RDPython

Modules

Python/

ClientForm	HTML form handling for web clients.
__init__	A module for Geometry stuff
RDBuild	variables and definitions for distutils builds
RDConfig	Configuration for Rational Discovery's Python code
RDLogger
RDRandom	making random numbers consistent so we get good regressions
TestRunner

Python/Chem/

AllChem	Import all RDKit chemistry modules
AvailDescriptors	constructs the list of available descriptors
BuildFragmentCatalog	command line utility for working with FragmentCatalogs (CASE-type analysis)
CDXMLWriter	Dumping CDXML from python
ChemicalFeatures
ChemicalForceFields
Crippen	Atom-based calculation of LogP and MR using Crippen's approach
DSViewer	uses DSViewer to interact with molecules
Descriptors
FeatFinderCLI
FragmentCatalog
FragmentMatcher	exposes a class for matching fragments of molecules.
Fragments	functions to match a bunch of fragment descriptors from a file
GraphDescriptors	Calculation of topological/topochemical descriptors.
Graphs	Python functions for manipulating molecular graphs
Lipinski	Calculation of Lipinski parameters for molecules
MACCSkeys	SMARTS definitions for the publically available MACCS keys
MolSurf	Exposes functionality for MOE-like approximate molecular surface area
PeriodicTable	periodic table data, obsolete
Polymers	Python functions for manipulating polymers
PyMol	uses pymol to interact with molecules
Randomize
SATIS	Functionality for SATIS typing atoms
ShowMols
TemplateAlign
UnitTestArom	unit testing code for the Crippen clogp and MR calculators
UnitTestCatalog
UnitTestChem	basic unit testing code for the molecule boost wrapper
UnitTestChemAtom	basic unit testing code for atoms
UnitTestChemBond	basic unit testing code for the Bond wrapper
UnitTestChemSmarts	basic unit testing code for the wrapper of the SMARTS matcher
UnitTestChemv2	basic unit testing code for the rdkit Boost wrapper
UnitTestCrippen	unit testing code for the Crippen clogp and MR calculators
UnitTestFragmentDescriptors	Unit Test code for Fragment Descriptors
UnitTestFragments	Unit Test code for cFragments module
UnitTestGraphDescriptors.2	unit testing code for graph-theoretical descriptors
UnitTestLipinski	unit testing code for Lipinski parameter calculation
UnitTestOldBugs	testing code inspired by old bugs
UnitTestSATIS	unit testing code for the SATIS numbers
UnitTestSmiles	basic unit testing code for SMILES canonicalization
UnitTestSubgraphs	unit testing code for the subgraph code
UnitTestSuppliers	unit testing code for molecule suppliers
UnitTestSurf	unit testing code for surface calculations
test_list

Python/Chem/AtomPairs/

Pairs	Contains an implementation of Atom-pair fingerprints, as
Torsions	Contains an implementation of Topological-torsion fingerprints, as

Python/Chem/ChemUtils/

BulkTester
SDFToCSV

Python/Chem/Draw/

DrawUtils
MolDrawing

Python/Chem/EState/

AtomTypes	contains SMARTS definitions and calculators for EState atom types
EState	Basic EState definitions
EState_VSA	Hybrid EState-VSA descriptors (like the MOE VSA descriptors)
Fingerprinter	EState fingerprinting
UnitTestEState	unit testing code for the EState indices
UnitTestTypes	unit testing code for the EState atom typing
UnitTestVSA	unit testing code for MOE-type descriptors with EStates

Python/Chem/Features/

FeatDirUtils

Python/Chem/Fingerprints/

ClusterMols	utility functionality for clustering molecules using fingerprints
DbFpSupplier	Supplies a class for working with fingerprints from databases
FingerprintMols	utility functionality for fingerprinting sets of molecules
Fingerprints	Python functions for path-based (like Daylight) molecular fingerprinting
MolSimilarity	utility functionality for molecular similarity
SimilarityScreener	class definitions for similarity screening
UnitTestFingerprints	unit testing code for fingerprinting
UnitTestSimScreener	unit testing code for the SimilarityScreeners

