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[ Module Hierarchy | Class Hierarchy ]

# Class Hierarchy

- rdkit.DataStructs.BitVect.BitVect
  - rdkit.DataStructs.BitVect.SparseBitVect
- rdkit.ML.CompositeRun.CompositeRun: class to store parameters for and results from Composite building
- rdkit.ML.Descriptors.Descriptors.DescriptorCalculator: abstract base class for descriptor calculators
  - rdkit.ML.Descriptors.CompoundDescriptors.CompoundDescriptorCalculator: used for calculating descriptors
  - rdkit.ML.Descriptors.MoleculeDescriptors.MolecularDescriptorCalculator: used for calculating descriptors for molecules
- rdkit.ML.Descriptors.DescriptorsCOM.DescriptorServer: exposes an interface for descriptor calculator COM servers
- exceptions.Exception
- rdkit.Chem.Pharm3D.Pharmacophore.ExplicitPharmacophore: this is a pharmacophore with explicit point locations and radii...
- rdkit.Logger.demo.Foo: a simple class...
- rdkit.DataStructs.LazySignature.LazySig
- rdkit.ML.NaiveBayes.ClassificationModel.NaiveBayesClassifier: _NaiveBayesClassifier_s can save the following pieces of internal state, accessible via standard setter/getter functions:
- rdkit.ML.Neural.NetNode.NetNode: a node in a neural network
- rdkit.ML.Neural.Network.Network: a neural network
- rdkit.Chem.Pharm3D.Pharmacophore.Pharmacophore
- rdkit.ML.files.ReFile: convenience class for dealing with files with comments
- rdkit.ML.DecTree.Tree.TreeNode: This is your bog standard Tree class.
  - rdkit.ML.DecTree.DecTree.DecTreeNode: This is used to represent decision trees
    - rdkit.ML.DecTree.QuantTree.QuantTreeNode:
    - rdkit.ML.DecTree.SigTree.SigTreeNode:
- rdkit.VLib.NodeLib.DbPickleSupplier._lazyDataSeq: These classes are used to speed up (a lot) the process of pulling pickled objects from PostgreSQL databases.
- object: The most base type
  - rdkit.ML.Neural.ActFuncs.ActFunc: "virtual base class" for activation functions
    - rdkit.ML.Neural.ActFuncs.Sigmoid: the standard sigmoidal function
    - rdkit.ML.Neural.ActFuncs.TanH: the standard hyperbolic tangent function
  - exceptions.BaseException: Common base class for all exceptions
    - exceptions.Exception: Common base class for all non-exit exceptions.
      - rdkit.ML.ModelPackage.Packager.ClassificationError: used to signal problems generating predictions
      - rdkit.ML.ModelPackage.Packager.DescriptorCalculationError: used to signal problems generating descriptor values
      - RDConfig.ObsoleteCodeError
      - exceptions.StandardError: Base class for all standard Python exceptions that do not represent interpreter exiting.
        - exceptions.AssertionError: Assertion failed.
        - exceptions.RuntimeError: Unspecified run-time error.
          - rdkit.Dbase.DbConnection.DbError
        - exceptions.ValueError: Inappropriate argument value (of correct type).
          - rdkit.Chem.FeatMaps.FeatMapParser.FeatMapParseError
      - RDConfig.UnimplementedCodeError
  - rdkit.ML.InfoTheory.BitClusterer.BitClusterer: Class to cluster a set of bits based on their correllation
  - rdkit.DataStructs.BitEnsemble.BitEnsemble: used to store a collection of bits and score BitVects (or signatures) against them.
  - rdkit.Chem.FragmentCatalog.BitGainsInfo
  - rdkit.Dbase.DbReport.CDXImageTransformer
  - rdkit.Dbase.DbReport.CactvsImageTransformer
  - rdkit.Logger.Logger.Callable: this is just a simple class with a __call__ method we'll use to pass any method invocations back to the caller.
