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Module Hierarchy
RDRandom
:
making random numbers consistent so we get good regressions
rdkit.Avalon
rdkit.Chem
:
A module for molecules and stuff
rdkit.Chem.AllChem
:
Import all RDKit chemistry modules
rdkit.Chem.AtomPairs
rdkit.Chem.AtomPairs.Pairs
:
Contains an implementation of Atom-pair fingerprints, as described in:
rdkit.Chem.AtomPairs.Torsions
:
Contains an implementation of Topological-torsion fingerprints, as described in:
rdkit.Chem.AtomPairs.Utils
rdkit.Chem.BRICS
:
Implementation of the BRICS algorithm from Degen et al.
rdkit.Chem.BuildFragmentCatalog
:
command line utility for working with FragmentCatalogs (CASE-type analysis)
rdkit.Chem.ChemUtils
rdkit.Chem.ChemUtils.AlignDepict
rdkit.Chem.ChemUtils.BulkTester
rdkit.Chem.ChemUtils.SDFToCSV
rdkit.Chem.ChemUtils.TemplateExpand
rdkit.Chem.ChemicalFeatures
rdkit.Chem.ChemicalForceFields
rdkit.Chem.Crippen
:
Atom-based calculation of LogP and MR using Crippen's approach
rdkit.Chem.DSViewer
:
uses DSViewer to interact with molecules
rdkit.Chem.Descriptors
rdkit.Chem.Draw
rdkit.Chem.Draw.IPythonConsole
rdkit.Chem.Draw.MolDrawing
rdkit.Chem.Draw.SimilarityMaps
rdkit.Chem.Draw.aggCanvas
rdkit.Chem.Draw.cairoCanvas
rdkit.Chem.Draw.canvasbase
rdkit.Chem.Draw.mplCanvas
rdkit.Chem.Draw.qtCanvas
rdkit.Chem.Draw.spingCanvas
rdkit.Chem.EState
:
A module for Kier and Hall's EState Descriptors
rdkit.Chem.EState.AtomTypes
:
contains SMARTS definitions and calculators for EState atom types
rdkit.Chem.EState.EState
:
Basic EState definitions
rdkit.Chem.EState.EState_VSA
:
Hybrid EState-VSA descriptors (like the MOE VSA descriptors)
rdkit.Chem.EState.Fingerprinter
:
EState fingerprinting
rdkit.Chem.FastSDMolSupplier
rdkit.Chem.FeatFinderCLI
rdkit.Chem.FeatMaps
rdkit.Chem.FeatMaps.FeatMapParser
rdkit.Chem.FeatMaps.FeatMapPoint
rdkit.Chem.FeatMaps.FeatMapUtils
rdkit.Chem.FeatMaps.FeatMaps
rdkit.Chem.Features
rdkit.Chem.Features.FeatDirUtilsRD
rdkit.Chem.Features.ShowFeats
rdkit.Chem.Fingerprints
rdkit.Chem.Fingerprints.ClusterMols
:
utility functionality for clustering molecules using fingerprints includes a command line app for clustering
rdkit.Chem.Fingerprints.DbFpSupplier
:
Supplies a class for working with fingerprints from databases...
rdkit.Chem.Fingerprints.FingerprintMols
:
utility functionality for fingerprinting sets of molecules includes a command line app for working with fingerprints and databases
rdkit.Chem.Fingerprints.MolSimilarity
:
utility functionality for molecular similarity includes a command line app for screening databases
rdkit.Chem.Fingerprints.SimilarityScreener
:
class definitions for similarity screening
rdkit.Chem.Fraggle
rdkit.Chem.Fraggle.FraggleSim
rdkit.Chem.FragmentCatalog
rdkit.Chem.FragmentMatcher
:
exposes a class for matching fragments of molecules.
rdkit.Chem.Fragments
:
functions to match a bunch of fragment descriptors from a file
rdkit.Chem.FunctionalGroups
rdkit.Chem.GraphDescriptors
:
Calculation of topological/topochemical descriptors.
