diff --git a/Docs/Code/index.html b/Docs/Code/index.html index 727053681..dbd43babb 100755 --- a/Docs/Code/index.html +++ b/Docs/Code/index.html @@ -1,799 +1,1541 @@ - - - - RDPython - - - - - -

Table of Contents

- - - - - - - - - -
RDPython -  
- - - - - - - - -
- - Modules  - - -   -
-

Python/

- - - -
RDConfig -Configuration for Rational Discovery's Python code - -
__init__
-

Python\Chem/

- - - - - - - - - - - - - - - - - - - - - - - - - - - -
CDXMLParser.OE
CanonSmiles -code for canonicalizing SMILES - -
DGeom -Python functions for working with dgeom - -
Fingerprints -Python functions for molecular fingerprinting - -
GraphDescriptors
Graphs -Python functions for manipulating molecular graphs - -
Lipinski
MACCSkeys
MolSurf
PeriodicTable
Polymers -Python functions for manipulating polymers - -
SATIS -Functionality for SATIS typing atoms - -
UnitTestChem -basic unit testing code for the OELib Boost wrapper - -
UnitTestChemAtom -basic unit testing code for the OELib atoms - -
UnitTestChemBond -basic unit testing code for the OELib Bond wrapper - -
UnitTestChemSmarts -basic unit testing code for the OELib Smarts matcher - -
UnitTestDGeom -basic unit testing code for DGeom usage - -
UnitTestFingerprints -unit testing code for fingerprinting - -
UnitTestGraphDescriptors -unit testing code for graph-theoretical descriptors - -
UnitTestLipinski -unit testing code for Lipinski parameter calculation - -
UnitTestPaths -unit testing code for graph-theoretical descriptors - -
UnitTestSATIS -unit testing code for the SATIS numbers - -
UnitTestSmiles -basic unit testing code for SMILES canonicalization - -
UnitTestSurf -unit testing code for surface calculations - -
cluster
uniquepaths
-

Python\Chem\Query/

- - - - - - - -
ComponentQuery
MolQuery
QueryObj
UnitTestComponentQuery -unit testing code for component query objects - -
UnitTestMolQuery -unit testing code for molecule query objects - -
UnitTestQueryObjs -unit testing code for query objects - -
-

Python\Chem\dbtest/

- - - -
builddb
test
-

Python\DataStructs/

- - - - - - - -
BitRank -Functionality for ranking bits - -
BitUtils
BitVect
UnitTestBitVect
UnitTestcBitVect
testScreen
-

Python\Dbase/

- - - - -
DbConnection -defines class DbConnect, for abstracting connections to databases - -
DbUtils -a set of functions for interacting with databases - -
ibase_tut -A brief little demo/tutorial on use of the python <-> interbase adaptor - -
-

Python\Excel/

- - -
ExcelWrapper -a wrapper for interacting with Excel - -
-

Python\ExptDesign/

- - - - - -
ActiveDesigner -A simple experimental designer which returns the first N actives - -
BaseDesigner -Assume the enumerator returns a 2-tuple: - -
DesignUtils -utilities for experimental design - -
UnitTestDesigner -unit testing code for experimental design - -
-

Python\GuiFramework/

- - - - - - - - - - - -
GuiDialog -defines a wrapper class for dialogs - -
GuiFrame -defines a wrapper class for frames (similar to windows) - -
GuiGrid -a Grid (spreadsheet like) class - -
GuiHistoryField -a widget which allows text entry or selection from a list and stores - -
GuiHtml -Defines a widget for rendering HTML in windows - -
GuiIDs -functionality for maintaing unique IDs - -
GuiNotebook -provides a wrapper around the wxNotebook class - -
MenuBar -provides a menu bar class - -
UnitTestGuiBase -does some voodoo magic to attach an xmlrpc server to a GUI - -
rpcMixin -provides xmlrpc server functionality for wxPython applications via a mixin class - -
-

Python\GuiFramework\GuiLib/

- - - - - - - - - - - - - - -
ClusterGui -mixin functionality for clustering data - -
DecTreeGui -GUI mixin for building decision trees - -
DescriptorCalc -GUI mixin for building descriptor calculators - -
ExcelStuff -GUI mixin for interacting with Excel - -
ForestVis -mixin functionality for visualizing decision forests - -
MolDb
MolViewers -GUI mixin for interacting with the WebLab and Accord OCX controls - -
MolecImage
NetVis
PCAGui -mixin functionality for clustering data - -
PiddleCanvas
TreeVis
WebLab -GUI mixin for interacting with the WebLab OCX control - -
-

