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<html>
<head>
<title>RDPython</title>
<link rel="stylesheet" type="text/css" href="RD.css">
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<body bgcolor="#ffffff">
<p><i><a href="index.html">Table of Contents</a></i></p>
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width="10%"><font color="#000000">RDPython</font>
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<th align="right"><font color="#000000">&nbsp;</font></th>
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<a name="Modules">Modules</a>&nbsp;
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<font color="#000000">&nbsp;</font>
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<h4>Python/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/ClientForm.py.html">ClientForm</a></td><td valign="top" align="left">
HTML form handling for web clients.
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Geometry.html">__init__</a></td><td valign="top" align="left">
A module for Geometry stuff
</td></tr>
<tr><td valign="top" align="left"><a href="Python/RDBuild.py.html">RDBuild</a></td><td valign="top" align="left">
variables and definitions for distutils builds
</td></tr>
<tr><td valign="top" align="left"><a href="Python/RDConfig.py.html">RDConfig</a></td><td valign="top" align="left">
Configuration for Rational Discovery's Python code
</td></tr>
<tr><td valign="top" align="left"><a href="Python/RDLogger.py.html">RDLogger</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/RDRandom.py.html">RDRandom</a></td><td valign="top" align="left">
making random numbers consistent so we get good regressions
</td></tr>
<tr><td valign="top" align="left"><a href="Python/TestRunner.py.html">TestRunner</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/Chem/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/Chem/AllChem.py.html">AllChem</a></td><td valign="top" align="left">
Import all RDKit chemistry modules
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/AvailDescriptors.py.html">AvailDescriptors</a></td><td valign="top" align="left">
constructs the list of available descriptors
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/BuildFragmentCatalog.py.html">BuildFragmentCatalog</a></td><td valign="top" align="left">
command line utility for working with FragmentCatalogs (CASE-type analysis)
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/CDXMLWriter.py.html">CDXMLWriter</a></td><td valign="top" align="left">
Dumping CDXML from python
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/ChemicalFeatures.py.html">ChemicalFeatures</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/ChemicalForceFields.py.html">ChemicalForceFields</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Crippen.py.html">Crippen</a></td><td valign="top" align="left">
Atom-based calculation of LogP and MR using Crippen's approach
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/DSViewer.py.html">DSViewer</a></td><td valign="top" align="left">
uses DSViewer to interact with molecules
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Descriptors.py.html">Descriptors</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/FeatFinderCLI.py.html">FeatFinderCLI</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/FragmentCatalog.py.html">FragmentCatalog</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/FragmentMatcher.py.html">FragmentMatcher</a></td><td valign="top" align="left">
exposes a class for matching fragments of molecules.
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Fragments.py.html">Fragments</a></td><td valign="top" align="left">
functions to match a bunch of fragment descriptors from a file
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/GraphDescriptors.py.html">GraphDescriptors</a></td><td valign="top" align="left">
Calculation of topological/topochemical descriptors.
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Graphs.py.html">Graphs</a></td><td valign="top" align="left">
Python functions for manipulating molecular graphs
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Lipinski.py.html">Lipinski</a></td><td valign="top" align="left">
Calculation of Lipinski parameters for molecules
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/MACCSkeys.py.html">MACCSkeys</a></td><td valign="top" align="left">
SMARTS definitions for the publically available MACCS keys
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/MolSurf.py.html">MolSurf</a></td><td valign="top" align="left">
Exposes functionality for MOE-like approximate molecular surface area
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/PeriodicTable.py.html">PeriodicTable</a></td><td valign="top" align="left">
periodic table data, <strong>obsolete</strong>
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Polymers.py.html">Polymers</a></td><td valign="top" align="left">
Python functions for manipulating polymers
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/PyMol.py.html">PyMol</a></td><td valign="top" align="left">
uses pymol to interact with molecules
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Randomize.py.html">Randomize</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/SATIS.py.html">SATIS</a></td><td valign="top" align="left">
Functionality for SATIS typing atoms
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/ShowMols.py.html">ShowMols</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/TemplateAlign.py.html">TemplateAlign</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/UnitTestArom.py.html">UnitTestArom</a></td><td valign="top" align="left">
unit testing code for the Crippen clogp and MR calculators
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/UnitTestCatalog.py.html">UnitTestCatalog</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/UnitTestChem.py.html">UnitTestChem</a></td><td valign="top" align="left">
basic unit testing code for the molecule boost wrapper
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/UnitTestChemAtom.py.html">UnitTestChemAtom</a></td><td valign="top" align="left">
basic unit testing code for atoms
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/UnitTestChemBond.py.html">UnitTestChemBond</a></td><td valign="top" align="left">
basic unit testing code for the Bond wrapper
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/UnitTestChemSmarts.py.html">UnitTestChemSmarts</a></td><td valign="top" align="left">
basic unit testing code for the wrapper of the SMARTS matcher
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/UnitTestChemv2.py.html">UnitTestChemv2</a></td><td valign="top" align="left">
basic unit testing code for the rdkit Boost wrapper
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/UnitTestCrippen.py.html">UnitTestCrippen</a></td><td valign="top" align="left">
unit testing code for the Crippen clogp and MR calculators
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/UnitTestFragmentDescriptors.py.html">UnitTestFragmentDescriptors</a></td><td valign="top" align="left">
Unit Test code for Fragment Descriptors
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/UnitTestFragments.py.html">UnitTestFragments</a></td><td valign="top" align="left">
Unit Test code for cFragments module
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/UnitTestGraphDescriptors.2.py.html">UnitTestGraphDescriptors.2</a></td><td valign="top" align="left">
unit testing code for graph-theoretical descriptors
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/UnitTestLipinski.py.html">UnitTestLipinski</a></td><td valign="top" align="left">
unit testing code for Lipinski parameter calculation
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/UnitTestOldBugs.py.html">UnitTestOldBugs</a></td><td valign="top" align="left">
testing code inspired by old bugs
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/UnitTestSATIS.py.html">UnitTestSATIS</a></td><td valign="top" align="left">
unit testing code for the SATIS numbers
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/UnitTestSmiles.py.html">UnitTestSmiles</a></td><td valign="top" align="left">
basic unit testing code for SMILES canonicalization
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/UnitTestSubgraphs.py.html">UnitTestSubgraphs</a></td><td valign="top" align="left">
unit testing code for the subgraph code
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/UnitTestSuppliers.py.html">UnitTestSuppliers</a></td><td valign="top" align="left">
unit testing code for molecule suppliers
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/UnitTestSurf.py.html">UnitTestSurf</a></td><td valign="top" align="left">
unit testing code for surface calculations
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/test_list.py.html">test_list</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/Chem/AtomPairs/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/Chem/AtomPairs/Pairs.py.html">Pairs</a></td><td valign="top" align="left">
Contains an implementation of Atom-pair fingerprints, as
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/AtomPairs/Torsions.py.html">Torsions</a></td><td valign="top" align="left">
