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<h3><a href="index.html">Table Of Contents</a></h3>
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<li class="toctree-l1 current"><a class="current reference internal" href="">An overview of the RDKit</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#what-is-it">What is it?</a></li>
<li class="toctree-l2"><a class="reference internal" href="#functionality-overview">Functionality overview</a></li>
<li class="toctree-l2"><a class="reference internal" href="#the-contrib-directory">The Contrib Directory</a></li>
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<div class="section" id="an-overview-of-the-rdkit">
<h1>An overview of the RDKit<a class="headerlink" href="#an-overview-of-the-rdkit" title="Permalink to this headline">¶</a></h1>
<div class="section" id="what-is-it">
<h2>What is it?<a class="headerlink" href="#what-is-it" title="Permalink to this headline">¶</a></h2>
<ul>
<li><p class="first">Open source toolkit for cheminformatics</p>
<ul class="simple">
<li>BSD licensed</li>
<li>Core data structures and algorithms in C++</li>
<li>Python (2.x) wrapper generated using Boost.Python</li>
<li>Java and C# wrappers generated with SWIG</li>
<li>2D and 3D molecular operations</li>
<li>Descriptor generation for machine learning</li>
<li>Molecular database cartridge for PostgreSQL</li>
<li>Cheminformatics nodes for KNIME (distributed from the KNIME community site: <a class="reference external" href="http://tech.knime.org/community/rdkit">http://tech.knime.org/community/rdkit</a>)</li>
</ul>
</li>
<li><p class="first">Operational:</p>
<ul>
<li><p class="first"><a class="reference external" href="http://www.rdkit.org">http://www.rdkit.org</a></p>
</li>
<li><p class="first">Supports Mac/Windows/Linux</p>
</li>
<li><p class="first">Releases every 6 months</p>
</li>
<li><p class="first">Web presence:</p>
<ul>
<li><p class="first">Homepage: <a class="reference external" href="http://www.rdkit.org">http://www.rdkit.org</a></p>
<p>Documentation, links</p>
</li>
<li><p class="first">Github (<a class="reference external" href="https://github.com/rdkit">https://github.com/rdkit</a>)</p>
<p>Bug tracker, git repository</p>
</li>
<li><p class="first">Sourceforge (<a class="reference external" href="http://sourceforge.net/projects/rdkit">http://sourceforge.net/projects/rdkit</a>)</p>
<p>Mailing lists, Downloads</p>
</li>
<li><p class="first">Google code (<a class="reference external" href="http://code.google.com/p/rdkit/">http://code.google.com/p/rdkit/</a>)</p>
<p>wiki</p>
</li>
</ul>
</li>
<li><dl class="first docutils">
<dt>Mailing lists at <a class="reference external" href="https://sourceforge.net/p/rdkit/mailman/">https://sourceforge.net/p/rdkit/mailman/</a>, searchable archives available for</dt>
<dd><p class="first last"><a class="reference external" href="http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/">rdkit-discuss</a> and
<a class="reference external" href="http://www.mail-archive.com/rdkit-devel@lists.sourceforge.net/">rdkit-devel</a></p>
</dd>
</dl>
</li>
</ul>
</li>
<li><p class="first">History:</p>
<ul class="simple">
<li>2000-2006: Developed and used at Rational Discovery for building predictive models for ADME, Tox, biological activity</li>
<li>June 2006: Open-source (BSD license) release of software, Rational Discovery shuts down</li>
<li>to present: Open-source development continues, use within Novartis, contributions from Novartis back to open-source version</li>
</ul>
</li>
</ul>
</div>
<div class="section" id="functionality-overview">
<h2>Functionality overview<a class="headerlink" href="#functionality-overview" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li>Input/Output: SMILES/SMARTS, SDF, TDT, SLN <a class="footnote-reference" href="#id11" id="id1">[1]</a>, Corina mol2 <a class="footnote-reference" href="#id11" id="id2">[1]</a>, PDB</li>
<li>“Cheminformatics”:<ul>
<li>Substructure searching</li>
<li>Canonical SMILES</li>
<li>Chirality support (i.e. R/S or E/Z labeling)</li>
<li>Chemical transformations (e.g. remove matching substructures)</li>
<li>Chemical reactions</li>
<li>Molecular serialization (e.g. mol <-> text)</li>
</ul>
</li>
<li>2D depiction, including constrained depiction</li>
<li>2D->3D conversion/conformational analysis via distance geometry</li>
<li>UFF and MMFF94/MMFF94S implementations for cleaning up structures</li>
<li>Fingerprinting: Daylight-like, atom pairs, topological torsions, Morgan algorithm, “MACCS keys”, etc.</li>
<li>Similarity/diversity picking</li>
