">&#39;label&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">label</span>
<span class="n">reaction_dict</span><span class="p">[</span><span class="s1">&#39;ts_label&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ts_label</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">ts_label</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">reaction_dict</span><span class="p">[</span><span class="s1">&#39;ts_label&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ts_label</span>
<span class="k">return</span> <span class="n">reaction_dict</span></div>

<div class="viewcode-block" id="ARCReaction.from_dict"><a class="viewcode-back" href="../../api/reaction.html#arc.reaction.ARCReaction.from_dict">[docs]</a> <span class="k">def</span> <span class="nf">from_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
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