Contains an implementation of Topological-torsion fingerprints, as
</td></tr>
</table>
<h4>Python/Chem/ChemUtils/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/Chem/ChemUtils/BulkTester.py.html">BulkTester</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/ChemUtils/SDFToCSV.py.html">SDFToCSV</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/Chem/Draw/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/Chem/Draw/DrawUtils.py.html">DrawUtils</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Draw/MolDrawing.py.html">MolDrawing</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/Chem/EState/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/Chem/EState/AtomTypes.py.html">AtomTypes</a></td><td valign="top" align="left">
contains SMARTS definitions and calculators for EState atom types
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/EState/EState.py.html">EState</a></td><td valign="top" align="left">
Basic EState definitions
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/EState/EState_VSA.py.html">EState_VSA</a></td><td valign="top" align="left">
Hybrid EState-VSA descriptors (like the MOE VSA descriptors)
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/EState/Fingerprinter.py.html">Fingerprinter</a></td><td valign="top" align="left">
EState fingerprinting
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/EState/UnitTestEState.py.html">UnitTestEState</a></td><td valign="top" align="left">
unit testing code for the EState indices
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/EState/UnitTestTypes.py.html">UnitTestTypes</a></td><td valign="top" align="left">
unit testing code for the EState atom typing
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/EState/UnitTestVSA.py.html">UnitTestVSA</a></td><td valign="top" align="left">
unit testing code for MOE-type descriptors with EStates
</td></tr>
</table>
<h4>Python/Chem/Features/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/Chem/Features/FeatDirUtils.py.html">FeatDirUtils</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/Chem/Fingerprints/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/Chem/Fingerprints/ClusterMols.py.html">ClusterMols</a></td><td valign="top" align="left">
utility functionality for clustering molecules using fingerprints
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Fingerprints/DbFpSupplier.py.html">DbFpSupplier</a></td><td valign="top" align="left">
Supplies a class for working with fingerprints from databases
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Fingerprints/FingerprintMols.py.html">FingerprintMols</a></td><td valign="top" align="left">
utility functionality for fingerprinting sets of molecules
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Fingerprints/Fingerprints.py.html">Fingerprints</a></td><td valign="top" align="left">
Python functions for path-based (like Daylight) molecular fingerprinting
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Fingerprints/MolSimilarity.py.html">MolSimilarity</a></td><td valign="top" align="left">
utility functionality for molecular similarity
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Fingerprints/SimilarityScreener.py.html">SimilarityScreener</a></td><td valign="top" align="left">
class definitions for similarity screening
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Fingerprints/UnitTestFingerprints.py.html">UnitTestFingerprints</a></td><td valign="top" align="left">
unit testing code for fingerprinting
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Fingerprints/UnitTestSimScreener.py.html">UnitTestSimScreener</a></td><td valign="top" align="left">
unit testing code for the SimilarityScreeners
</td></tr>
</table>
<h4>Python/Chem/Pharm2D/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/Chem/Pharm2D/Generate.py.html">Generate</a></td><td valign="top" align="left">
generation of 2D pharmacophores
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Pharm2D/Gobbi_Pharm2D.py.html">Gobbi_Pharm2D</a></td><td valign="top" align="left">
Definitions for 2D Pharmacophores from:
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Pharm2D/LazyGenerator.py.html">LazyGenerator</a></td><td valign="top" align="left">
lazy generator of 2D pharmacophore signature data
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Pharm2D/Matcher.py.html">Matcher</a></td><td valign="top" align="left">
functionality for finding pharmacophore matches in molecules
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Pharm2D/SigFactory.py.html">SigFactory</a></td><td valign="top" align="left">
contains factory class for producing signatures
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Pharm2D/Signature.py.html">Signature</a></td><td valign="top" align="left">
data structures for holding 2D pharmacophore signatures
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Pharm2D/UnitTestGobbi.py.html">UnitTestGobbi</a></td><td valign="top" align="left">
unit testing code for the signatures
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Pharm2D/UnitTestLazyGenerator.py.html">UnitTestLazyGenerator</a></td><td valign="top" align="left">
unit testing code for the lazy signature generator
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Pharm2D/UnitTestMatcher.py.html">UnitTestMatcher</a></td><td valign="top" align="left">
unit testing code for the signatures
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Pharm2D/UnitTestSignature.py.html">UnitTestSignature</a></td><td valign="top" align="left">
unit testing code for the signatures
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Pharm2D/UnitTestUtils.py.html">UnitTestUtils</a></td><td valign="top" align="left">
unit testing code for the signature utils
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Pharm2D/Utils.py.html">Utils</a></td><td valign="top" align="left">
utility functionality for the 2D pharmacophores code
</td></tr>
</table>
<h4>Python/Chem/Pharm3D/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/Chem/Pharm3D/EmbedLib.py.html">EmbedLib</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Pharm3D/ExcludedVolume.py.html">ExcludedVolume</a></td><td valign="top" align="left">
$Id: ExcludedVolume.py 2 2006-05-06 22:54:39Z glandrum $
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Pharm3D/Pharmacophore.py.html">Pharmacophore</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Pharm3D/UnitTestEmbed.py.html">UnitTestEmbed</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Pharm3D/UnitTestPharmacophore.py.html">UnitTestPharmacophore</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/Chem/Suppliers/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/Chem/Suppliers/DbMolSupplier.py.html">DbMolSupplier</a></td><td valign="top" align="left">
Supplies a class for working with molecules from databases
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Suppliers/MolSupplier.py.html">MolSupplier</a></td><td valign="top" align="left">
Supplies an abstract class for working with sequences of molecules
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Suppliers/SDMolSupplier.py.html">SDMolSupplier</a></td><td valign="top" align="left">
Supplies a class for working with molecules from SD files
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Suppliers/SmilesMolSupplier.py.html">SmilesMolSupplier</a></td><td valign="top" align="left">
Supplies a class for working with molecules from SMILES tables and CSV files
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Suppliers/UnitTestSDMolSupplier.py.html">UnitTestSDMolSupplier</a></td><td valign="top" align="left">
unit testing code for the SD file handling stuff
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/Suppliers/UnitTestSmilesMolSupplier.py.html">UnitTestSmilesMolSupplier</a></td><td valign="top" align="left">
unit testing code for the Smiles file handling stuff
</td></tr>
</table>
<h4>Python/Chem/tests/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/Chem/tests/BuildCrippenTestSet.py.html">BuildCrippenTestSet</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/Chem/tests/BuildDescrsTestSet.py.html">BuildDescrsTestSet</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/ClientCookie/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/ClientCookie/_BSDDBCookieJar.py.html">_BSDDBCookieJar</a></td><td valign="top" align="left">
Persistent CookieJar based on bsddb standard library module.
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ClientCookie/_ClientCookie.py.html">_ClientCookie</a></td><td valign="top" align="left">
HTTP cookie handling for web clients, plus some other stuff.
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ClientCookie/_Debug.py.html">_Debug</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/ClientCookie/_HeadersUtil.py.html">_HeadersUtil</a></td><td valign="top" align="left">
Utility functions for HTTP header value parsing and construction.
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ClientCookie/_LWPCookieJar.py.html">_LWPCookieJar</a></td><td valign="top" align="left">
Load / save to libwww-perl (LWP) format files.