rdkit.Chem.Graphs
:
Python functions for manipulating molecular graphs
rdkit.Chem.Lipinski
:
Calculation of Lipinski parameters for molecules
rdkit.Chem.MACCSkeys
:
SMARTS definitions for the publically available MACCS keys and a MACCS fingerprinter
rdkit.Chem.MCS
rdkit.Chem.MolCatalog
rdkit.Chem.MolDb
rdkit.Chem.MolDb.FingerprintUtils
rdkit.Chem.MolDb.Loader
rdkit.Chem.MolDb.Loader_orig
rdkit.Chem.MolDb.Loader_sa
rdkit.Chem.MolSurf
:
Exposes functionality for MOE-like approximate molecular surface area descriptors.
rdkit.Chem.PandasTools
:
Importing pandasTools enables several features that allow for using RDKit molecules as columns of a Pandas dataframe.
rdkit.Chem.PeriodicTable
:
periodic table data, **obsolete**
rdkit.Chem.Pharm2D
:
module with functionality for 2D pharmacophores
rdkit.Chem.Pharm2D.Generate
:
generation of 2D pharmacophores
rdkit.Chem.Pharm2D.Gobbi_Pharm2D
:
Definitions for 2D Pharmacophores from: Gobbi and Poppinger, Biotech.
rdkit.Chem.Pharm2D.LazyGenerator
rdkit.Chem.Pharm2D.Matcher
:
functionality for finding pharmacophore matches in molecules
rdkit.Chem.Pharm2D.SigFactory
:
contains factory class for producing signatures
rdkit.Chem.Pharm2D.Utils
:
utility functionality for the 2D pharmacophores code
rdkit.Chem.Pharm3D
rdkit.Chem.Pharm3D.EmbedLib
rdkit.Chem.Pharm3D.ExcludedVolume
rdkit.Chem.Pharm3D.Pharmacophore
rdkit.Chem.PropertyMol
rdkit.Chem.PyMol
:
uses pymol to interact with molecules
rdkit.Chem.Randomize
rdkit.Chem.Recap
:
Implementation of the RECAP algorithm from Lewell et al.
rdkit.Chem.SATIS
:
Functionality for SATIS typing atoms
rdkit.Chem.SaltRemover
rdkit.Chem.Scaffolds
rdkit.Chem.Scaffolds.MurckoScaffold
:
Generation of Murcko scaffolds from a molecule
rdkit.Chem.ShowMols
rdkit.Chem.SimpleEnum
rdkit.Chem.SimpleEnum.Enumerator
rdkit.Chem.Subshape
rdkit.Chem.Subshape.BuilderUtils
rdkit.Chem.Subshape.SubshapeAligner
rdkit.Chem.Subshape.SubshapeBuilder
rdkit.Chem.Subshape.SubshapeObjects
rdkit.Chem.Suppliers
rdkit.Chem.Suppliers.DbMolSupplier
:
Supplies a class for working with molecules from databases...
rdkit.Chem.Suppliers.MolSupplier
:
Supplies an abstract class for working with sequences of molecules
rdkit.Chem.TemplateAlign
rdkit.Chem.TorsionFingerprints
:
Torsion Fingerprints (Deviation) (TFD) According to a paper from Schulz-Gasch et al., JCIM, 52, 1499-1512 (2012).
rdkit.Chem.fmcs
:
Actual implementation of the FMCS algorithm...
rdkit.Chem.fmcs.fmcs
:
FMCS - Find Maximum Common Substructure
rdkit.Chem.inchi
rdkit.DataManip
rdkit.DataManip.Metric
rdkit.DataStructs
rdkit.DataStructs.BitEnsemble
:
#DOC
rdkit.DataStructs.BitEnsembleDb
:
This functionality gets mixed into the BitEnsemble class
rdkit.DataStructs.BitUtils
rdkit.DataStructs.BitVect
:
This has all be re-implemented in the C++ code
rdkit.DataStructs.HierarchyVis
:
functionality for drawing hierarchical catalogs on sping...