Python\GuiFramework\GuiLib\tests/

- - -
TestTemplate
-

Python\HybridDB/

- - - -
HybridBase
ZHybrid
-

Python\HybridDB\test/

- - - - -
UnitTest1 -unit testing code for the HybridDB - -
buildtest1
test1
-

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 - -
demo
-

Python\ML/

- - - - - - - - -
AnalyzeComposite -command line utility to report on the contributions of descriptors to - -
BuildComposite -command line utility for building composite models - -
DataFilter -command line utility for filtering data - -
EnrichPlot -Command line tool to construct an enrichment plot from saved composite models - -
MatOps -Matrix operations which may or may not come in handy some day - -
ScreenComposite -command line utility for screening composite models - -
files -Generic file manipulation stuff - -
-

Python\ML\Cluster/

- - - - - - - - - - - - - - - -
Algorithms -Specific clustering algorithms - -
Classify -functionality for using clusters as classifiers - -
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 - -
Driver -Drivers for generating cluster hierarchies - -
Murtagh
Resemblance -code for dealing with resemblance (metric) matrices - -
Standardize -contains code for standardization of data matrices for clustering - -
UnitTestClassify -unit testing code for cluster classification and the ClusterModel - -
UnitTestCluster -unit testing code for clustering - -
murtagh_test
testdivide
-

Python\ML\Composite/

- - - - - -
BayesComposite -code for dealing with Bayesian composite models - -
Composite -code for dealing with composite models - -
CompositeCOM -the COM server for Composite models - -
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 - -
Stats -various statistical operations on data - -
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/

- - - - - - - - - - - - - - - - - -
AutoQuantTree
BuildQuantTree
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 - -
Tree -Implements a class used to represent N-ary trees - -
TreeUtils -Utilities for working with trees - -
UnitTestID3 -unit tests for the ID3 implementation - -
UnitTestQuantTree -unit tests for the QuantTree implementation - -
UnitTestTree -unit testing code for trees and decision trees (not learning/xvalidation) - -
UnitTestXVal -unit testing code for cross validation - -
entropy -Informational Entropy functions - -
randomforest
randomtest
-

Python\ML\Descriptors/

- - - - - - - -
Descriptors -Various bits and pieces for calculating descriptors - -
DescriptorsCOM -the COM server for Descriptor Calculators - -
Parser -The "parser" for compound descriptors. - -
UnitTestCOMServer -unit testing code for the descriptor COM server - -
UnitTestDescriptors -unit testing code for descriptors - -
UnitTestParser -unit testing code for compound descriptors - -
-

Python\ML\MLUtils/

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

Python\ML\Neural/

- - - - - - - -
ActFuncs -Activation functions for neural network nodes - -
CrossValidate -handles doing cross validation with neural nets - -
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\RDJobMan/

- - - - - - - - - -
RDJM_Clients
RDJM_User
RDJobMan
RDJobManImpl
Server
UnitTestJobMan -unit testing code for the RDJobManager - -
testclient
ztest
-

Python\RDToDo/

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

Python\RDToDo\forms/

- - - - - -
itemdialog
mainform
taskdialog
textview
-

Python\VLib/

- - - - - - - - -
EnumNodes -Functionality for nodes in a virtual library enumerator - -
EnumUtils -Utility functions for virtual library enumerators - -
EnumVis -visualization code for Virtual Library Enumerators - -
Results -defines a class used to store and manipulate results from - -
UnitTestEnum -unit testing code for the virtual library enumerator - -
VLibCOM -the COM server for virtual library enumerators - -
catalenum
-

Python\VLib\NodeLib/

- - - - - -
DupFilter
HeteroInserter
SDFSupply
testhetero
-

Python\Zope/

- - -
NCIload
-

Python\mixins/

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

Python\qtGui/

- - - - - - - - -
Gui -Mixin GUI launcher - -
GuiBase
GuiShell
GuiUndo -undo functionality - -
base
qtUtils
rpcClient -required components to add an xml-rpc server to a qt application - -
-

Python\qtGui\Graph/

- - -
Node
-

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.orig
VPIcons
VPItems
VPLib
VPLink.orig
VPLink
VPUtils
genicons
icons
-