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ClientCookie/_MSIECookieJar.py.html">_MSIECookieJar</a></td><td valign="top" align="left">
Microsoft Internet Explorer cookie loading on Windows.
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ClientCookie/_MSIEDBCookieJar.py.html">_MSIEDBCookieJar</a></td><td valign="top" align="left">
Persistent CookieJar based on MS Internet Explorer cookie database.
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ClientCookie/_MozillaCookieJar.py.html">_MozillaCookieJar</a></td><td valign="top" align="left">
Mozilla / Netscape cookie loading / saving.
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ClientCookie/_Util.py.html">_Util</a></td><td valign="top" align="left">
Python backwards-compat., date/time routines, seekable file object wrapper.
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ClientCookie/_urllib2_support.py.html">_urllib2_support</a></td><td valign="top" align="left">
Integration with Python standard library module urllib2.
</td></tr>
</table>
<h4>Python/DataStructs/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/DataStructs/BitEnsemble.py.html">BitEnsemble</a></td><td valign="top" align="left">
#DOC
</td></tr>
<tr><td valign="top" align="left"><a href="Python/DataStructs/BitEnsembleDb.py.html">BitEnsembleDb</a></td><td valign="top" align="left">
This functionality gets mixed into the BitEnsemble class
</td></tr>
<tr><td valign="top" align="left"><a href="Python/DataStructs/BitUtils.py.html">BitUtils</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/DataStructs/BitVect.py.html">BitVect</a></td><td valign="top" align="left">
This has all be re-implemented in the C++ code
</td></tr>
<tr><td valign="top" align="left"><a href="Python/DataStructs/HierarchyVis.py.html">HierarchyVis</a></td><td valign="top" align="left">
functionality for drawing hierarchical catalogs on sping
</td></tr>
<tr><td valign="top" align="left"><a href="Python/DataStructs/TopNContainer.py.html">TopNContainer</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/DataStructs/UnitTestBitEnsemble.py.html">UnitTestBitEnsemble</a></td><td valign="top" align="left">
unit testing code for BitEnsembles
</td></tr>
<tr><td valign="top" align="left"><a href="Python/DataStructs/UnitTestBitVect.py.html">UnitTestBitVect</a></td><td valign="top" align="left">
unit testing code for the python BitVects
</td></tr>
<tr><td valign="top" align="left"><a href="Python/DataStructs/UnitTestTopNContainer.py.html">UnitTestTopNContainer</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/DataStructs/UnitTestcBitVect.py.html">UnitTestcBitVect</a></td><td valign="top" align="left">
unit testing code for the C++ BitVects
</td></tr>
<tr><td valign="top" align="left"><a href="Python/DataStructs/UnitTestcBitVect2.py.html">UnitTestcBitVect2</a></td><td valign="top" align="left">
unit testing code for the C++ ExplicitBitVects
</td></tr>
<tr><td valign="top" align="left"><a href="Python/DataStructs/VectCollection.py.html">VectCollection</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/DataStructs/testScreen.py.html">testScreen</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/Dbase/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/Dbase/DbConnection.py.html">DbConnection</a></td><td valign="top" align="left">
defines class <u>DbConnect</u>, for abstracting connections to databases
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Dbase/DbInfo.py.html">DbInfo</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/Dbase/DbModule.py.html">DbModule</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/Dbase/DbReport.py.html">DbReport</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/Dbase/DbResultSet.py.html">DbResultSet</a></td><td valign="top" align="left">
defines class <u>DbResultSet</u> for lazy interactions with Db query results
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Dbase/DbUtils.py.html">DbUtils</a></td><td valign="top" align="left">
a set of functions for interacting with databases
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Dbase/Gui.py.html">Gui</a></td><td valign="top" align="left">
simple GUI tools for interacting with databases
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Dbase/StorageUtils.py.html">StorageUtils</a></td><td valign="top" align="left">
Various storage (molecular and otherwise) functionality
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Dbase/UnitTestDbConnect.py.html">UnitTestDbConnect</a></td><td valign="top" align="left">
unit testing code for database connection objects
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Dbase/UnitTestDbResultSet.py.html">UnitTestDbResultSet</a></td><td valign="top" align="left">
unit testing code for the DbResultSet object
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Dbase/UnitTestDbUtils.py.html">UnitTestDbUtils</a></td><td valign="top" align="left">
unit testing code for the database utilities
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Dbase/ibase_tut.py.html">ibase_tut</a></td><td valign="top" align="left">
A brief little demo/tutorial on use of the python &lt;-&gt; interbase adaptor
</td></tr>
</table>
<h4>Python/Dbase/Pubmed/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/Dbase/Pubmed/PubmedUtils.py.html">PubmedUtils</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/Dbase/Pubmed/QueryParams.py.html">QueryParams</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/Dbase/Pubmed/Records.py.html">Records</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/Dbase/Pubmed/Searches.py.html">Searches</a></td><td valign="top" align="left">
Tools for doing PubMed searches and processing the results
</td></tr>
</table>
<h4>Python/Excel/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/Excel/ExcelWrapper.py.html">ExcelWrapper</a></td><td valign="top" align="left">
a wrapper for interacting with Excel
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Excel/Molecules.py.html">Molecules</a></td><td valign="top" align="left">
mixin class for dealing with ChemDraw for Excel
</td></tr>
</table>
<h4>Python/Logger/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/Logger/Logger.py.html">Logger</a></td><td valign="top" align="left">
Provides a Logger class which can be wrapped around another
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Logger/SpingDemo.py.html">SpingDemo</a></td><td valign="top" align="left">
demo code for the Logger class
</td></tr>
<tr><td valign="top" align="left"><a href="Python/Logger/UnitTestLogger.py.html">UnitTestLogger</a></td><td valign="top" align="left">
unit testing code for the logger
</td></tr>
</table>
<h4>Python/ML/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/ML/AnalyzeComposite.py.html">AnalyzeComposite</a></td><td valign="top" align="left">
command line utility to report on the contributions of descriptors to
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/BuildComposite.py.html">BuildComposite</a></td><td valign="top" align="left">
command line utility for building composite models
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/CompositeRun.py.html">CompositeRun</a></td><td valign="top" align="left">
contains a class to store parameters for and results from
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/DataFilter.py.html">DataFilter</a></td><td valign="top" align="left">
command line utility for filtering data
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/EnrichPlot.py.html">EnrichPlot</a></td><td valign="top" align="left">
Command line tool to construct an enrichment plot from saved composite models
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/GrowComposite.py.html">GrowComposite</a></td><td valign="top" align="left">
command line utility for growing composite models
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/MatOps.py.html">MatOps</a></td><td valign="top" align="left">
Matrix operations which may or may not come in handy some day
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/ScreenComposite.py.html">ScreenComposite</a></td><td valign="top" align="left">
command line utility for screening composite models
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/UnitTestAnalyzeComposite.py.html">UnitTestAnalyzeComposite</a></td><td valign="top" align="left">
unit testing code for the AnalyzeComposite functionality
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/UnitTestBuildComposite.py.html">UnitTestBuildComposite</a></td><td valign="top" align="left">
unit testing code for the BuildComposite functionality
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/UnitTestScreenComposite.py.html">UnitTestScreenComposite</a></td><td valign="top" align="left">