  - rdkit.Chem.Draw.cairoCanvas.Canvas
  - rdkit.ML.Cluster.Clusters.Cluster: a class for storing clusters/data
  - rdkit.ML.Cluster.ClusterVis.ClusterRenderer
  - rdkit.ML.Composite.Composite.Composite: a composite model
    - rdkit.ML.Composite.BayesComposite.BayesComposite: a composite model using Bayesian statistics in the Decision Proxy
  - rdkit.ML.Composite.CompositeCOM.CompositeServer: exposes an interface for composite COM servers
  - rdkit.Dbase.DbConnection.DbConnect: This class is intended to abstract away many of the details of interacting with databases.
  - rdkit.Dbase.DbResultSet.DbResultBase
    - rdkit.Dbase.DbResultSet.DbResultSet: Only supports forward iteration
    - rdkit.Dbase.DbResultSet.RandomAccessDbResultSet: Supports random access
  - rdkit.Chem.FeatMaps.FeatMapUtils.DirMergeMode
  - rdkit.Chem.DSViewer.Displayable
  - rdkit.Chem.Pharm3D.ExcludedVolume.ExcludedVolume
  - rdkit.Chem.FastSDMolSupplier.FastSDMolSupplier: A wrapper around an SDMolSupplier that precomputes and stores molecular indices (via text processing) to allow quick length calculations and random access.
  - rdkit.Chem.FeatMaps.FeatMaps.FeatDirScoreMode
  - rdkit.Chem.FeatMaps.FeatMaps.FeatMap
  - rdkit.Chem.FeatMaps.FeatMaps.FeatMapParams: one of these should be instantiated for each...
  - rdkit.Chem.FeatMaps.FeatMapParser.FeatMapParser
  - rdkit.Chem.FeatMaps.FeatMaps.FeatMapScoreMode
  - rdkit.Chem.FeatMaps.FeatMaps.FeatMapParams.FeatProfile: scoring profile of the feature
  - rdkit.Chem.Fingerprints.FingerprintMols.FingerprinterDetails: class for storing the details of a fingerprinting run,...
  - rdkit.Chem.Draw.MolDrawing.Font
  - rdkit.ML.DecTree.Forest.Forest: a forest of unique decision trees.
  - rdkit.Chem.FragmentMatcher.FragmentMatcher
  - rdkit.Chem.Pharm2D.LazyGenerator.Generator: Important attributes:
  - rdkit.SimDivFilters.SimilarityPickers.GenericPicker
    - rdkit.SimDivFilters.SimilarityPickers.SpreadPicker: A class for picking the best matches across a library
    - rdkit.SimDivFilters.SimilarityPickers.TopNOverallPicker: A class for picking the top N overall best matches across a library
  - rdkit.ML.KNN.KNNModel.KNNModel: This is a base class used by KNNClassificationModel and KNNRegressionModel to represent a k-nearest neighbor predictor.
    - rdkit.ML.KNN.KNNClassificationModel.KNNClassificationModel: This is used to represent a k-nearest neighbor classifier
    - rdkit.ML.KNN.KNNRegressionModel.KNNRegressionModel: This is used to represent a k-nearest neighbor classifier
  - rdkit.Logger.Logger.Logger: This is the actual wrapper class.
  - rdkit.ML.Data.MLData.MLDataSet: A data set for holding general data (floats, ints, and strings)
    - rdkit.ML.Data.MLData.MLQuantDataSet: a data set for holding quantized data
  - rdkit.Chem.FeatMaps.FeatMapUtils.MergeMethod
  - rdkit.Chem.FeatMaps.FeatMapUtils.MergeMetric
  - rdkit.ML.ModelPackage.Packager.ModelPackage: a container class to package a composite model with a descriptor...
  - rdkit.Chem.Draw.MolDrawing.MolDrawing
  - rdkit.Chem.Suppliers.MolSupplier.MolSupplier: we must, at minimum, support forward iteration
    - rdkit.Chem.Suppliers.DbMolSupplier.DbMolSupplier: new molecules come back with all additional fields from the...
