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Deployed d17dfd3 to latest with MkDocs 1.6.1 and mike 2.1.3
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actions-user committed Feb 14, 2025
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203 changes: 167 additions & 36 deletions latest/api/config/index.html
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</span>
</a>

</li>

<li class="md-nav__item">
<a href="#ties.Config._guess_ligands_contain_q" class="md-nav__link">
<span class="md-ellipsis">
<code class="doc-symbol doc-symbol-toc doc-symbol-method"></code>&nbsp;_guess_ligands_contain_q
</span>
</a>

</li>

<li class="md-nav__item">
<a href="#ties.Config._get_first_ligand_net_q" class="md-nav__link">
<span class="md-ellipsis">
<code class="doc-symbol doc-symbol-toc doc-symbol-method"></code>&nbsp;_get_first_ligand_net_q
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</a>

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</span>
</a>

</li>

<li class="md-nav__item">
<a href="#ties.Config._guess_ligands_contain_q" class="md-nav__link">
<span class="md-ellipsis">
<code class="doc-symbol doc-symbol-toc doc-symbol-method"></code>&nbsp;_guess_ligands_contain_q
</span>
</a>

</li>

<li class="md-nav__item">
<a href="#ties.Config._get_first_ligand_net_q" class="md-nav__link">
<span class="md-ellipsis">
<code class="doc-symbol doc-symbol-toc doc-symbol-method"></code>&nbsp;_get_first_ligand_net_q
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Expand Down Expand Up @@ -3382,6 +3418,101 @@ <h2 id="ties.Config.lig_dir" class="doc doc-heading">
<div class="doc doc-object doc-function">


<h2 id="ties.Config._guess_ligands_contain_q" class="doc doc-heading">
<code class="doc-symbol doc-symbol-heading doc-symbol-method"></code> <span class="doc doc-object-name doc-function-name">_guess_ligands_contain_q</span>


</h2>
<div class="doc-signature highlight"><pre><span></span><code><span class="nf">_guess_ligands_contain_q</span><span class="p">()</span>
</code></pre></div>

<div class="doc doc-contents ">

<p>Checks if the first .mol2 file contains charges.
:return:</p>

<details class="quote">
<summary>Source code in <code>ties/config.py</code></summary>
<div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">456</span>
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<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Checks if the first .mol2 file contains charges.</span>
<span class="sd"> :return:</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="c1"># if all ligands are .mol2, then charges are provided</span>
<span class="k">if</span> <span class="nb">all</span><span class="p">(</span><span class="n">l</span><span class="o">.</span><span class="n">suffix</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;.mol2&#39;</span> <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">ligand_files</span><span class="p">):</span>
<span class="c1"># if all atoms have q = 0 that means they&#39;re a placeholder</span>
<span class="n">u</span> <span class="o">=</span> <span class="n">parmed</span><span class="o">.</span><span class="n">load_file</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ligand_files</span><span class="p">)[</span><span class="mi">0</span><span class="p">]),</span> <span class="n">structure</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">all_q_0</span> <span class="o">=</span> <span class="nb">all</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">charge</span> <span class="o">==</span> <span class="mi">0</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">u</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span>
<span class="k">if</span> <span class="n">all_q_0</span><span class="p">:</span>
<span class="k">return</span> <span class="kc">False</span>

<span class="k">return</span> <span class="kc">True</span>

<span class="k">return</span> <span class="kc">False</span>
</code></pre></div></td></tr></table></div>
</details>
</div>

</div>

<div class="doc doc-object doc-function">


<h2 id="ties.Config._get_first_ligand_net_q" class="doc doc-heading">
<code class="doc-symbol doc-symbol-heading doc-symbol-method"></code> <span class="doc doc-object-name doc-function-name">_get_first_ligand_net_q</span>


</h2>
<div class="doc-signature highlight"><pre><span></span><code><span class="nf">_get_first_ligand_net_q</span><span class="p">()</span>
</code></pre></div>

<div class="doc doc-contents ">

<p>:return: Returns the net charge from the parmed file with partial charges.</p>

<details class="quote">
<summary>Source code in <code>ties/config.py</code></summary>
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<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> :return: Returns the net charge from the parmed file with partial charges.</span>
<span class="sd"> &quot;&quot;&quot;</span>

<span class="c1"># if all atoms have q = 0 that means they&#39;re a placeholder</span>
<span class="n">u</span> <span class="o">=</span> <span class="n">parmed</span><span class="o">.</span><span class="n">load_file</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ligand_files</span><span class="p">)[</span><span class="mi">0</span><span class="p">]),</span> <span class="n">structure</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">net_q</span> <span class="o">=</span> <span class="nb">sum</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">charge</span> <span class="o">==</span> <span class="mi">0</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">u</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span>
<span class="k">return</span> <span class="n">net_q</span>
</code></pre></div></td></tr></table></div>
</details>
</div>

</div>

<div class="doc doc-object doc-function">


<h2 id="ties.Config.get_element_map" class="doc doc-heading">
<code class="doc-symbol doc-symbol-heading doc-symbol-method"></code> <span class="doc doc-object-name doc-function-name">get_element_map</span>

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<details class="quote">
<summary>Source code in <code>ties/config.py</code></summary>
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<span class="k">def</span><span class="w"> </span><span class="nf">get_element_map</span><span class="p">():</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>

Expand Down Expand Up @@ -3470,23 +3601,7 @@ <h2 id="ties.Config.get_serializable" class="doc doc-heading">

<details class="quote">
<summary>Source code in <code>ties/config.py</code></summary>
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<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Get a JSON serializable structure of the config.</span>

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