unit testing code for the ScreenComposite functionality
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/files.py.html">files</a></td><td valign="top" align="left">
Generic file manipulation stuff
</td></tr>
</table>
<h4>Python/ML/Cluster/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/ML/Cluster/ClusterModel.py.html">ClusterModel</a></td><td valign="top" align="left">
defines the ClusterModel
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Cluster/ClusterUtils.py.html">ClusterUtils</a></td><td valign="top" align="left">
utility functions for clustering
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Cluster/ClusterVis.py.html">ClusterVis</a></td><td valign="top" align="left">
Cluster tree visualization using Sping
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Cluster/Clusters.py.html">Clusters</a></td><td valign="top" align="left">
contains the Cluster class for representing hierarchical cluster trees
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Cluster/Murtagh.py.html">Murtagh</a></td><td valign="top" align="left">
Interface to the C++ Murtagh hierarchic clustering code
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Cluster/Resemblance.py.html">Resemblance</a></td><td valign="top" align="left">
code for dealing with resemblance (metric) matrices
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Cluster/Standardize.py.html">Standardize</a></td><td valign="top" align="left">
contains code for standardization of data matrices for clustering
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Cluster/UnitTestCluster.py.html">UnitTestCluster</a></td><td valign="top" align="left">
unit testing code for clustering
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Cluster/murtagh_test.py.html">murtagh_test</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/ML/Composite/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/ML/Composite/AdjustComposite.py.html">AdjustComposite</a></td><td valign="top" align="left">
functionality to allow adjusting composite model contents
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Composite/BayesComposite.py.html">BayesComposite</a></td><td valign="top" align="left">
code for dealing with Bayesian composite models
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Composite/Composite.py.html">Composite</a></td><td valign="top" align="left">
code for dealing with composite models
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Composite/CompositeCOM.py.html">CompositeCOM</a></td><td valign="top" align="left">
the COM server for Composite models
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Composite/UnitTestCOMServer.py.html">UnitTestCOMServer</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Composite/UnitTestComposite.py.html">UnitTestComposite</a></td><td valign="top" align="left">
unit testing code for composite models
</td></tr>
</table>
<h4>Python/ML/Data/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/ML/Data/DataUtils.py.html">DataUtils</a></td><td valign="top" align="left">
Utilities for data manipulation
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Data/FindQuantBounds.py.html">FindQuantBounds</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Data/MLData.py.html">MLData</a></td><td valign="top" align="left">
classes to be used to help work with data sets
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Data/Quantize.py.html">Quantize</a></td><td valign="top" align="left">
Automatic search for quantization bounds
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Data/SplitData.py.html">SplitData</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Data/Stats.py.html">Stats</a></td><td valign="top" align="left">
various statistical operations on data
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Data/Transforms.py.html">Transforms</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Data/UnitTestFilter.py.html">UnitTestFilter</a></td><td valign="top" align="left">
unit testing code for variable quantization
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Data/UnitTestMLData.py.html">UnitTestMLData</a></td><td valign="top" align="left">
unit testing code for MLData sets
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Data/UnitTestQuantize.py.html">UnitTestQuantize</a></td><td valign="top" align="left">
unit testing code for variable quantization
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Data/UnitTestStats.py.html">UnitTestStats</a></td><td valign="top" align="left">
unit testing code for the Stats module
</td></tr>
</table>
<h4>Python/ML/DecTree/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/ML/DecTree/AutoQuantTree.py.html">AutoQuantTree</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/DecTree/BuildQuantTree.py.html">BuildQuantTree</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/DecTree/BuildSigTree.py.html">BuildSigTree</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/DecTree/DecTree.py.html">DecTree</a></td><td valign="top" align="left">
Defines the class <u>DecTreeNode</u>, used to represent decision trees
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/DecTree/Forest.py.html">Forest</a></td><td valign="top" align="left">
code for dealing with forests (collections) of decision trees
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/DecTree/ID3.py.html">ID3</a></td><td valign="top" align="left">
ID3 Decision Trees
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/DecTree/PruneTree.py.html">PruneTree</a></td><td valign="top" align="left">
Contains functionality for doing tree pruning
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/DecTree/QuantTree.py.html">QuantTree</a></td><td valign="top" align="left">
Defines the class <u>QuantTreeNode</u>, used to represent decision trees with automatic
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/DecTree/SigTree.py.html">SigTree</a></td><td valign="top" align="left">
Defines the class SigTreeNode, used to represent trees that
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/DecTree/Tree.py.html">Tree</a></td><td valign="top" align="left">
Implements a class used to represent N-ary trees
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/DecTree/TreeUtils.py.html">TreeUtils</a></td><td valign="top" align="left">
Utilities for working with trees
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/DecTree/TreeVis.py.html">TreeVis</a></td><td valign="top" align="left">
functionality for drawing trees on sping canvases
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/DecTree/UnitTestID3.py.html">UnitTestID3</a></td><td valign="top" align="left">
unit tests for the ID3 implementation
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/DecTree/UnitTestPrune.py.html">UnitTestPrune</a></td><td valign="top" align="left">
<TABLE BORDER=1 CELLPADDING=2>
</TABLE>
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/DecTree/UnitTestQuantTree.py.html">UnitTestQuantTree</a></td><td valign="top" align="left">
unit tests for the QuantTree implementation
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/DecTree/UnitTestSigTree.py.html">UnitTestSigTree</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/DecTree/UnitTestTree.py.html">UnitTestTree</a></td><td valign="top" align="left">
unit testing code for trees and decision trees (not learning/xvalidation)
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/DecTree/UnitTestXVal.py.html">UnitTestXVal</a></td><td valign="top" align="left">
unit testing code for cross validation
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/DecTree/randomforest.py.html">randomforest</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/DecTree/randomtest.py.html">randomtest</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/ML/Descriptors/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/ML/Descriptors/CompoundDescriptors.py.html">CompoundDescriptors</a></td><td valign="top" align="left">
descriptor calculator for compounds defined by a composition alone
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Descriptors/DescriptorsCOM.py.html">DescriptorsCOM</a></td><td valign="top" align="left">
the COM server for Descriptor Calculators
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Descriptors/MoleculeDescriptors.py.html">MoleculeDescriptors</a></td><td valign="top" align="left">
Various bits and pieces for calculating Molecular descriptors
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Descriptors/Parser.py.html">Parser</a></td><td valign="top" align="left">
The &quot;parser&quot; for compound descriptors.