      - rdkit.Chem.Suppliers.DbMolSupplier.ForwardDbMolSupplier: DbMol supplier supporting only forward iteration
      - rdkit.Chem.Suppliers.DbMolSupplier.RandomAccessDbMolSupplier
  - rdkit.Chem.DSViewer.MolViewer
  - rdkit.Chem.PyMol.MolViewer
  - rdkit.Chem.Pharm2D.Signature.Pharm2DSig: **Notes on Use**
  - rdkit.Dbase.DbReport.RDImageTransformer
  - rdkit.Chem.Recap.RecapHierarchyNode: This class is used to hold the Recap hiearchy...
  - rdkit.Dbase.Pubmed.Records.Record
    - rdkit.Dbase.Pubmed.Records.JournalArticleRecord
    - rdkit.Dbase.Pubmed.Records.LinkRecord
    - rdkit.Dbase.Pubmed.Records.SummaryRecord
  - rdkit.Dbase.DbReport.ReportLabImageTransformer
  - rdkit.Chem.BuildFragmentCatalog.RunDetails
  - rdkit.Chem.Subshape.SubshapeObjects.ShapeWithSkeleton
  - rdkit.Chem.Pharm2D.SigFactory.SigFactory: SigFactory's are used by creating one, setting the relevant parameters, then calling the GetSignature() method each time a signature is required.
  - rdkit.PySVD.SVDSimilarity.SimilarityCalculator
  - rdkit.Chem.Fingerprints.SimilarityScreener.SimilarityScreener: base class
    - rdkit.Chem.Fingerprints.SimilarityScreener.ThresholdScreener: Used to return all compounds that have a similarity to the probe beyond a threshold value
    - rdkit.Chem.Fingerprints.SimilarityScreener.TopNScreener: A screener that only returns the top N hits found
  - rdkit.Chem.Subshape.SubshapeObjects.SkeletonPoint
  - rdkit.Chem.Subshape.SubshapeAligner.SubshapeAligner
  - rdkit.Chem.Subshape.SubshapeAligner.SubshapeAlignment
  - rdkit.Chem.Subshape.SubshapeBuilder.SubshapeBuilder
  - rdkit.Chem.Subshape.SubshapeBuilder.SubshapeCombineOperations
  - rdkit.Chem.Subshape.SubshapeAligner.SubshapeDistanceMetric
  - rdkit.Chem.Subshape.SubshapeObjects.SubshapeShape
  - unittest.TestCase: A class whose instances are single test cases.
    - rdkit.Chem.ChemUtils.SDFToCSV.TestCase
  - rdkit.DataStructs.TopNContainer.TopNContainer: maintains a sorted list of a particular number of data elements.
  - rdkit.ML.Neural.Trainers.Trainer: "virtual base class" for network trainers
    - rdkit.ML.Neural.Trainers.BackProp: implement back propagation (algorithm on pp 153-154 of Patterson)
  - rdkit.VLib.Node.VLibNode: base class for all virtual library nodes,...
    - rdkit.Chem.Fingerprints.DbFpSupplier.DbFpSupplier: new fps come back with all additional fields from the...
