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[ Module Hierarchy | Class Hierarchy ]

# Class Hierarchy

- rdkit.Chem.Draw.canvasbase.CanvasBase: Base class for specialized canvas backends
  - rdkit.Chem.Draw.spingCanvas.Canvas
  - rdkit.Chem.Draw.qtCanvas.Canvas
  - rdkit.Chem.Draw.mplCanvas.Canvas
  - rdkit.Chem.Draw.cairoCanvas.Canvas
- 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.Chem.Pharm3D.Pharmacophore.ExplicitPharmacophore: this is a pharmacophore with explicit point locations and radii...
- rdkit.Chem.SaltRemover.InputFormat
- rdkit.Chem.MolDb.FingerprintUtils.LayeredOptions
- 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.Chem.MolKey.MolKey.BadMoleculeException
      - rdkit.ML.ModelPackage.Packager.ClassificationError: used to signal problems generating predictions
      - rdkit.ML.ModelPackage.Packager.DescriptorCalculationError: used to signal problems generating descriptor values
      - rdkit.Chem.inchi.InchiReadWriteError
      - rdkit.Chem.Pharm2D.Matcher.MatchError
      - rdkit.Chem.MolKey.MolKey.MolIdentifierException
      - RDConfig.ObsoleteCodeError
      - exceptions.StandardError: Base class for all standard Python exceptions that do not represent interpreter exiting.
        - exceptions.RuntimeError: Unspecified run-time error.
          - rdkit.Dbase.DbConnection.DbError
        - exceptions.ValueError: Inappropriate argument value (of correct type).
          - rdkit.Chem.FeatMaps.FeatMapParser.FeatMapParseError
          - rdkit.Chem.FunctionalGroups.FuncGroupFileParseError
      - 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.Chem.fmcs.fmcs'.CangenNode
  - 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.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.fmcs.fmcs'.Default
  - rdkit.Chem.FeatMaps.FeatMapUtils.DirMergeMode
  - rdkit.Chem.DSViewer.Displayable
  - rdkit.Chem.Draw.MolDrawing'.DrawingOptions
  - rdkit.Chem.Pharm3D.ExcludedVolume.ExcludedVolume
  - rdkit.Chem.FunctionalGroups.FGHierarchyNode
  - 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.fmcs.fmcs'.FragmentedTypedMolecule
  - 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.Chem.MolKey.InchiInfo.InchiInfo
  - 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.Chem.MCS.MCSResult
  - rdkit.Chem.fmcs.fmcs'.MCSResult
  - 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.Dbase.DbReport.RDImageTransformer
  - rdkit.Chem.Recap.RecapHierarchyNode: This class is used to hold the Recap hiearchy...
  - rdkit.Dbase.DbReport.ReportLabImageTransformer
  - rdkit.Chem.BuildFragmentCatalog.RunDetails
  - rdkit.Chem.SaltRemover.SaltRemover
  - 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.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.EnumerateStereoisomers.StereoEnumerationOptions: - tryEmbedding: if set the process attempts to generate a standard RDKit distance geometry conformation for the stereisomer.
  - 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
  - rdkit.Chem.fmcs.fmcs'.Timer
  - 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.Chem.fmcs.fmcs'.TypedFragment
  - rdkit.Chem.fmcs.fmcs'.TypedMolecule
  - 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 import RDConfig >>> 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.Chem.fmcs.fmcs'.VerboseCachingTargetsMatcher
  - rdkit.Chem.fmcs.fmcs'.VerboseHeapOps
  - rdkit.ML.Cluster.ClusterVis.VisOpts: stores visualization options for cluster viewing
  - rdkit.DataStructs.HierarchyVis.VisOpts
  - rdkit.ML.DecTree.TreeVis.VisOpts
  - rdkit.Chem.EnumerateStereoisomers._AtomFlipper
  - rdkit.Chem.EnumerateStereoisomers._BondFlipper
  - rdkit.Chem.EnumerateStereoisomers._RangeBitsGenerator
  - rdkit.Chem.fmcs.fmcs'._SingleBest
    - rdkit.Chem.fmcs.fmcs'.SingleBestAtoms
    - rdkit.Chem.fmcs.fmcs'.SingleBestAtomsCompleteRingsOnly
    - rdkit.Chem.fmcs.fmcs'.SingleBestBonds
    - rdkit.Chem.fmcs.fmcs'.SingleBestBondsCompleteRingsOnly
  - rdkit.Chem.EnumerateStereoisomers._UniqueRandomBitsGenerator
  - dict: dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object's (key, value) pairs dict(iterable) -> new dictionary initialized as if via: d = {} for k, v in iterable: d[k] = v dict(**kwargs) -> new dictionary initialized with the name=value pairs in the keyword argument list.
    - rdkit.Chem.fmcs.fmcs'.AtomSmartsNoAromaticity
    - rdkit.Chem.fmcs.fmcs'.CachingTargetsMatcher
    - rdkit.Chem.fmcs.fmcs'.Uniquer
  - unreachable.instance
    - rdkit.Chem.rdmolops.AdjustQueryParameters: Parameters controlling which components of the query atoms are adjusted.
    - rdkit.Chem.rdchem.Atom: The class to store Atoms.
      - rdkit.Chem.rdchem.QueryAtom: The class to store QueryAtoms.