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Descriptors/UnitTestDescriptors.py.html">UnitTestDescriptors</a></td><td valign="top" align="left">
unit testing code for descriptors
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Descriptors/UnitTestMolDescriptors.py.html">UnitTestMolDescriptors</a></td><td valign="top" align="left">
unit testing code for molecular descriptor calculators
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Descriptors/UnitTestParser.py.html">UnitTestParser</a></td><td valign="top" align="left">
unit testing code for compound descriptors
</td></tr>
</table>
<h4>Python/ML/FeatureSelect/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/ML/FeatureSelect/CMIM.py.html">CMIM</a></td><td valign="top" align="left">
for the moment this is using Francois Fleuret's cmim library
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/FeatureSelect/UnitTestCMIM.py.html">UnitTestCMIM</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/ML/InfoTheory/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/ML/InfoTheory/BitClusterer.py.html">BitClusterer</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/InfoTheory/BitRank.py.html">BitRank</a></td><td valign="top" align="left">
Functionality for ranking bits using info gains
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/InfoTheory/entropy.py.html">entropy</a></td><td valign="top" align="left">
Informational Entropy functions
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/InfoTheory/testBitRanker.py.html">testBitRanker</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/InfoTheory/testCorrMatGen.py.html">testCorrMatGen</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/ML/KNN/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/ML/KNN/DistFunctions.py.html">DistFunctions</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/KNN/KNNClassificationModel.py.html">KNNClassificationModel</a></td><td valign="top" align="left">
Define the class <u>KNNClassificationModel</u>, used to represent a k-nearest neighbhors classification model
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/KNN/KNNModel.py.html">KNNModel</a></td><td valign="top" align="left">
Define the class <u>KNNModel</u>, used to represent a k-nearest neighbhors model
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/KNN/KNNRegressionModel.py.html">KNNRegressionModel</a></td><td valign="top" align="left">
Define the class <u>KNNRegressionModel</u>, used to represent a k-nearest neighbhors
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/KNN/UnitTestKNN.py.html">UnitTestKNN</a></td><td valign="top" align="left">
unit testing code for knn models
</td></tr>
</table>
<h4>Python/ML/MLUtils/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/ML/MLUtils/VoteImg.py.html">VoteImg</a></td><td valign="top" align="left">
functionality for generating an image showing the results of a composite model voting on a data set
</td></tr>
</table>
<h4>Python/ML/ModelPackage/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/ML/ModelPackage/PackageUtils.py.html">PackageUtils</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/ModelPackage/Packager.py.html">Packager</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/ModelPackage/UnitTestPackage.py.html">UnitTestPackage</a></td><td valign="top" align="left">
unit tests for the model and descriptor packager
</td></tr>
</table>
<h4>Python/ML/NaiveBayes/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/ML/NaiveBayes/ClassificationModel.py.html">ClassificationModel</a></td><td valign="top" align="left">
Defines Naive Baysean classification model
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/NaiveBayes/CrossValidate.py.html">CrossValidate</a></td><td valign="top" align="left">
handles doing cross validation with naive bayes models
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/NaiveBayes/UnitTestNB.py.html">UnitTestNB</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/ML/Neural/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/ML/Neural/ActFuncs.py.html">ActFuncs</a></td><td valign="top" align="left">
Activation functions for neural network nodes
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Neural/NetNode.py.html">NetNode</a></td><td valign="top" align="left">
Contains the class <u>NetNode</u> which is used to represent nodes in neural nets
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Neural/Network.py.html">Network</a></td><td valign="top" align="left">
Contains the class <u>Network</u> which is used to represent neural nets
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Neural/Trainers.py.html">Trainers</a></td><td valign="top" align="left">
Training algorithms for feed-forward neural nets
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/Neural/UnitTestTrainer.py.html">UnitTestTrainer</a></td><td valign="top" align="left">
unit tests for the Neural network trainer implementation
</td></tr>
</table>
<h4>Python/ML/SLT/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/ML/SLT/Risk.py.html">Risk</a></td><td valign="top" align="left">
code for calculating empirical risk
</td></tr>
<tr><td valign="top" align="left"><a href="Python/ML/SLT/UnitTestRisk.py.html">UnitTestRisk</a></td><td valign="top" align="left">
unit testing code for SLT Risk functions
</td></tr>
</table>
<h4>Python/ML/test_data/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/ML/test_data/populate.py.html">populate</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/PySVD/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/PySVD/SVDPack.py.html">SVDPack</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/PySVD/SVDSimilarity.py.html">SVDSimilarity</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/PySVD/UnitTestSVD.py.html">UnitTestSVD</a></td><td valign="top" align="left">
unit testing code for the SVD wrapper
</td></tr>
</table>
<h4>Python/RDToDo/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/RDToDo/HelpData.py.html">HelpData</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/RDToDo/ItemEditImpl.py.html">ItemEditImpl</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/RDToDo/OutlUtils.py.html">OutlUtils</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/RDToDo/OutlineTree.py.html">OutlineTree</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/RDToDo/OutlineTreeItem.py.html">OutlineTreeItem</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/RDToDo/RDOutline.py.html">RDOutline</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/RDToDo/RDToDo.py.html">RDToDo</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/RDToDo/TaskEditImpl.py.html">TaskEditImpl</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/RDToDo/TextViewImpl.py.html">TextViewImpl</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/RDToDo/ToDoListItem.py.html">ToDoListItem</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/RDToDo/ToDoListView.py.html">ToDoListView</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/RDToDo/ToDoTree.py.html">ToDoTree</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/RDToDo/ToDoTreeItem.py.html">ToDoTreeItem</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/RDToDo/ToDoUtils.py.html">ToDoUtils</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/RDToDo/forms/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/RDToDo/forms/itemdialog.py.html">itemdialog</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/RDToDo/forms/mainform.py.html">mainform</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/RDToDo/forms/taskdialog.py.html">taskdialog</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/RDToDo/forms/textview.py.html">textview</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/RDToDo/icons/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/RDToDo/icons/icons.py.html">icons</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/Reports/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/Reports/HTMLReport.py.html">HTMLReport</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/Reports/PDFReport.py.html">PDFReport</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/Reports/ReportUtils.py.html">ReportUtils</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/SimDivFilters/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/SimDivFilters/SimilarityPickers.py.html">SimilarityPickers</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/SimDivFilters/test_data/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/SimDivFilters/test_data/genfps.py.html">genfps</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/VLib/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/VLib/Filter.py.html">Filter</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/VLib/Node.py.html">Node</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/VLib/Output.py.html">Output</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/VLib/Supply.py.html">Supply</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/VLib/Transform.py.html">Transform</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/VLib/UnitTestEnum.py.html">UnitTestEnum</a></td><td valign="top" align="left">
unit testing code for the virtual library enumerator
</td></tr>