      - rdkit.Chem.Fingerprints.DbFpSupplier.ForwardDbFpSupplier: DbFp supplier supporting only forward iteration
      - rdkit.Chem.Fingerprints.DbFpSupplier.RandomAccessDbFpSupplier: DbFp supplier supporting random access: >>> import os.path >>> from rdkit.Dbase.DbConnection import DbConnect >>> fName = RDConfig.RDTestDatabase >>> conn = DbConnect(fName,'simple_combined') >>> suppl = RandomAccessDbFpSupplier(conn.GetData()) >>> len(suppl) 12
    - rdkit.VLib.Filter.FilterNode: base class for nodes which filter their input
      - rdkit.VLib.NodeLib.SmilesDupeFilter.DupeFilter: canonical-smiles based duplicate filter
      - rdkit.VLib.NodeLib.SmartsMolFilter.SmartsFilter: filter out molecules matching one or more SMARTS patterns
    - rdkit.VLib.Output.OutputNode: base class for nodes which dump output
      - rdkit.VLib.NodeLib.SmilesOutput.OutputNode: dumps smiles output
    - rdkit.VLib.Supply.SupplyNode: base class for nodes which supply things
      - rdkit.VLib.NodeLib.DbMolSupply.DbMolSupplyNode: Supplies molecules from a db result set:
      - rdkit.VLib.NodeLib.DbPickleSupplier.DbPickleSupplyNode: Supplies pickled objects from a db result set:
      - rdkit.VLib.NodeLib.SDSupply.SDSupplyNode: SD supplier
      - rdkit.VLib.NodeLib.SmilesSupply.SmilesSupplyNode: Smiles supplier
    - rdkit.VLib.Transform.TransformNode: base class for nodes which filter their input
      - rdkit.VLib.NodeLib.SmartsRemover.SmartsRemover: transforms molecules by removing atoms matching smarts patterns
  - rdkit.DataStructs.VectCollection.VectCollection: >>> vc = VectCollection() >>> bv1 = DataStructs.ExplicitBitVect(10) >>> bv1.SetBitsFromList((1,3,5)) >>> vc.AddVect(1,bv1) >>> bv1 = DataStructs.ExplicitBitVect(10) >>> bv1.SetBitsFromList((6,8)) >>> vc.AddVect(2,bv1) >>> len(vc) 10 >>> vc.GetNumBits() 10 >>> vc[0] 0 >>> vc[1] 1 >>> vc[9] 0 >>> vc[6] 1 >>> vc.GetBit(6) 1 >>> list(vc.GetOnBits()) [1, 3, 5, 6, 8]
  - rdkit.DataStructs.HierarchyVis.VisOpts
  - rdkit.ML.Cluster.ClusterVis.VisOpts: stores visualization options for cluster viewing
  - rdkit.ML.DecTree.TreeVis.VisOpts
  - unreachable.instance
    - rdkit.Chem.rdchem.Atom: The class to store Atoms.
    - rdkit.Chem.rdMolDescriptors.AtomPairsParameters
    - rdkit.ML.InfoTheory.rdInfoTheory.BitCorrMatGenerator: A class to generate a pariwise correlation matrix between a list of bits The mode of operation for this class is something like this >>> cmg = BitCorrMatGenerator() >>> cmg.SetBitList(blist) >>> for fp in fpList: >>> cmg.CollectVotes(fp) >>> corrMat = cmg.GetCorrMatrix()
    - rdkit.Chem.rdchem.Bond: The class to store Bonds.
    - rdkit.Chem.rdChemReactions.ChemicalReaction: A class for storing and applying chemical reactions.
    - rdkit.Chem.rdchem.Conformer: The class to store 2D or 3D conformation of a molecule
    - rdkit.DataStructs.cDataStructs.DiscreteValueVect: A container class for storing unsigned integer values within a particular range.
    - rdkit.Chem.rdchem.EditableMol: an editable molecule class
    - rdkit.DataStructs.cDataStructs.ExplicitBitVect: A class to store explicit bit vectors.
    - rdkit.ForceField.rdForceField.ForceField: A force field
    - rdkit.Chem.rdfragcatalog.FragCatGenerator
    - rdkit.Chem.rdfragcatalog.FragCatParams
    - rdkit.Chem.rdfragcatalog.FragCatalog
    - rdkit.Chem.rdfragcatalog.FragFPGenerator
    - rdkit.Chem.rdChemicalFeatures.FreeChemicalFeature: Class to represent a free chemical features.
      - rdkit.Chem.FeatMaps.FeatMapPoint.FeatMapPoint
    - rdkit.SimDivFilters.rdSimDivPickers.HierarchicalClusterPicker: A class for diversity picking of items using Hierarchical Clustering
    - rdkit.ML.InfoTheory.rdInfoTheory.InfoBitRanker: A class to rank the bits from a series of labelled fingerprints A simple demonstration may help clarify what this class does.
    - rdkit.DataStructs.cDataStructs.IntSparseIntVect: A container class for storing integer values within a particular range.
