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Deployed 2619c61 to stable with MkDocs 1.5.0 and mike 1.1.2
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@hadim
hadim committed Jul 27, 2023
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8 changes: 4 additions & 4 deletions stable/404.html
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<link rel="icon" href="/images/logo-black.png">
<meta name="generator" content="mkdocs-1.4.3, mkdocs-material-9.1.16">
<meta name="generator" content="mkdocs-1.5.0, mkdocs-material-9.1.19">



<title>datamol</title>



<link rel="stylesheet" href="/assets/stylesheets/main.26e3688c.min.css">
<link rel="stylesheet" href="/assets/stylesheets/main.eebd395e.min.css">



Expand Down Expand Up @@ -937,10 +937,10 @@ <h1>404 - Not found</h1>
<div class="md-dialog__inner md-typeset"></div>
</div>

<script id="__config" type="application/json">{"base": "/", "features": ["navigation.tabs", "navigation.expand"], "search": "/assets/javascripts/workers/search.208ed371.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": {"provider": "mike"}}</script>
<script id="__config" type="application/json">{"base": "/", "features": ["navigation.tabs", "navigation.expand"], "search": "/assets/javascripts/workers/search.74e28a9f.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": {"provider": "mike"}}</script>


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43 changes: 27 additions & 16 deletions stable/api/datamol.align.html
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<link rel="next" href="datamol.cluster.html">

<link rel="icon" href="../images/logo-black.png">
<meta name="generator" content="mkdocs-1.4.3, mkdocs-material-9.1.16">
<meta name="generator" content="mkdocs-1.5.0, mkdocs-material-9.1.19">



<title>datamol.align - datamol</title>



<link rel="stylesheet" href="../assets/stylesheets/main.26e3688c.min.css">
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Expand Down Expand Up @@ -1038,6 +1038,7 @@ <h1 id="datamolalign"><code>datamol.align</code><a class="headerlink" href="#dat




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


Expand All @@ -1059,6 +1060,8 @@ <h3 id="datamol.align.auto_align_many" class="doc doc-heading">
<li><code>dm.auto_align_many.core</code>: the smiles/smarts of the core of the cluster.</li>
</ul>



<p><strong>Parameters:</strong></p>
<table>
<thead>
Expand Down Expand Up @@ -1170,9 +1173,9 @@ <h3 id="datamol.align.auto_align_many" class="doc doc-heading">
</tbody>
</table>

<details class="quote">
<summary>Source code in <code>datamol/align.py</code></summary>
<div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">128</span>
<details class="quote">
<summary>Source code in <code>datamol/align.py</code></summary>
<div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">128</span>
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Expand Down Expand Up @@ -1426,11 +1429,12 @@ <h3 id="datamol.align.auto_align_many" class="doc doc-heading">

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

</div>


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


Expand All @@ -1445,6 +1449,8 @@ <h3 id="datamol.align.compute_2d_coords" class="doc doc-heading">

<p>Compute 2D coordinates for a molecule.</p>



<p><strong>Parameters:</strong></p>
<table>
<thead>
Expand Down Expand Up @@ -1487,9 +1493,9 @@ <h3 id="datamol.align.compute_2d_coords" class="doc doc-heading">
</tbody>
</table>

<details class="quote">
<summary>Source code in <code>datamol/align.py</code></summary>
<div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">20</span>
<details class="quote">
<summary>Source code in <code>datamol/align.py</code></summary>
<div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">20</span>
<span class="normal">21</span>
<span class="normal">22</span>
<span class="normal">23</span>
Expand Down Expand Up @@ -1517,11 +1523,12 @@ <h3 id="datamol.align.compute_2d_coords" class="doc doc-heading">

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

</div>


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


Expand All @@ -1537,6 +1544,8 @@ <h3 id="datamol.align.template_align" class="doc doc-heading">
<p>Align an input molecule to a template. If the template is not provided then the input molecule is
returned.</p>



<p><strong>Parameters:</strong></p>
<table>
<thead>
Expand Down Expand Up @@ -1638,6 +1647,8 @@ <h3 id="datamol.align.template_align" class="doc doc-heading">
</tbody>
</table>