<tr><td valign="top" align="left"><a href="Python/VLib/catalenum.py.html">catalenum</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/VLib/NodeLib/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/VLib/NodeLib/DbMolSupply.py.html">DbMolSupply</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/VLib/NodeLib/DbPickleSupplier.py.html">DbPickleSupplier</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/VLib/NodeLib/SDSupply.py.html">SDSupply</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/VLib/NodeLib/SmartsMolFilter.py.html">SmartsMolFilter</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/VLib/NodeLib/SmartsRemover.py.html">SmartsRemover</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/VLib/NodeLib/SmilesDupeFilter.py.html">SmilesDupeFilter</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/VLib/NodeLib/SmilesOutput.py.html">SmilesOutput</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/VLib/NodeLib/SmilesSupply.py.html">SmilesSupply</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/VLib/NodeLib/demo.py.html">demo</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/WebUtils/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/WebUtils/ChemdrawPlugin.py.html">ChemdrawPlugin</a></td><td valign="top" align="left">
Code for dealing with the ChemDraw Plugin on web pages
</td></tr>
<tr><td valign="top" align="left"><a href="Python/WebUtils/General.py.html">General</a></td><td valign="top" align="left">
General functionality used by the RDOnline Web Interfaces
</td></tr>
<tr><td valign="top" align="left"><a href="Python/WebUtils/Storage.py.html">Storage</a></td><td valign="top" align="left">
A simple, primitive, shelve-based data storage system for persistence
</td></tr>
<tr><td valign="top" align="left"><a href="Python/WebUtils/WebStore.py.html">WebStore</a></td><td valign="top" align="left">
A simple, primitive, shelve-based data storage system for persistence
</td></tr>
</table>
<h4>Python/mixins/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/mixins/Loader.py.html">Loader</a></td><td valign="top" align="left">
Everything required to load and initialize mixins
</td></tr>
<tr><td valign="top" align="left"><a href="Python/mixins/StateSaver.py.html">StateSaver</a></td><td valign="top" align="left">
Allows mixins to save their state
</td></tr>
</table>
<h4>Python/qtGui/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/qtGui/DbConnDialog.py.html">DbConnDialog</a></td><td valign="top" align="left">
dialog for establishing db connections
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/DbConnWidgetImpl.py.html">DbConnWidgetImpl</a></td><td valign="top" align="left">
implementation bits for DbConnWidgets
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/DbDialog.py.html">DbDialog</a></td><td valign="top" align="left">
contains simple dialog box for holding db widgets
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/DbQueryDialog.py.html">DbQueryDialog</a></td><td valign="top" align="left">
dialog for setting up db queries
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/DbQueryWidgetImpl.py.html">DbQueryWidgetImpl</a></td><td valign="top" align="left">
implementation bits for DbQueryWidgets
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/DbWidget.py.html">DbWidget</a></td><td valign="top" align="left">
contains a mixin class for the various Database widgets
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiBase.py.html">GuiBase</a></td><td valign="top" align="left">
base class for the main window in the qt MixinGui
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiShell.py.html">GuiShell</a></td><td valign="top" align="left">
provides a window with an interactive python shell
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiTable.py.html">GuiTable</a></td><td valign="top" align="left">
defines classes to make QTables more useful for us
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiTextViewer.py.html">GuiTextViewer</a></td><td valign="top" align="left">
defines a class for viewing rich text
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiUndo.py.html">GuiUndo</a></td><td valign="top" align="left">
undo functionality
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/PiddleWindowImpl.py.html">PiddleWindowImpl</a></td><td valign="top" align="left">
implementation bits for PiddleWindows
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/qtActiveX.py.html">qtActiveX</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/qtUtils.py.html">qtUtils</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/rpcClient.py.html">rpcClient</a></td><td valign="top" align="left">
components required to add an xml-rpc server to a qt application
</td></tr>
</table>
<h4>Python/qtGui/GuiLib/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/BuildClusterDialogImpl.py.html">BuildClusterDialogImpl</a></td><td valign="top" align="left">
implementation bits for BuildClusterDialogs
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/BuildCompositeDialogImpl.py.html">BuildCompositeDialogImpl</a></td><td valign="top" align="left">
implementation bits for BuildCompositeDialogs
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/ClusterWindow.py.html">ClusterWindow</a></td><td valign="top" align="left">
defines classes required for interacting with Clusters
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/CompositeUtils.py.html">CompositeUtils</a></td><td valign="top" align="left">
general utilities for interacting with composites from GUIs
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/CompositeWindowImpl.py.html">CompositeWindowImpl</a></td><td valign="top" align="left">
implementation bits for CompositeWindows
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/DecTreeWindow.py.html">DecTreeWindow</a></td><td valign="top" align="left">
defines classes required for interacting with Dec Trees
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/DescTable.py.html">DescTable</a></td><td valign="top" align="left">
defines the DescTable class
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/FingerprintDbWidget.py.html">FingerprintDbWidget</a></td><td valign="top" align="left">
Defines a widget for working with fingerprints in databases
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/ModelBrowserDialogImpl.py.html">ModelBrowserDialogImpl</a></td><td valign="top" align="left">
implementation bits for Model Browsers
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/ModelTable.py.html">ModelTable</a></td><td valign="top" align="left">
defines classes required to put models in QTables
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/MolBrowserImpl.py.html">MolBrowserImpl</a></td><td valign="top" align="left">
implementation bits for MolBrowsers
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/MolCanvas.py.html">MolCanvas</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/MolDescriptorWinImpl.py.html">MolDescriptorWinImpl</a></td><td valign="top" align="left">
implementation bits for MolDescriptorWins
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/MolTable.py.html">MolTable</a></td><td valign="top" align="left">
defines classes required for using molecules in QTables
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/PubmedRecordImpl.py.html">PubmedRecordImpl</a></td><td valign="top" align="left">
implementation bits for Pubmed searching
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/PubmedSearchImpl.py.html">PubmedSearchImpl</a></td><td valign="top" align="left">
implementation bits for Pubmed searching
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/ScreenCompositeDialogImpl.py.html">ScreenCompositeDialogImpl</a></td><td valign="top" align="left">
implementation bits for ScreenCompositeDialogs
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/SignatureTable.py.html">SignatureTable</a></td><td valign="top" align="left">
defines classes required for using 2D pharmacophore signatures in QTables
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/SignatureViewDialogImpl.py.html">SignatureViewDialogImpl</a></td><td valign="top" align="left">
implementation bits for SignatureViewDialogs, which are for working with
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/SimilarityParamsImpl.py.html">SimilarityParamsImpl</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/SimilaritySearchWidgetImpl.py.html">SimilaritySearchWidgetImpl</a></td><td valign="top" align="left">
implementation bits for Similarity Searching
</td></tr>
</table>
<h4>Python/qtGui/GuiLib/Proto/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/Proto/DataTransformWidgetImpl.py.html">DataTransformWidgetImpl</a></td><td valign="top" align="left">
implementation bits for DataTransformWidgets
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/Proto/LoaderWidgetImpl.py.html">LoaderWidgetImpl</a></td><td valign="top" align="left">
implementation bits for SupplierWindows (for editing supplier
</td></tr>
</table>
<h4>Python/qtGui/GuiLib/Proto/forms/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/Proto/forms/DataTransformWidget.py.html">DataTransformWidget</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/Proto/forms/LoaderWidget.py.html">LoaderWidget</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/qtGui/GuiLib/forms/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/forms/BuildClusterDialog.py.html">BuildClusterDialog</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/forms/BuildCompositeDialog.py.html">BuildCompositeDialog</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/forms/CompositeWindow.py.html">CompositeWindow</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/forms/ModelBrowserDialog.py.html">ModelBrowserDialog</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/forms/MolBrowser.py.html">MolBrowser</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/forms/MolDescriptorWin.py.html">MolDescriptorWin</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/forms/MolEditDisplayWidget2.py.html">MolEditDisplayWidget2</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/forms/PubmedRecordWidget.py.html">PubmedRecordWidget</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/forms/PubmedSearchWidget.py.html">PubmedSearchWidget</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/forms/ScreenCompositeDialog.py.html">ScreenCompositeDialog</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/forms/SignatureViewDialog.py.html">SignatureViewDialog</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/forms/SimilarityParams.py.html">SimilarityParams</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/forms/SimilaritySearch.py.html">SimilaritySearch</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/forms/TextViewer.py.html">TextViewer</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/GuiLib/forms/orig.py.html">orig</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/qtGui/HierarchyBrowser/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/qtGui/HierarchyBrowser/BrowserInputImpl.py.html">BrowserInputImpl</a></td><td valign="top" align="left">