<li>2D pharmacophores <a class="footnote-reference" href="#id11" id="id3">[1]</a></li>
<li>Gasteiger-Marsili charges</li>
<li>Hierarchical subgraph/fragment analysis</li>
<li>Bemis and Murcko scaffold determination</li>
<li>RECAP and BRICS implementations</li>
<li>Multi-molecule maximum common substructure <a class="footnote-reference" href="#id12" id="id4">[2]</a></li>
<li>Feature maps</li>
<li>Shape-based similarity</li>
<li>RMSD-based molecule-molecule alignment</li>
<li>Shape-based alignment (subshape alignment <a class="footnote-reference" href="#id13" id="id5">[3]</a>) <a class="footnote-reference" href="#id11" id="id6">[1]</a></li>
<li>Unsupervised molecule-molecule alignment using Open3DAlign algorithm <a class="footnote-reference" href="#id14" id="id7">[4]</a></li>
<li>Integration with PyMOL for 3D visualization</li>
<li>Functional group filtering</li>
<li>Salt stripping</li>
<li>Molecular descriptor library:<ul>
<li>Topological (κ3, Balaban J, etc.)</li>
<li>Compositional (Number of Rings, Number of Aromatic Heterocycles, etc.)</li>
<li>Electrotopological state (Estate)</li>
<li>clogP, MR (Wildman and Crippen approach)</li>
<li>“MOE like” VSA descriptors</li>
<li>Feature-map vectors <a class="footnote-reference" href="#id15" id="id8">[5]</a></li>
<li>MQN <a class="footnote-reference" href="#id16" id="id9">[6]</a></li>
</ul>
</li>
<li>Similarity Maps <a class="footnote-reference" href="#id17" id="id10">[7]</a></li>
<li>Machine Learning:<ul>
<li>Clustering (hierarchical, Butina)</li>
<li>Information theory (Shannon entropy, information gain, etc.)</li>
</ul>
</li>
<li>Tight integration with the <a class="reference external" href="http://ipython.org">IPython</a> notebook and qtconsole.</li>
</ul>
<table class="docutils footnote" frame="void" id="id11" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
<tr><td class="label">[1]</td><td><em>(<a class="fn-backref" href="#id1">1</a>, <a class="fn-backref" href="#id2">2</a>, <a class="fn-backref" href="#id3">3</a>, <a class="fn-backref" href="#id6">4</a>)</em> These implementations are functional but are not necessarily the best, fastest, or most complete.</td></tr>
</tbody>
</table>
<table class="docutils footnote" frame="void" id="id12" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
<tr><td class="label"><a class="fn-backref" href="#id4">[2]</a></td><td>Contribution from Andrew Dalke</td></tr>
</tbody>
</table>
<table class="docutils footnote" frame="void" id="id13" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
<tr><td class="label"><a class="fn-backref" href="#id5">[3]</a></td><td>Putta, S., Eksterowicz, J., Lemmen, C. & Stanton, R. “A Novel Subshape Molecular Descriptor” <em>Journal of Chemical Information and Computer Sciences</em> <strong>43:1623–35</strong> (2003).</td></tr>
</tbody>
</table>
<table class="docutils footnote" frame="void" id="id14" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
<tr><td class="label"><a class="fn-backref" href="#id7">[4]</a></td><td>Tosco, P., Balle, T. & Shiri, F. Open3DALIGN: an open-source software aimed at unsupervised ligand alignment. <em>J Comput Aided Mol Des</em> <strong>25:777–83</strong> (2011).</td></tr>
</tbody>
</table>
<table class="docutils footnote" frame="void" id="id15" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
<tr><td class="label"><a class="fn-backref" href="#id8">[5]</a></td><td>Landrum, G., Penzotti, J. & Putta, S. “Feature-map vectors: a new class of informative descriptors for computational drug discovery” <em>Journal of Computer-Aided Molecular Design</em> <strong>20:751–62</strong> (2006).</td></tr>
</tbody>
</table>
<table class="docutils footnote" frame="void" id="id16" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
<tr><td class="label"><a class="fn-backref" href="#id9">[6]</a></td><td>Nguyen, K. T., Blum, L. C., van Deursen, R. & Reymond, J.-L. Classification of Organic Molecules by Molecular Quantum Numbers. <em>ChemMedChem</em> <strong>4:1803–5</strong> (2009).</td></tr>
</tbody>
</table>
<table class="docutils footnote" frame="void" id="id17" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
<tr><td class="label"><a class="fn-backref" href="#id10">[7]</a></td><td>Riniker, S. & Landrum, G. A. Similarity maps - a visualization strategy for molecular fingerprints and machine-learning methods. <em>Journal of Cheminformatics</em> <strong>5:43</strong> (2013).</td></tr>
</tbody>
</table>
</div>
<div class="section" id="the-contrib-directory">
<h2>The Contrib Directory<a class="headerlink" href="#the-contrib-directory" title="Permalink to this headline">¶</a></h2>