Python/Chem/Pharm2D/

Generate	generation of 2D pharmacophores
Gobbi_Pharm2D	Definitions for 2D Pharmacophores from:
LazyGenerator	lazy generator of 2D pharmacophore signature data
Matcher	functionality for finding pharmacophore matches in molecules
SigFactory	contains factory class for producing signatures
Signature	data structures for holding 2D pharmacophore signatures
UnitTestGobbi	unit testing code for the signatures
UnitTestLazyGenerator	unit testing code for the lazy signature generator
UnitTestMatcher	unit testing code for the signatures
UnitTestSignature	unit testing code for the signatures
UnitTestUtils	unit testing code for the signature utils
Utils	utility functionality for the 2D pharmacophores code

Python/Chem/Pharm3D/

EmbedLib
ExcludedVolume	$Id: ExcludedVolume.py 2 2006-05-06 22:54:39Z glandrum $
Pharmacophore
UnitTestEmbed
UnitTestPharmacophore

Python/Chem/Suppliers/

DbMolSupplier	Supplies a class for working with molecules from databases
MolSupplier	Supplies an abstract class for working with sequences of molecules
SDMolSupplier	Supplies a class for working with molecules from SD files
SmilesMolSupplier	Supplies a class for working with molecules from SMILES tables and CSV files
UnitTestSDMolSupplier	unit testing code for the SD file handling stuff
UnitTestSmilesMolSupplier	unit testing code for the Smiles file handling stuff

Python/Chem/tests/

BuildCrippenTestSet
BuildDescrsTestSet

Python/ClientCookie/

_BSDDBCookieJar	Persistent CookieJar based on bsddb standard library module.
_ClientCookie	HTTP cookie handling for web clients, plus some other stuff.
_Debug
_HeadersUtil	Utility functions for HTTP header value parsing and construction.
_LWPCookieJar	Load / save to libwww-perl (LWP) format files.
_MSIECookieJar	Microsoft Internet Explorer cookie loading on Windows.
_MSIEDBCookieJar	Persistent CookieJar based on MS Internet Explorer cookie database.
_MozillaCookieJar	Mozilla / Netscape cookie loading / saving.
_Util	Python backwards-compat., date/time routines, seekable file object wrapper.
_urllib2_support	Integration with Python standard library module urllib2.

Python/DataStructs/

BitEnsemble	#DOC
BitEnsembleDb	This functionality gets mixed into the BitEnsemble class
BitUtils
BitVect	This has all be re-implemented in the C++ code
HierarchyVis	functionality for drawing hierarchical catalogs on sping
TopNContainer
UnitTestBitEnsemble	unit testing code for BitEnsembles
UnitTestBitVect	unit testing code for the python BitVects
UnitTestTopNContainer
UnitTestcBitVect	unit testing code for the C++ BitVects
UnitTestcBitVect2	unit testing code for the C++ ExplicitBitVects
VectCollection
testScreen

Python/Dbase/

DbConnection	defines class DbConnect, for abstracting connections to databases
DbInfo
DbModule
DbReport
DbResultSet	defines class DbResultSet for lazy interactions with Db query results
DbUtils	a set of functions for interacting with databases
Gui	simple GUI tools for interacting with databases
StorageUtils	Various storage (molecular and otherwise) functionality
UnitTestDbConnect	unit testing code for database connection objects
UnitTestDbResultSet	unit testing code for the DbResultSet object
UnitTestDbUtils	unit testing code for the database utilities
ibase_tut	A brief little demo/tutorial on use of the python <-> interbase adaptor

Python/Dbase/Pubmed/

PubmedUtils
QueryParams
Records
Searches	Tools for doing PubMed searches and processing the results

Python/Excel/

ExcelWrapper	a wrapper for interacting with Excel
Molecules	mixin class for dealing with ChemDraw for Excel

Python/Logger/

Logger	Provides a Logger class which can be wrapped around another
SpingDemo	demo code for the Logger class
UnitTestLogger	unit testing code for the logger

Python/ML/

AnalyzeComposite	command line utility to report on the contributions of descriptors to
BuildComposite	command line utility for building composite models
CompositeRun	contains a class to store parameters for and results from
DataFilter	command line utility for filtering data
EnrichPlot	Command line tool to construct an enrichment plot from saved composite models
GrowComposite	command line utility for growing composite models
MatOps	Matrix operations which may or may not come in handy some day
ScreenComposite	command line utility for screening composite models
UnitTestAnalyzeComposite	unit testing code for the AnalyzeComposite functionality
UnitTestBuildComposite	unit testing code for the BuildComposite functionality
UnitTestScreenComposite	unit testing code for the ScreenComposite functionality
files	Generic file manipulation stuff

