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<p>You can run this notebook online in a <a href="https://mybinder.org/v2/gh/MolSSI/QCArchiveInfrastructureWebsite/master?urlpath=lab/tree/basic_examples/QCPortal.ipynb" target="_blank">Binder</a>
session or view it <a class="reference external" href="https://github.com/MolSSI/QCArchiveInfrastructureWebsite/blob/master/basic_examples/QCPortal.ipynb">on Github</a>.</p>
<section id="QCPortal">
<h1>QCPortal<a class="headerlink" href="#QCPortal" title="Permalink to this headline"></a></h1>
<p>Full <a class="reference external" href="http://docs.qcarchive.molssi.org/projects/QCPortal">QCPortal documentation</a> is available.</p>
<p>QCPortal is a data viewer for a QCFractal server. QCPortal can be used with any QCFractal server including one that you build on your own, but for these examples we will use the MolSSI QCArchive server. To begin we first construct a client that points to a QCFractal server instance, here we explicitly add the <code class="docutils literal notranslate"><span class="pre">molssi.org</span></code> server.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[1]:
</pre></div>
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<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="kn">import</span> <span class="nn">qcportal</span> <span class="k">as</span> <span class="nn">ptl</span>
<span class="n">client</span> <span class="o">=</span> <span class="n">ptl</span><span class="o">.</span><span class="n">FractalClient</span><span class="p">(</span><span class="s2">"api.qcarchive.molssi.org"</span><span class="p">)</span>
<span class="n">client</span>
</pre></div>
</div>
</div>
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<h3>FractalClient</h3>
<ul>
<li><b>Server: </b>The MolSSI QCArchive Server</li>
<li><b>Address: </b>https://api.qcarchive.molssi.org/</li>
<li><b>Username: </b>None</li>
</ul></div>
</div>
<section id="Finding-Collections">
<h2>Finding Collections<a class="headerlink" href="#Finding-Collections" title="Permalink to this headline"></a></h2>
<p>One of the main ways to explore the QCArchive is to examine <code class="docutils literal notranslate"><span class="pre">Collection</span></code>s which are structures that allow easy manipulation of data in preset ways. Several example of <code class="docutils literal notranslate"><span class="pre">Collection</span></code>s contained within the QCArchive are as follows:</p>
<ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">Dataset</span></code> - A dataset where each record is a single molecule and many methods can be applied to each record.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">ReactionDataset</span></code> - A dataset where each record is a combinations of molecule (e.g. interaction and reaction energies) and many methods can be applied to each record.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">OpenFFWorkflow</span></code> - A workflow collection for torsiondrives and contstrained optimization developed with the <a class="reference external" href="https://openforcefield.org">Open Force Field Iniative</a>.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">TorsionDriveDataset</span></code> - A datas set which organizes many molecular torsion scans together for data exploration, analysis, and methodology comparison (see the TorsionDrive Dataset example for more details).</p></li>
</ul>
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</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">client</span><span class="o">.</span><span class="n">list_collections</span><span class="p">()</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[2]:
</pre></div>
</div>
<div class="output_area rendered_html docutils container">
<div>
<style scoped>
.dataframe tbody tr th:only-of-type {
vertical-align: middle;
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.dataframe tbody tr th {
vertical-align: top;
}
.dataframe thead th {
text-align: right;
}
</style>
<table border="1" class="dataframe">
<thead>
<tr style="text-align: right;">
<th></th>
<th></th>
<th>tagline</th>
</tr>
<tr>
<th>collection</th>
<th>name</th>
<th></th>
</tr>
</thead>
<tbody>
<tr>
<th rowspan="5" valign="top">Dataset</th>
<th>OpenFF Discrepancy Benchmark 1</th>
<td>None</td>
</tr>
<tr>
<th>OpenFF NCI250K Boron 1</th>
<td>None</td>
</tr>
<tr>
<th>OpenFF Optimization Set 1</th>
<td>None</td>
</tr>
<tr>
<th>OpenFF VEHICLe Set 1</th>
<td>None</td>
</tr>
<tr>
<th>SMIRNOFF Coverage Set 1</th>