<p><strong>Returns:</strong></p>
<table>
<thead>
Expand All @@ -1660,9 +1671,9 @@ <h3 id="datamol.align.template_align" class="doc doc-heading">
</tbody>
</table>

<details class="quote">
<summary>Source code in <code>datamol/align.py</code></summary>
<div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 36</span>
<details class="quote">
<summary>Source code in <code>datamol/align.py</code></summary>
<div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 36</span>
<span class="normal"> 37</span>
<span class="normal"> 38</span>
<span class="normal"> 39</span>
Expand Down Expand Up @@ -1842,7 +1853,7 @@ <h3 id="datamol.align.template_align" class="doc doc-heading">

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

</div>
Expand Down Expand Up @@ -1895,10 +1906,10 @@ <h3 id="datamol.align.template_align" class="doc doc-heading">
<div class="md-dialog__inner md-typeset"></div>
</div>

<script id="__config" type="application/json">{"base": "..", "features": ["navigation.tabs", "navigation.expand"], "search": "../assets/javascripts/workers/search.208ed371.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": {"provider": "mike"}}</script>
<script id="__config" type="application/json">{"base": "..", "features": ["navigation.tabs", "navigation.expand"], "search": "../assets/javascripts/workers/search.74e28a9f.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": {"provider": "mike"}}</script>


<script src="../assets/javascripts/bundle.a51614de.min.js"></script>
<script src="../assets/javascripts/bundle.220ee61c.min.js"></script>


<script src="../assets/js/google-analytics.js"></script>
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58 changes: 38 additions & 20 deletions stable/api/datamol.cluster.html
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<link rel="next" href="datamol.conformers.html">

<link rel="icon" href="../images/logo-black.png">
<meta name="generator" content="mkdocs-1.4.3, mkdocs-material-9.1.16">
<meta name="generator" content="mkdocs-1.5.0, mkdocs-material-9.1.19">



<title>datamol.cluster - datamol</title>



<link rel="stylesheet" href="../assets/stylesheets/main.26e3688c.min.css">
<link rel="stylesheet" href="../assets/stylesheets/main.eebd395e.min.css">



Expand Down Expand Up @@ -1052,6 +1052,7 @@ <h1 id="datamolcluster"><code>datamol.cluster</code><a class="headerlink" href="




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


Expand All @@ -1066,6 +1067,8 @@ <h3 id="datamol.cluster.assign_to_centroids" class="doc doc-heading">

<p>Assign molecules to centroids. Each molecule will be assigned to the closest centroid.</p>



<p><strong>Parameters:</strong></p>
<table>
<thead>
Expand Down Expand Up @@ -1155,6 +1158,8 @@ <h3 id="datamol.cluster.assign_to_centroids" class="doc doc-heading">
</tbody>
</table>



<p><strong>Returns:</strong></p>
<table>
<thead>
Expand Down Expand Up @@ -1188,9 +1193,9 @@ <h3 id="datamol.cluster.assign_to_centroids" class="doc doc-heading">
</tbody>
</table>

<details class="quote">
<summary>Source code in <code>datamol/cluster.py</code></summary>
<div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">211</span>
<details class="quote">
<summary>Source code in <code>datamol/cluster.py</code></summary>
<div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">211</span>
<span class="normal">212</span>
<span class="normal">213</span>
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Expand Down Expand Up @@ -1288,11 +1293,12 @@ <h3 id="datamol.cluster.assign_to_centroids" class="doc doc-heading">
<span class="n">clusters_list</span><span class="p">[</span><span class="n">cluster_ind</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">mols</span><span class="p">[</span><span class="n">ind</span><span class="p">])</span>
<span class="k">return</span> <span class="n">clusters_map</span><span class="p">,</span> <span class="n">clusters_list</span>
</code></pre></div></td></tr></table></div>
</details>
</details>
</div>

</div>


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


Expand All @@ -1307,6 +1313,8 @@ <h3 id="datamol.cluster.cluster_mols" class="doc doc-heading">

<p>Cluster a set of molecules using the butina clustering algorithm and a given threshold.</p>



<p><strong>Parameters:</strong></p>
<table>
<thead>
Expand Down Expand Up @@ -1380,9 +1388,9 @@ <h3 id="datamol.cluster.cluster_mols" class="doc doc-heading">
</tbody>
</table>