Python/ML/Cluster/

ClusterModel	defines the ClusterModel
ClusterUtils	utility functions for clustering
ClusterVis	Cluster tree visualization using Sping
Clusters	contains the Cluster class for representing hierarchical cluster trees
Murtagh	Interface to the C++ Murtagh hierarchic clustering code
Resemblance	code for dealing with resemblance (metric) matrices
Standardize	contains code for standardization of data matrices for clustering
UnitTestCluster	unit testing code for clustering
murtagh_test

Python/ML/Composite/

AdjustComposite	functionality to allow adjusting composite model contents
BayesComposite	code for dealing with Bayesian composite models
Composite	code for dealing with composite models
CompositeCOM	the COM server for Composite models
UnitTestCOMServer
UnitTestComposite	unit testing code for composite models

Python/ML/Data/

DataUtils	Utilities for data manipulation
FindQuantBounds
MLData	classes to be used to help work with data sets
Quantize	Automatic search for quantization bounds
SplitData
Stats	various statistical operations on data
Transforms
UnitTestFilter	unit testing code for variable quantization
UnitTestMLData	unit testing code for MLData sets
UnitTestQuantize	unit testing code for variable quantization
UnitTestStats	unit testing code for the Stats module

Python/ML/DecTree/

Defines the class DecTreeNode, used to represent decision trees

Forest

code for dealing with forests (collections) of decision trees

ID3

ID3 Decision Trees

PruneTree

Contains functionality for doing tree pruning

QuantTree

Defines the class QuantTreeNode, used to represent decision trees with automatic

SigTree

Defines the class SigTreeNode, used to represent trees that

Tree

Implements a class used to represent N-ary trees

TreeUtils

Utilities for working with trees

TreeVis

functionality for drawing trees on sping canvases

UnitTestID3

unit tests for the ID3 implementation

UnitTestPrune

UnitTestQuantTree

unit tests for the QuantTree implementation

UnitTestSigTree

UnitTestTree

unit testing code for trees and decision trees (not learning/xvalidation)

UnitTestXVal

unit testing code for cross validation

randomforest

randomtest

Python/ML/Descriptors/

CompoundDescriptors	descriptor calculator for compounds defined by a composition alone
DescriptorsCOM	the COM server for Descriptor Calculators
MoleculeDescriptors	Various bits and pieces for calculating Molecular descriptors
Parser	The "parser" for compound descriptors.
UnitTestDescriptors	unit testing code for descriptors
UnitTestMolDescriptors	unit testing code for molecular descriptor calculators
UnitTestParser	unit testing code for compound descriptors

Python/ML/FeatureSelect/

CMIM	for the moment this is using Francois Fleuret's cmim library
UnitTestCMIM

Python/ML/InfoTheory/

BitClusterer
BitRank	Functionality for ranking bits using info gains
entropy	Informational Entropy functions
testBitRanker
testCorrMatGen

Python/ML/KNN/

DistFunctions
KNNClassificationModel	Define the class KNNClassificationModel, used to represent a k-nearest neighbhors classification model
KNNModel	Define the class KNNModel, used to represent a k-nearest neighbhors model
KNNRegressionModel	Define the class KNNRegressionModel, used to represent a k-nearest neighbhors
UnitTestKNN	unit testing code for knn models

Python/ML/MLUtils/

VoteImg

functionality for generating an image showing the results of a composite model voting on a data set

Python/ML/ModelPackage/

PackageUtils
Packager
UnitTestPackage	unit tests for the model and descriptor packager

Python/ML/NaiveBayes/

ClassificationModel	Defines Naive Baysean classification model
CrossValidate	handles doing cross validation with naive bayes models
UnitTestNB

Python/ML/Neural/

ActFuncs	Activation functions for neural network nodes
NetNode	Contains the class NetNode which is used to represent nodes in neural nets
Network	Contains the class Network which is used to represent neural nets
Trainers	Training algorithms for feed-forward neural nets
UnitTestTrainer	unit tests for the Neural network trainer implementation

Python/ML/SLT/

Risk	code for calculating empirical risk
UnitTestRisk	unit testing code for SLT Risk functions