<p>The Contrib directory, part of the standard RDKit distribution, includes code that has been contributed by members of the community.</p>
<ul>
<li><p class="first"><strong>LEF</strong>: Local Environment Fingerprints</p>
<p>Contains python source code from the publications:</p>
<ul class="simple">
<li><ol class="first upperalpha">
<li>Vulpetti, U. Hommel, G. Landrum, R. Lewis and C. Dalvit, “Design and NMR-based screening of LEF, a library of chemical fragments with different Local Environment of Fluorine” <em>J. Am. Chem. Soc.</em> <strong>131</strong> (2009) 12949-12959. <a class="reference external" href="http://dx.doi.org/10.1021/ja905207t">http://dx.doi.org/10.1021/ja905207t</a></li>
</ol>
</li>
<li><ol class="first upperalpha">
<li>Vulpetti, G. Landrum, S. Ruedisser, P. Erbel and C. Dalvit, “19F NMR Chemical Shift Prediction with Fluorine Fingerprint Descriptor” <em>J. of Fluorine Chemistry</em> <strong>131</strong> (2010) 570-577. <a class="reference external" href="http://dx.doi.org/10.1016/j.jfluchem.2009.12.024">http://dx.doi.org/10.1016/j.jfluchem.2009.12.024</a></li>
</ol>
</li>
</ul>
<p>Contribution from Anna Vulpetti</p>
</li>
<li><p class="first"><strong>M_Kossner</strong>:</p>
<p>Contains a set of pharmacophoric feature definitions as well as code for finding molecular frameworks.</p>
<p>Contribution from Markus Kossner</p>
</li>
<li><p class="first"><strong>PBF</strong>: Plane of best fit</p>
<p>Contains C++ source code and sample data from the publication:</p>
<ol class="upperalpha simple" start="14">
<li><ol class="first upperalpha" start="3">
<li>Firth, N. Brown, and J. Blagg, “Plane of Best Fit: A Novel Method to Characterize the Three-Dimensionality of Molecules” <em>Journal of Chemical Information and Modeling</em> <strong>52</strong> 2516-2525 (2012). <a class="reference external" href="http://pubs.acs.org/doi/abs/10.1021/ci300293f">http://pubs.acs.org/doi/abs/10.1021/ci300293f</a></li>
</ol>
</li>
</ol>
<p>Contribution from Nicholas Firth</p>
</li>
<li><p class="first"><strong>mmpa</strong>: Matched molecular pairs</p>
<p>Python source and sample data for an implementation of the matched-molecular pair algorithm described in the publication:</p>
<p>Hussain, J., & Rea, C. “Computationally efficient algorithm to identify matched molecular pairs (MMPs) in large data sets.” <em>Journal of chemical information and modeling</em> <strong>50</strong> 339-348 (2010). <a class="reference external" href="http://dx.doi.org/10.1021/ci900450m">http://dx.doi.org/10.1021/ci900450m</a></p>
<p>Includes a fragment indexing algorithm from the publication:</p>
<p>Wagener, M., & Lommerse, J. P. “The quest for bioisosteric replacements.” <em>Journal of chemical information and modeling</em> <strong>46</strong> 677-685 (2006).</p>
<p>Contribution from Jameed Hussain.</p>
</li>
<li><p class="first"><strong>SA_Score</strong>: Synthetic assessibility score</p>
<p>Python source for an implementation of the SA score algorithm described in the publication:</p>
<p>Ertl, P. and Schuffenhauer A. “Estimation of Synthetic Accessibility Score of Drug-like Molecules based on Molecular Complexity and Fragment Contributions” <em>Journal of Cheminformatics</em> <strong>1:8</strong> (2009)</p>
<p>Contribution from Peter Ertl</p>
</li>
<li><p class="first"><strong>fraggle</strong>: A fragment-based molecular similarity algorithm</p>
<p>Python source for an implementation of the fraggle similarity algorithm developed at GSK and described in this RDKit UGM presentation:
<a class="reference external" href="https://github.com/rdkit/UGM_2013/blob/master/Presentations/Hussain.Fraggle.pdf">https://github.com/rdkit/UGM_2013/blob/master/Presentations/Hussain.Fraggle.pdf</a></p>
<p>Contribution from Jameed Hussain</p>
</li>
</ul>
</div>
<div class="section" id="license">
<h2>License<a class="headerlink" href="#license" title="Permalink to this headline">¶</a></h2>
<p>This document is copyright (C) 2013-2014 by Greg Landrum</p>
<p>This work is licensed under the Creative Commons Attribution-ShareAlike 3.0 License.
To view a copy of this license, visit <a class="reference external" href="http://creativecommons.org/licenses/by-sa/3.0/">http://creativecommons.org/licenses/by-sa/3.0/</a> or send a letter to Creative Commons, 543 Howard Street, 5th Floor, San Francisco, California, 94105, USA.</p>
<p>The intent of this license is similar to that of the RDKit itself.
In simple words: “Do whatever you want with it, but please give us some credit.”</p>
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