<details class="quote">
<summary>Source code in <code>datamol/cluster.py</code></summary>
<div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">31</span>
<details class="quote">
<summary>Source code in <code>datamol/cluster.py</code></summary>
<div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">31</span>
<span class="normal">32</span>
<span class="normal">33</span>
<span class="normal">34</span>
Expand Down Expand Up @@ -1462,11 +1470,12 @@ <h3 id="datamol.cluster.cluster_mols" class="doc doc-heading">

<span class="k">return</span> <span class="n">cluster_indices</span><span class="p">,</span> <span class="n">cluster_mols</span>
</code></pre></div></td></tr></table></div>
</details>
</details>
</div>

</div>


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


Expand All @@ -1481,6 +1490,8 @@ <h3 id="datamol.cluster.pick_centroids" class="doc doc-heading">

<p>Pick a set of <code>npick</code> centroids from a list of molecules.</p>



<p><strong>Parameters:</strong></p>
<table>
<thead>
Expand Down Expand Up @@ -1628,6 +1639,8 @@ <h3 id="datamol.cluster.pick_centroids" class="doc doc-heading">
</tbody>
</table>



<p><strong>Returns:</strong></p>
<table>
<thead>
Expand Down Expand Up @@ -1660,9 +1673,9 @@ <h3 id="datamol.cluster.pick_centroids" class="doc doc-heading">
</tbody>
</table>

<details class="quote">
<summary>Source code in <code>datamol/cluster.py</code></summary>
<div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">124</span>
<details class="quote">
<summary>Source code in <code>datamol/cluster.py</code></summary>
<div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">124</span>
<span class="normal">125</span>
<span class="normal">126</span>
<span class="normal">127</span>
Expand Down Expand Up @@ -1832,11 +1845,12 @@ <h3 id="datamol.cluster.pick_centroids" class="doc doc-heading">

<span class="k">return</span> <span class="n">picked_inds</span><span class="p">,</span> <span class="n">picked_mols</span>
</code></pre></div></td></tr></table></div>
</details>
</details>
</div>

</div>


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


Expand All @@ -1851,6 +1865,8 @@ <h3 id="datamol.cluster.pick_diverse" class="doc doc-heading">

<p>Pick a set of diverse molecules based on they fingerprint.</p>



<p><strong>Parameters:</strong></p>
<table>
<thead>
Expand Down Expand Up @@ -1969,6 +1985,8 @@ <h3 id="datamol.cluster.pick_diverse" class="doc doc-heading">
</tbody>
</table>



<p><strong>Returns:</strong></p>
<table>
<thead>
Expand Down Expand Up @@ -2001,9 +2019,9 @@ <h3 id="datamol.cluster.pick_diverse" class="doc doc-heading">
</tbody>
</table>

<details class="quote">
<summary>Source code in <code>datamol/cluster.py</code></summary>
<div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 73</span>
<details class="quote">
<summary>Source code in <code>datamol/cluster.py</code></summary>
<div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 73</span>
<span class="normal"> 74</span>
<span class="normal"> 75</span>
<span class="normal"> 76</span>
Expand Down Expand Up @@ -2101,7 +2119,7 @@ <h3 id="datamol.cluster.pick_diverse" class="doc doc-heading">

<span class="k">return</span> <span class="n">picked_inds</span><span class="p">,</span> <span class="n">picked_mols</span>
</code></pre></div></td></tr></table></div>
</details>
</details>
</div>

</div>
Expand Down Expand Up @@ -2154,10 +2172,10 @@ <h3 id="datamol.cluster.pick_diverse" class="doc doc-heading">
<div class="md-dialog__inner md-typeset"></div>
</div>

<script id="__config" type="application/json">{"base": "..", "features": ["navigation.tabs", "navigation.expand"], "search": "../assets/javascripts/workers/search.208ed371.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": {"provider": "mike"}}</script>
<script id="__config" type="application/json">{"base": "..", "features": ["navigation.tabs", "navigation.expand"], "search": "../assets/javascripts/workers/search.74e28a9f.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": {"provider": "mike"}}</script>


<script src="../assets/javascripts/bundle.a51614de.min.js"></script>
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<script src="../assets/js/google-analytics.js"></script>
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