<td>None</td>
</tr>
</tbody>
</table>
</div></div>
</div>
<p>Specific <code class="docutils literal notranslate"><span class="pre">Collection</span></code> types can be queried to limit the amount of collections to browse through:</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[4]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">client</span><span class="o">.</span><span class="n">list_collections</span><span class="p">(</span><span class="s2">"ReactionDataset"</span><span class="p">)</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[4]:
</pre></div>
</div>
<div class="output_area rendered_html docutils container">
<div>
<style scoped>
.dataframe tbody tr th:only-of-type {
vertical-align: middle;
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.dataframe tbody tr th {
vertical-align: top;
}
.dataframe thead th {
text-align: right;
}
</style>
<table border="1" class="dataframe">
<thead>
<tr style="text-align: right;">
<th></th>
<th></th>
<th>tagline</th>
</tr>
<tr>
<th>collection</th>
<th>name</th>
<th></th>
</tr>
</thead>
<tbody>
<tr>
<th rowspan="5" valign="top">ReactionDataset</th>
<th>A21</th>
<td>Equilibrium complexes from A24 database of sma...</td>
</tr>
<tr>
<th>A24</th>
<td>Interaction energies for small bimolecular com...</td>
</tr>
<tr>
<th>ACONF</th>
<td>Conformation energies for alkanes</td>
</tr>
<tr>
<th>AlkBind12</th>
<td>Binding energies of saturated and unsaturated ...</td>
</tr>
<tr>
<th>AlkIsod14</th>
<td>Isodesmic reaction energies for alkanes N=3--8</td>
</tr>
</tbody>
</table>
</div></div>
</div>
</section>
<section id="Exploring-Collections">
<h2>Exploring Collections<a class="headerlink" href="#Exploring-Collections" title="Permalink to this headline"></a></h2>
<p>Collections can be obtained by pulling their data from the centeral server. A collection is primarily metadata and extremely large collections can be pulled in a few seconds. For this example we will explore S22 dataset which is a small interaction energy dataset of 22 common dimers such as the water dimer, methane dimer, and more. To obtain this collection:</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[5]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">ds</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">get_collection</span><span class="p">(</span><span class="s2">"ReactionDataset"</span><span class="p">,</span> <span class="s2">"S22"</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">ds</span><span class="p">)</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt empty docutils container">
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
ReactionDataset(name=`S22`, id='1', client='https://api.qcarchive.molssi.org/')
</pre></div></div>
</div>
</section>
<section id="Stastistics-and-Visualization">
<h2>Stastistics and Visualization<a class="headerlink" href="#Stastistics-and-Visualization" title="Permalink to this headline"></a></h2>
<p>Visual statics and plotting can be generated by the <code class="docutils literal notranslate"><span class="pre">visualize</span></code> command:</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[6]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">ds</span><span class="o">.</span><span class="n">visualize</span><span class="p">(</span><span class="n">method</span><span class="o">=</span><span class="s2">"B2PLYP"</span><span class="p">,</span> <span class="n">basis</span><span class="o">=</span><span class="p">[</span><span class="s2">"def2-svp"</span><span class="p">,</span> <span class="s2">"def2-tzvp"</span><span class="p">],</span> <span class="n">bench</span><span class="o">=</span><span class="s2">"S220"</span><span class="p">,</span> <span class="n">kind</span><span class="o">=</span><span class="s2">"violin"</span><span class="p">)</span>
</pre></div>
</div>
</div>
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<section id="Conclusion">
<h2>Conclusion<a class="headerlink" href="#Conclusion" title="Permalink to this headline"></a></h2>
<p>These are just some of the capabilities QCPortal offers; check out <a class="reference external" href="https://qcarchive.molssi.org/examples/">more examples</a> and the <a class="reference external" href="http://docs.qcarchive.molssi.org/projects/QCPortal">QCPortal documentation</a>. If you like the project, consider starring us on <a class="reference external" href="https://github.com/MolSSI/QCFractal">GitHub</a> or if you have any questions, join our
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