rdkit.DataStructs.LazySignature
rdkit.DataStructs.SparseIntVect
rdkit.DataStructs.TopNContainer
rdkit.DataStructs.VectCollection
rdkit.Dbase
:
a module for interacting with databases
rdkit.Dbase.DbConnection
:
defines class _DbConnect_, for abstracting connections to databases
rdkit.Dbase.DbInfo
rdkit.Dbase.DbModule
rdkit.Dbase.DbReport
rdkit.Dbase.DbResultSet
:
defines class _DbResultSet_ for lazy interactions with Db query results
rdkit.Dbase.DbUtils
:
a set of functions for interacting with databases
rdkit.Dbase.Pubmed
rdkit.Dbase.Pubmed.PubmedUtils
rdkit.Dbase.Pubmed.QueryParams
rdkit.Dbase.Pubmed.Records
rdkit.Dbase.Pubmed.Searches
:
Tools for doing PubMed searches and processing the results
rdkit.Dbase.StorageUtils
:
Various storage (molecular and otherwise) functionality
rdkit.DistanceGeometry
rdkit.ForceField
rdkit.Geometry
:
A module for Geometry stuff ...
rdkit.ML
:
module containing machine learning code
rdkit.ML.AnalyzeComposite
:
command line utility to report on the contributions of descriptors to tree-based composite models
rdkit.ML.BuildComposite
:
command line utility for building composite models
rdkit.ML.Cluster
rdkit.ML.Cluster.Butina
:
Implementation of the clustering algorithm published in:...
rdkit.ML.Cluster.ClusterUtils
:
utility functions for clustering
rdkit.ML.Cluster.ClusterVis
:
Cluster tree visualization using Sping
rdkit.ML.Cluster.Clusters
:
contains the Cluster class for representing hierarchical cluster trees
rdkit.ML.Cluster.Murtagh
:
Interface to the C++ Murtagh hierarchic clustering code
rdkit.ML.Cluster.Resemblance
:
code for dealing with resemblance (metric) matrices
rdkit.ML.Cluster.Standardize
:
contains code for standardization of data matrices for clustering
rdkit.ML.Composite
rdkit.ML.Composite.AdjustComposite
:
functionality to allow adjusting composite model contents
rdkit.ML.Composite.BayesComposite
:
code for dealing with Bayesian composite models
rdkit.ML.Composite.Composite
:
code for dealing with composite models
rdkit.ML.CompositeRun
:
contains a class to store parameters for and results from...
rdkit.ML.Data
rdkit.ML.Data.DataUtils
:
Utilities for data manipulation
rdkit.ML.Data.FindQuantBounds
rdkit.ML.Data.MLData
:
classes to be used to help work with data sets
rdkit.ML.Data.Quantize
:
Automatic search for quantization bounds
rdkit.ML.Data.SplitData
rdkit.ML.Data.Stats
:
various statistical operations on data
rdkit.ML.Data.Transforms
rdkit.ML.DecTree
:
Here we're implementing the Decision Tree stuff found in Chapter 3 of Tom Mitchell's Machine Learning Book.
rdkit.ML.DecTree.BuildQuantTree
:
rdkit.ML.DecTree.BuildSigTree
:
rdkit.ML.DecTree.CrossValidate
:
handles doing cross validation with decision trees
rdkit.ML.DecTree.DecTree
:
Defines the class _DecTreeNode_, used to represent decision trees
rdkit.ML.DecTree.Forest
:
code for dealing with forests (collections) of decision trees
rdkit.ML.DecTree.ID3
:
ID3 Decision Trees
rdkit.ML.DecTree.PruneTree
:
Contains functionality for doing tree pruning
rdkit.ML.DecTree.QuantTree
:
Defines the class _QuantTreeNode_, used to represent decision trees with automatic quantization bounds
rdkit.ML.DecTree.SigTree
:
Defines the class SigTreeNode, used to represent trees that use signatures (bit vectors) to represent data.