Python/ML/test_data/

populate

Python/PySVD/

SVDPack
SVDSimilarity
UnitTestSVD	unit testing code for the SVD wrapper

Python/RDToDo/

HelpData
ItemEditImpl
OutlUtils
OutlineTree
OutlineTreeItem
RDOutline
RDToDo
TaskEditImpl
TextViewImpl
ToDoListItem
ToDoListView
ToDoTree
ToDoTreeItem
ToDoUtils

Python/RDToDo/forms/

itemdialog
mainform
taskdialog
textview

Python/RDToDo/icons/

icons

Python/Reports/

HTMLReport
PDFReport
ReportUtils

Python/SimDivFilters/

SimilarityPickers

Python/SimDivFilters/test_data/

genfps

Python/VLib/

Filter
Node
Output
Supply
Transform
UnitTestEnum	unit testing code for the virtual library enumerator
catalenum

Python/VLib/NodeLib/

DbMolSupply
DbPickleSupplier
SDSupply
SmartsMolFilter
SmartsRemover
SmilesDupeFilter
SmilesOutput
SmilesSupply
demo

Python/WebUtils/

ChemdrawPlugin	Code for dealing with the ChemDraw Plugin on web pages
General	General functionality used by the RDOnline Web Interfaces
Storage	A simple, primitive, shelve-based data storage system for persistence
WebStore	A simple, primitive, shelve-based data storage system for persistence

Python/mixins/

Loader	Everything required to load and initialize mixins
StateSaver	Allows mixins to save their state

Python/qtGui/

DbConnDialog	dialog for establishing db connections
DbConnWidgetImpl	implementation bits for DbConnWidgets
DbDialog	contains simple dialog box for holding db widgets
DbQueryDialog	dialog for setting up db queries
DbQueryWidgetImpl	implementation bits for DbQueryWidgets
DbWidget	contains a mixin class for the various Database widgets
GuiBase	base class for the main window in the qt MixinGui
GuiShell	provides a window with an interactive python shell
GuiTable	defines classes to make QTables more useful for us
GuiTextViewer	defines a class for viewing rich text
GuiUndo	undo functionality
PiddleWindowImpl	implementation bits for PiddleWindows
qtActiveX
qtUtils
rpcClient	components required to add an xml-rpc server to a qt application

Python/qtGui/GuiLib/

BuildClusterDialogImpl	implementation bits for BuildClusterDialogs
BuildCompositeDialogImpl	implementation bits for BuildCompositeDialogs
ClusterWindow	defines classes required for interacting with Clusters
CompositeUtils	general utilities for interacting with composites from GUIs
CompositeWindowImpl	implementation bits for CompositeWindows
DecTreeWindow	defines classes required for interacting with Dec Trees
DescTable	defines the DescTable class
FingerprintDbWidget	Defines a widget for working with fingerprints in databases
ModelBrowserDialogImpl	implementation bits for Model Browsers
ModelTable	defines classes required to put models in QTables
MolBrowserImpl	implementation bits for MolBrowsers
MolCanvas
MolDescriptorWinImpl	implementation bits for MolDescriptorWins
MolTable	defines classes required for using molecules in QTables
PubmedRecordImpl	implementation bits for Pubmed searching
PubmedSearchImpl	implementation bits for Pubmed searching
ScreenCompositeDialogImpl	implementation bits for ScreenCompositeDialogs
SignatureTable	defines classes required for using 2D pharmacophore signatures in QTables
SignatureViewDialogImpl	implementation bits for SignatureViewDialogs, which are for working with
SimilarityParamsImpl
SimilaritySearchWidgetImpl	implementation bits for Similarity Searching

Python/qtGui/GuiLib/Proto/

DataTransformWidgetImpl	implementation bits for DataTransformWidgets
LoaderWidgetImpl	implementation bits for SupplierWindows (for editing supplier

Python/qtGui/GuiLib/Proto/forms/

DataTransformWidget
LoaderWidget

Python/qtGui/GuiLib/forms/

BuildClusterDialog
BuildCompositeDialog
CompositeWindow
ModelBrowserDialog
MolBrowser
MolDescriptorWin
MolEditDisplayWidget2
PubmedRecordWidget
PubmedSearchWidget
ScreenCompositeDialog
SignatureViewDialog
SimilarityParams
SimilaritySearch
TextViewer
orig

Python/qtGui/HierarchyBrowser/

BrowserInputImpl	Implementation of the BrowserInput widget
HierarchyCatalogWindow	defines classes required for interacting with hierarchical catalogs