Implementation of the BrowserInput widget
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/HierarchyBrowser/HierarchyCatalogWindow.py.html">HierarchyCatalogWindow</a></td><td valign="top" align="left">
defines classes required for interacting with hierarchical catalogs
</td></tr>
</table>
<h4>Python/qtGui/HierarchyBrowser/forms/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/qtGui/HierarchyBrowser/forms/BrowserInput.py.html">BrowserInput</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/qtGui/MixIns/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/qtGui/MixIns/ClusterInteract.py.html">ClusterInteract</a></td><td valign="top" align="left">
Mixin for interacting with cluster trees
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/MixIns/CompositeBase.py.html">CompositeBase</a></td><td valign="top" align="left">
Base composite interaction mixin
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/MixIns/CompositeBuilder.py.html">CompositeBuilder</a></td><td valign="top" align="left">
Mixin for building composite models
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/MixIns/CompositeInteract.py.html">CompositeInteract</a></td><td valign="top" align="left">
Mixin for interacting with composite models
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/MixIns/MolCluster.py.html">MolCluster</a></td><td valign="top" align="left">
Ties the MolBrowser and ClusterInteract widgets together
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/MixIns/MolDescriptors.py.html">MolDescriptors</a></td><td valign="top" align="left">
Allows calculation of molecular descriptors
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/MixIns/PiddleCanvas.py.html">PiddleCanvas</a></td><td valign="top" align="left">
Allows calculation of molecular descriptors
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/MixIns/SigViewer.py.html">SigViewer</a></td><td valign="top" align="left">
#DOC
</td></tr>
</table>
<h4>Python/qtGui/PointSprinkler/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/qtGui/PointSprinkler/PointCanvas.py.html">PointCanvas</a></td><td valign="top" align="left">
point-sprinkler canvas
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/PointSprinkler/PointCanvasItems.py.html">PointCanvasItems</a></td><td valign="top" align="left">
point classes for the point-sprinkler canvas
</td></tr>
</table>
<h4>Python/qtGui/Search3D/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/qtGui/Search3D/ExcludedVolumeMixin.py.html">ExcludedVolumeMixin</a></td><td valign="top" align="left">
------------------------------------------------------------------------
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/Search3D/LocalConfig.py.html">LocalConfig</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/Search3D/MolAlignmentList.py.html">MolAlignmentList</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/Search3D/Persist.py.html">Persist</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/Search3D/PharmacophoreDefWidgets.py.html">PharmacophoreDefWidgets</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/Search3D/PharmacophoreMixin.py.html">PharmacophoreMixin</a></td><td valign="top" align="left">
------------------------------------------------------------------------
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/Search3D/ReplaceConfigCLI.py.html">ReplaceConfigCLI</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/Search3D/ReplaceFDefCLI.py.html">ReplaceFDefCLI</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/Search3D/Search3D.py.html">Search3D</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/Search3D/SearchUtils.py.html">SearchUtils</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/qtGui/Search3D/forms/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/qtGui/Search3D/forms/AtomCorrespondenceDialog.py.html">AtomCorrespondenceDialog</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/Search3D/forms/Search3DWidget.py.html">Search3DWidget</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/qtGui/VisProg/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/qtGui/VisProg/FilterWindowImpl.py.html">FilterWindowImpl</a></td><td valign="top" align="left">
implementation bits for FilterWindows
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/VisProg/NewReactionDialogImpl.py.html">NewReactionDialogImpl</a></td><td valign="top" align="left">
implementation bits for NewReactionDialogs
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/VisProg/ReactionBuilder.py.html">ReactionBuilder</a></td><td valign="top" align="left">
mixin providing reaction-cascade builder functionality on a visual programming
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/VisProg/ReactionWindowImpl.py.html">ReactionWindowImpl</a></td><td valign="top" align="left">
implementation bits for ReactionWindows (for editing reaction
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/VisProg/SinkWindowImpl.py.html">SinkWindowImpl</a></td><td valign="top" align="left">
implementation bits for SinkWindows
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/VisProg/SupplierWindowImpl.py.html">SupplierWindowImpl</a></td><td valign="top" align="left">
implementation bits for SupplierWindows (for editing supplier
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/VisProg/VPCanvas.py.html">VPCanvas</a></td><td valign="top" align="left">
mixin providing a visual programming canvas
</td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/VisProg/VPIcons.py.html">VPIcons</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/VisProg/VPItems.py.html">VPItems</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/VisProg/VPLib.py.html">VPLib</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/VisProg/VPLink.py.html">VPLink</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/VisProg/VPUtils.py.html">VPUtils</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/VisProg/genicons.py.html">genicons</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/qtGui/VisProg/forms/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/qtGui/VisProg/forms/FilterWindow.py.html">FilterWindow</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/VisProg/forms/NewReactionDialog.py.html">NewReactionDialog</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/VisProg/forms/ReactionWindow.py.html">ReactionWindow</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/VisProg/forms/SinkWindow.py.html">SinkWindow</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/VisProg/forms/SupplierWindow.py.html">SupplierWindow</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/qtGui/forms/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/qtGui/forms/BaseDialog.py.html">BaseDialog</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/forms/CountDialog.py.html">CountDialog</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/forms/DbConnWidget.py.html">DbConnWidget</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/forms/DbQueryWidget.py.html">DbQueryWidget</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/forms/ListSelectorDialog.py.html">ListSelectorDialog</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/forms/PiddleWindow.py.html">PiddleWindow</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/qtGui/forms/pyshell.py.html">pyshell</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/sping/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/sping/README.html">README.html</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/sping/colors.py.html">colors</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/sping/pagesizes.py.html">pagesizes</a></td><td valign="top" align="left">
pagesizes.py
</td></tr>
<tr><td valign="top" align="left"><a href="Python/sping/pid.py.html">pid</a></td><td valign="top" align="left">
PIDDLE (Plug-In Drawing, Does Little Else)
</td></tr>
<tr><td valign="top" align="left"><a href="Python/sping/stringformat.py.html">stringformat</a></td><td valign="top" align="left">
Module StringFormat
</td></tr>
<tr><td valign="top" align="left"><a href="Python/sping/utils.py.html">utils</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/sping/PDF/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/sping/PDF/pdfdoc.py.html">pdfdoc</a></td><td valign="top" align="left">
PDFgen is a library to generate PDF files containing text and graphics. It is the
</td></tr>
<tr><td valign="top" align="left"><a href="Python/sping/PDF/pdfgen.py.html">pdfgen</a></td><td valign="top" align="left">
PDFgen is a library to generate PDF files containing text and graphics. It is the
</td></tr>
<tr><td valign="top" align="left"><a href="Python/sping/PDF/pdfgeom.py.html">pdfgeom</a></td><td valign="top" align="left">
This module includes any mathematical methods needed for PIDDLE.