rdkit.ML.DecTree.Tree
:
Implements a class used to represent N-ary trees
rdkit.ML.DecTree.TreeUtils
:
Utilities for working with trees
rdkit.ML.DecTree.TreeVis
:
functionality for drawing trees on sping canvases
rdkit.ML.Descriptors
rdkit.ML.Descriptors.CompoundDescriptors
:
descriptor calculator for compounds defined by a composition alone...
rdkit.ML.Descriptors.Descriptors
:
Various bits and pieces for calculating descriptors
rdkit.ML.Descriptors.MoleculeDescriptors
:
Various bits and pieces for calculating Molecular descriptors
rdkit.ML.Descriptors.Parser
:
The "parser" for compound descriptors.
rdkit.ML.EnrichPlot
:
Command line tool to construct an enrichment plot from saved composite models
rdkit.ML.GrowComposite
:
command line utility for growing composite models
rdkit.ML.InfoTheory
:
Information Theory functionality
rdkit.ML.InfoTheory.BitClusterer
rdkit.ML.InfoTheory.BitRank
:
Functionality for ranking bits using info gains
rdkit.ML.InfoTheory.entropy
:
Informational Entropy functions
rdkit.ML.KNN
:
rdkit.ML.KNN.CrossValidate
:
handles doing cross validation with k-nearest neighbors model
rdkit.ML.KNN.DistFunctions
rdkit.ML.KNN.KNNClassificationModel
:
Define the class _KNNClassificationModel_, used to represent a k-nearest neighbhors classification model
rdkit.ML.KNN.KNNModel
:
Define the class _KNNModel_, used to represent a k-nearest neighbhors model
rdkit.ML.KNN.KNNRegressionModel
:
Define the class _KNNRegressionModel_, used to represent a k-nearest neighbhors regression model
rdkit.ML.MLUtils
rdkit.ML.MLUtils.VoteImg
:
functionality for generating an image showing the results of a composite model voting on a data set
rdkit.ML.MatOps
:
Matrix operations which may or may not come in handy some day
rdkit.ML.ModelPackage
rdkit.ML.ModelPackage.PackageUtils
rdkit.ML.ModelPackage.Packager
rdkit.ML.NaiveBayes
:
rdkit.ML.NaiveBayes.ClassificationModel
:
Defines Naive Baysean classification model...
rdkit.ML.NaiveBayes.CrossValidate
:
handles doing cross validation with naive bayes models...
rdkit.ML.Neural
rdkit.ML.Neural.ActFuncs
:
Activation functions for neural network nodes
rdkit.ML.Neural.CrossValidate
:
handles doing cross validation with neural nets
rdkit.ML.Neural.NetNode
:
Contains the class _NetNode_ which is used to represent nodes in neural nets
rdkit.ML.Neural.Network
:
Contains the class _Network_ which is used to represent neural nets
rdkit.ML.Neural.Trainers
:
Training algorithms for feed-forward neural nets
rdkit.ML.SLT
rdkit.ML.SLT.Risk
:
code for calculating empirical risk
rdkit.ML.Scoring
rdkit.ML.Scoring.Scoring
:
$Id$
rdkit.ML.ScreenComposite
:
command line utility for screening composite models
rdkit.ML.files
:
Generic file manipulation stuff
rdkit.Numerics
:
A module for Numerics stuff ...
rdkit.SimDivFilters
rdkit.SimDivFilters.SimilarityPickers
rdkit.VLib
rdkit.VLib.Filter
rdkit.VLib.Node
rdkit.VLib.NodeLib
rdkit.VLib.NodeLib.DbMolSupply
rdkit.VLib.NodeLib.DbPickleSupplier
rdkit.VLib.NodeLib.SDSupply
rdkit.VLib.NodeLib.SmartsMolFilter
rdkit.VLib.NodeLib.SmartsRemover
rdkit.VLib.NodeLib.SmilesDupeFilter
rdkit.VLib.NodeLib.SmilesOutput
rdkit.VLib.NodeLib.SmilesSupply
rdkit.VLib.NodeLib.demo
rdkit.VLib.Output
rdkit.VLib.Supply
rdkit.VLib.Transform
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