Python/qtGui/HierarchyBrowser/forms/

BrowserInput

Python/qtGui/MixIns/

ClusterInteract	Mixin for interacting with cluster trees
CompositeBase	Base composite interaction mixin
CompositeBuilder	Mixin for building composite models
CompositeInteract	Mixin for interacting with composite models
MolCluster	Ties the MolBrowser and ClusterInteract widgets together
MolDescriptors	Allows calculation of molecular descriptors
PiddleCanvas	Allows calculation of molecular descriptors
SigViewer	#DOC

Python/qtGui/PointSprinkler/

PointCanvas	point-sprinkler canvas
PointCanvasItems	point classes for the point-sprinkler canvas

Python/qtGui/Search3D/

ExcludedVolumeMixin	------------------------------------------------------------------------
LocalConfig
MolAlignmentList
Persist
PharmacophoreDefWidgets
PharmacophoreMixin	------------------------------------------------------------------------
ReplaceConfigCLI
ReplaceFDefCLI
Search3D
SearchUtils

Python/qtGui/Search3D/forms/

AtomCorrespondenceDialog
Search3DWidget

Python/qtGui/VisProg/

FilterWindowImpl	implementation bits for FilterWindows
NewReactionDialogImpl	implementation bits for NewReactionDialogs
ReactionBuilder	mixin providing reaction-cascade builder functionality on a visual programming
ReactionWindowImpl	implementation bits for ReactionWindows (for editing reaction
SinkWindowImpl	implementation bits for SinkWindows
SupplierWindowImpl	implementation bits for SupplierWindows (for editing supplier
VPCanvas	mixin providing a visual programming canvas
VPIcons
VPItems
VPLib
VPLink
VPUtils
genicons

Python/qtGui/VisProg/forms/

FilterWindow
NewReactionDialog
ReactionWindow
SinkWindow
SupplierWindow

Python/qtGui/forms/

BaseDialog
CountDialog
DbConnWidget
DbQueryWidget
ListSelectorDialog
PiddleWindow
pyshell

Python/sping/

README.html
colors
pagesizes	pagesizes.py
pid	PIDDLE (Plug-In Drawing, Does Little Else)
stringformat	Module StringFormat
utils

Python/sping/PDF/

pdfdoc	PDFgen is a library to generate PDF files containing text and graphics. It is the
pdfgen	PDFgen is a library to generate PDF files containing text and graphics. It is the
pdfgeom	This module includes any mathematical methods needed for PIDDLE.
pdfmetrics	This contains pre-canned text metrics for the PDFgen package, and may also
pdfutils
pidPDF	This is the PIDDLE back end for PDF. It acts as a wrapper

Python/sping/PIL/

pidPIL

Python/sping/PIL/pilfonts/

removemedium

Python/sping/PS/

fontinfo
latin1MetricsCache
pidPS	piddlePS - a PostScript backend for the PIDDLE drawing module
psmetrics

Python/sping/Pyart/

Fontmapping
pidPyart

Python/sping/Qt/

pidQt

piddleQt

Python/sping/ReportLab/

pidReportLab

Python/sping/SVG/

pidSVG

piddleSVG

Python/sping/TK/

pidTK

A Tkinter based backend for piddle.

Python/sping/WX/

pidWX	WXCanvas
pidWxDc	\

Python/sping/examples/

formatted-strings
tkCanvas-with-scrollbars
tkCanvasPIL-with-scrollbars

Python/sping/tests/

pidtest	piddletest.py
pstests
testallps

Python/sping/util/

HTMLPiddler

Python/utils/

GUIDs
GenLicense	generates license files for our primitive license handler
Licensing	primitive license handler
PiddleTools	Tools to be used with Piddle/Sping canvases
PilTools	tools for working with PIL images
REFile	contains class REFile, for working with files containing comments
SliceTools	tools for working with python slices
cactvs
chemdraw	tools for interacting with chemdraw
chemdraw_qax
chemutils	utility functions with "chemical know-how"
comhack	$Id: comhack.py 2 2006-05-06 22:54:39Z glandrum $
fileutils	utility functions to help work with files
listutils	utility functions for lists
pydoc_local	Generate Python documentation in HTML or text for interactive use.
spiral

Table of Contents

This document was automatically generated on Mon May 8 07:11:15 2006 by HappyDoc as modified by Greg Landrum