</td></tr>
<tr><td valign="top" align="left"><a href="Python/sping/PDF/pdfmetrics.py.html">pdfmetrics</a></td><td valign="top" align="left">
This contains pre-canned text metrics for the PDFgen package, and may also
</td></tr>
<tr><td valign="top" align="left"><a href="Python/sping/PDF/pdfutils.py.html">pdfutils</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/sping/PDF/pidPDF.py.html">pidPDF</a></td><td valign="top" align="left">
This is the PIDDLE back end for PDF. It acts as a wrapper
</td></tr>
</table>
<h4>Python/sping/PIL/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/sping/PIL/pidPIL.py.html">pidPIL</a></td><td valign="top" align="left">
pidPIL
</td></tr>
</table>
<h4>Python/sping/PIL/pilfonts/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/sping/PIL/pilfonts/removemedium.py.html">removemedium</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/sping/PS/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/sping/PS/fontinfo.py.html">fontinfo</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/sping/PS/latin1MetricsCache.py.html">latin1MetricsCache</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/sping/PS/pidPS.py.html">pidPS</a></td><td valign="top" align="left">
piddlePS - a PostScript backend for the PIDDLE drawing module
</td></tr>
<tr><td valign="top" align="left"><a href="Python/sping/PS/psmetrics.py.html">psmetrics</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/sping/Pyart/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/sping/Pyart/Fontmapping.py.html">Fontmapping</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/sping/Pyart/pidPyart.py.html">pidPyart</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/sping/Qt/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/sping/Qt/pidQt.py.html">pidQt</a></td><td valign="top" align="left">
piddleQt
</td></tr>
</table>
<h4>Python/sping/ReportLab/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/sping/ReportLab/pidReportLab.py.html">pidReportLab</a></td><td valign="top" align="left">
pidReportLab
</td></tr>
</table>
<h4>Python/sping/SVG/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/sping/SVG/pidSVG.py.html">pidSVG</a></td><td valign="top" align="left">
piddleSVG
</td></tr>
</table>
<h4>Python/sping/TK/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/sping/TK/pidTK.py.html">pidTK</a></td><td valign="top" align="left">
A Tkinter based backend for piddle.
</td></tr>
</table>
<h4>Python/sping/WX/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/sping/WX/pidWX.py.html">pidWX</a></td><td valign="top" align="left">
WXCanvas
</td></tr>
<tr><td valign="top" align="left"><a href="Python/sping/WX/pidWxDc.py.html">pidWxDc</a></td><td valign="top" align="left">
\
</td></tr>
</table>
<h4>Python/sping/examples/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/sping/examples/formatted-strings.py.html">formatted-strings</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/sping/examples/tkCanvas-with-scrollbars.py.html">tkCanvas-with-scrollbars</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/sping/examples/tkCanvasPIL-with-scrollbars.py.html">tkCanvasPIL-with-scrollbars</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/sping/tests/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/sping/tests/pidtest.py.html">pidtest</a></td><td valign="top" align="left">
piddletest.py
</td></tr>
<tr><td valign="top" align="left"><a href="Python/sping/tests/pstests.py.html">pstests</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/sping/tests/testallps.py.html">testallps</a></td><td valign="top" align="left"></td></tr>
</table>
<h4>Python/sping/util/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/sping/util/HTMLPiddler.py.html">HTMLPiddler</a></td><td valign="top" align="left">
\
</td></tr>
</table>
<h4>Python/utils/</h4>
<table border="0" cellpadding="5">
<tr><td valign="top" align="left"><a href="Python/utils/GUIDs.py.html">GUIDs</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/utils/GenLicense.py.html">GenLicense</a></td><td valign="top" align="left">
generates license files for our primitive license handler
</td></tr>
<tr><td valign="top" align="left"><a href="Python/utils/Licensing.py.html">Licensing</a></td><td valign="top" align="left">
primitive license handler
</td></tr>
<tr><td valign="top" align="left"><a href="Python/utils/PiddleTools.py.html">PiddleTools</a></td><td valign="top" align="left">
Tools to be used with Piddle/Sping canvases
</td></tr>
<tr><td valign="top" align="left"><a href="Python/utils/PilTools.py.html">PilTools</a></td><td valign="top" align="left">
tools for working with PIL images
</td></tr>
<tr><td valign="top" align="left"><a href="Python/utils/REFile.py.html">REFile</a></td><td valign="top" align="left">
contains class REFile, for working with files containing comments
</td></tr>
<tr><td valign="top" align="left"><a href="Python/utils/SliceTools.py.html">SliceTools</a></td><td valign="top" align="left">
tools for working with python slices
</td></tr>
<tr><td valign="top" align="left"><a href="Python/utils/cactvs.py.html">cactvs</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/utils/chemdraw.py.html">chemdraw</a></td><td valign="top" align="left">
tools for interacting with chemdraw
</td></tr>
<tr><td valign="top" align="left"><a href="Python/utils/chemdraw_qax.py.html">chemdraw_qax</a></td><td valign="top" align="left"></td></tr>
<tr><td valign="top" align="left"><a href="Python/utils/chemutils.py.html">chemutils</a></td><td valign="top" align="left">
utility functions with &quot;chemical know-how&quot;
</td></tr>
<tr><td valign="top" align="left"><a href="Python/utils/comhack.py.html">comhack</a></td><td valign="top" align="left">
$Id: comhack.py 2 2006-05-06 22:54:39Z glandrum $
</td></tr>
<tr><td valign="top" align="left"><a href="Python/utils/fileutils.py.html">fileutils</a></td><td valign="top" align="left">
utility functions to help work with files
</td></tr>
<tr><td valign="top" align="left"><a href="Python/utils/listutils.py.html">listutils</a></td><td valign="top" align="left">
utility functions for lists
</td></tr>
<tr><td valign="top" align="left"><a href="Python/utils/pydoc_local.py.html">pydoc_local</a></td><td valign="top" align="left">
Generate Python documentation in HTML or text for interactive use.
</td></tr>
<tr><td valign="top" align="left"><a href="Python/utils/spiral.py.html">spiral</a></td><td valign="top" align="left"></td></tr>
</table>
</td></tr>
</table>
</td>
</tr>
</table>
<hr>
<p><i><a href="index.html">Table of Contents</a></i></p>
<p>
This document and the software it describes are Copyright &copy; 2001-2005 Greg Landrum and Rational Discovery LLC.
<p>
<i>This document was automatically generated on Mon May 8 07:11:15 2006
by <a href="http://happydoc.sourceforge.net">HappyDoc</a> as modified by Greg Landrum</i>
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