    - rdkit.DataStructs.cDataStructs.LongSparseIntVect: A container class for storing integer values within a particular range.
    - rdkit.SimDivFilters.rdSimDivPickers.MaxMinPicker: A class for diversity picking of items using the MaxMin Algorithm
    - rdkit.Chem.rdchem.Mol: The Molecule class.
    - rdkit.Chem.rdMolCatalog.MolCatalog
    - rdkit.Chem.rdMolCatalog.MolCatalogEntry
    - rdkit.Chem.rdMolChemicalFeatures.MolChemicalFeature: Class to represent a chemical feature.
    - rdkit.Chem.rdMolChemicalFeatures.MolChemicalFeatureFactory: Class to featurize a molecule
    - rdkit.Chem.rdchem.PeriodicTable: A class which stores information from the Periodic Table.
    - rdkit.Geometry.rdGeometry.Point2D: A class to represent a two-dimensional point
    - rdkit.Geometry.rdGeometry.Point3D: A class to represent a three-dimensional point The x, y, and z coordinates can be read and written using either attributes (i.e.
    - rdkit.Geometry.rdGeometry.PointND: A class to represent an N-dimensional point
    - rdkit.Chem.rdchem.RingInfo: contains information about a molecule's rings
    - rdkit.Chem.rdmolfiles.SDMolSupplier: A class which supplies molecules from an SD file.
    - rdkit.Chem.rdmolfiles.SDWriter: A class for writing molecules to SD files.
    - rdkit.Chem.rdmolfiles.SmilesMolSupplier: A class which supplies molecules from a text file.
    - rdkit.Chem.rdmolfiles.SmilesWriter: A class for writing molecules to text files.
    - rdkit.DataStructs.cDataStructs.SparseBitVect: A class to store sparse bit vectors.
    - rdkit.Chem.rdmolfiles.TDTMolSupplier: A class which supplies molecules from a TDT file.
    - rdkit.Chem.rdmolfiles.TDTWriter: A class for writing molecules to TDT files.
    - rdkit.DataStructs.cDataStructs.UIntSparseIntVect: A container class for storing integer values within a particular range.
    - rdkit.DataStructs.cDataStructs.ULongSparseIntVect: A container class for storing integer values within a particular range.
    - rdkit.Geometry.rdGeometry.UniformGrid3D_: Class to represent a uniform three-dimensional cubic grid.
    - rdkit.Chem.rdchem._ROAtomSeq: Read-only sequence of atoms, not constructable from Python.
    - rdkit.Chem.rdchem._ROBondSeq: Read-only sequence of bonds, not constructable from Python.
    - rdkit.Chem.rdchem._listPN5RDKit4AtomE
    - rdkit.Chem.rdchem._listPN5RDKit4BondE
    - rdkit.rdBase._listSt6vectorIiSaIiEE
    - rdkit.rdBase._listi
    - rdkit.rdBase._vectSs
    - rdkit.rdBase._vectSt6vectorIdSaIdEE
    - rdkit.rdBase._vectSt6vectorIiSaIiEE
    - rdkit.rdBase._vectSt6vectorIjSaIjEE
    - rdkit.rdBase._vectd
    - rdkit.rdBase._vecti
    - rdkit.rdBase._vectj
  - int: int(x[, base]) -> integer
    - unreachable.enum
      - rdkit.Chem.rdchem.BondDir
      - rdkit.Chem.rdchem.BondStereo
      - rdkit.Chem.rdchem.BondType
      - rdkit.Chem.rdchem.ChiralType
      - rdkit.SimDivFilters.rdSimDivPickers.ClusterMethod
      - rdkit.DataStructs.cDataStructs.DiscreteValueType
      - rdkit.Chem.rdchem.HybridizationType
      - rdkit.ML.InfoTheory.rdInfoTheory.InfoType
  - RDLogger.logger
  - rdkit.DataStructs.SparseIntVect.pySparseIntVect: this class is pretty much obsolete (it's in C++ now)