Python\qtGui\VisProg\forms/

- - - - - - -
FilterWindow
NewReactionDialog
ReactionWindow
SinkWindow
SupplierWindow
-

Python\qtGui\forms/

- - -
pyshell
-

Python\utils/

- - - - - - - - -
PiddleTools -Tools to be used with Piddle/Sping canvases - -
PilTools -tools for working with PIL images and wxPython - -
REFile -contains class REFile, for working with files containing comments - -
SliceTools -tools for working with python slices - -
chemdraw
chemutils -utility functions with "chemical know-how" - -
fileutils -utility functions to help work with files - -
-
- -
- -
- -

Table of Contents

- -

- This document and the software it describes are Copyright © 2001 Greg Landrum and Rational Discovery LLC. - -

- This document was automatically generated on Sat Jun 29 07:16:25 2002 - by HappyDoc as modified by Greg Landrum - - - + + + + RDPython + + + + + +

Table of Contents

+ + + + + + + + + +
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/

+ + + + + + + + + + + + + + + + + + + + + +
AutoQuantTree
BuildQuantTree
BuildSigTree
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 +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 +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 and the software it describes are Copyright © 2001-2005 Greg Landrum and Rational Discovery LLC. + +

+ This document was automatically generated on Mon May 8 07:11:15 2006 + by HappyDoc as modified by Greg Landrum + + + \ No newline at end of file diff --git a/Scripts/MailResults.py b/Scripts/MailResults.py index b52e93974..c66a48fbd 100755 --- a/Scripts/MailResults.py +++ b/Scripts/MailResults.py @@ -2,6 +2,10 @@ import sys, smtplib, base64, cStringIO, time, os.path from email import Message, Utils +SMTP_HOSTNAME='' +FROM_ADDR='' +TO_ADDR='' + def sendLog(fileName,summaryName=""): msg = Message.Message() @@ -39,9 +43,9 @@ def sendLog(fileName,summaryName=""): msg.attach(subMsg) - smtp = smtplib.SMTP('mail.sbcglobal.net') - smtp.sendmail('Build@RationalDiscovery.com', - ['Landrum@RationalDiscovery.com'], + smtp = smtplib.SMTP(SMTP_HOSTNAME) + smtp.sendmail(FROM_ADDR, + [TO_ADDR], msg.as_string()) smtp.quit() diff --git a/Scripts/NightlyBuildAndTest.sh b/Scripts/NightlyBuildAndTest.sh index 310350f2e..26b9eee26 100755 --- a/Scripts/NightlyBuildAndTest.sh +++ b/Scripts/NightlyBuildAndTest.sh @@ -49,18 +49,17 @@ echo "**** PULL ****" >> $LOGFILE 2>&1 echo "**** PULL ****" echo >> $LOGFILE 2>&1 echo >> $LOGFILE 2>&1 -SVNROOT=svn://marten/RD/trunk -svn checkout --username=NightlyBuild --password=rdnightly -N $SVNROOT RD &> /dev/null +SVNROOT=https://svn.sourceforge.net/svnroot/rdkit/trunk +svn checkout -N $SVNROOT RD &> /dev/null cd RD -svn checkout --username=NightlyBuild --password=rdnightly -N $SVNROOT/Data Data &> /dev/null -svn checkout --username=NightlyBuild --password=rdnightly -N $SVNROOT/Data/Proprietary/SPECS Data/Proprietary/SPECS &> /dev/null -svn checkout --username=NightlyBuild --password=rdnightly -N $SVNROOT/Data/NCI Data/NCI &> /dev/null +svn checkout -N $SVNROOT/Data Data &> /dev/null +svn checkout -N $SVNROOT/Data/NCI Data/NCI &> /dev/null for foo in Code bin Python; do - svn checkout --username=NightlyBuild --password=rdnightly $SVNROOT/$foo $foo &> /dev/null + svn checkout $SVNROOT/$foo $foo &> /dev/null done -svn checkout --username=NightlyBuild --password=rdnightly -N $SVNROOT/External External &> /dev/null +svn checkout -N $SVNROOT/External External &> /dev/null for foo in Lapack++ libsvm svdlibc svdpackc vflib-2.0 cmim-1.0 HappyDoc-r1_3; do - svn checkout --username=NightlyBuild --password=rdnightly $SVNROOT/External/$foo External/$foo &> /dev/null + svn checkout $SVNROOT/External/$foo External/$foo &> /dev/null done # ------------------------- -------------------------