    - rdkit.Chem.rdchem.AtomMonomerInfo: The class to store monomer information attached to Atoms
      - rdkit.Chem.rdchem.AtomPDBResidueInfo: The class to store PDB residue information attached to 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.rdchem.QueryBond: The class to store QueryBonds.
    - 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.Chem.rdDistGeom.EmbedParameters: Parameters controlling embedding
    - rdkit.Chem.rdChemReactions.EnumerateLibraryBase
      - rdkit.Chem.rdChemReactions.EnumerateLibrary: EnumerateLibrary This class allows easy enumeration of reactions.
    - rdkit.Chem.rdChemReactions.EnumerationParams: EnumerationParams Controls some aspects of how the enumeration is performed.
    - rdkit.Chem.rdChemReactions.EnumerationStrategyBase
      - rdkit.Chem.rdChemReactions.CartesianProductStrategy: CartesianProductStrategy produces a standard walk through all possible reagent combinations:
      - rdkit.Chem.rdChemReactions.EvenSamplePairsStrategy: Randomly sample Pairs evenly from a collection of building blocks This is a good strategy for choosing a relatively small selection of building blocks from a larger set.
      - rdkit.Chem.rdChemReactions.RandomSampleAllBBsStrategy: RandomSampleAllBBsStrategy randomly samples from the reagent sets with the constraint that all building blocks are samples as early as possible.
      - rdkit.Chem.rdChemReactions.RandomSampleStrategy: RandomSampleStrategy simply randomly samples from the reagent sets.
    - rdkit.DataStructs.cDataStructs.ExplicitBitVect: A class to store explicit bit vectors.
    - rdkit.DataStructs.cDataStructs.FPBReader: A class for reading and searching FPB files from Andrew Dalke's chemfp.
    - rdkit.Chem.rdSubstructLibrary.FPHolderBase:
      - rdkit.Chem.rdSubstructLibrary.PatternHolder: Holds fingerprints used for filtering of molecules.
    - rdkit.Chem.rdfiltercatalog.FilterCatalog
    - rdkit.Chem.rdfiltercatalog.FilterCatalogEntry: FilterCatalogEntry A filter catalog entry is an entry in a filter catalog.
    - rdkit.Chem.rdfiltercatalog.FilterCatalogEntryList
    - rdkit.Chem.rdfiltercatalog.FilterCatalogParams
    - rdkit.Chem.rdfiltercatalog.FilterMatch: Object that holds the result of running FilterMatcherBase::GetMatches
    - rdkit.Chem.rdfiltercatalog.FilterMatcherBase: Base class for matching molecules to filters.
      - rdkit.Chem.rdfiltercatalog.ExclusionList
      - rdkit.Chem.rdfiltercatalog.FilterHierarchyMatcher: Hierarchical Filter basic constructors: FilterHierarchyMatcher( matcher ) where can be any FilterMatcherBase (SmartsMatcher, etc) FilterHierarchyMatcher's have children and can form matching trees.
      - rdkit.Chem.rdfiltercatalog.PythonFilterMatcher
        - rdkit.Chem.FilterCatalog.FilterMatcher: FilterMatcher - This class allows creation of Python based filters.
      - rdkit.Chem.rdfiltercatalog.SmartsMatcher: Smarts Matcher Filter basic constructors: SmartsMatcher( name, smarts_pattern, minCount=1, maxCount=UINT_MAX ) SmartsMatcher( name, molecule, minCount=1, maxCount=UINT_MAX )
    - rdkit.ForceField.rdForceField.ForceField: A force field
    - rdkit.Chem.rdmolfiles.ForwardSDMolSupplier: A class which supplies molecules from file-like object containing SD data.
    - 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.Chem.rdfiltercatalog.IntPair
    - rdkit.DataStructs.cDataStructs.IntSparseIntVect: A container class for storing integer values within a particular range.
    - rdkit.Chem.Draw.rdMolDraw2D.IntStringMap
    - rdkit.DataStructs.cDataStructs.LongSparseIntVect: A container class for storing integer values within a particular range.
    - rdkit.Chem.rdFMCS.MCSAtomCompareParameters: Parameters controlling how atom-atom matching is done
    - rdkit.Chem.rdFMCS.MCSBondCompareParameters: Parameters controlling how bond-bond matching is done
    - rdkit.Chem.rdFMCS.MCSParameters: Parameters controlling how the MCS is constructed
    - rdkit.Chem.rdFMCS.MCSResult: used to return MCS results
    - rdkit.ForceField.rdForceField.MMFFMolProperties: MMFF molecular properties
    - rdkit.Chem.rdRGroupDecomposition.MOL_SPTR_VECT
    - rdkit.Chem.rdfiltercatalog.MatchTypeVect
    - rdkit.SimDivFilters.rdSimDivPickers.MaxMinPicker: A class for diversity picking of items using the MaxMin Algorithm
    - rdkit.Chem.rdchem.Mol: The Molecule class.
      - rdkit.Chem.PropertyMol.PropertyMol: allows rdkit molecules to be pickled with their properties saved.
      - rdkit.Chem.rdchem.RWMol: The RW molecule class (read/write)
    - rdkit.Chem.rdchem.MolBundle: A class for storing gropus of related molecules.
    - 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.Draw.rdMolDraw2D.MolDraw2D: Drawer abstract base class
      - rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DSVG: SVG molecule drawer
    - rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions: Drawing options
    - rdkit.Chem.rdSubstructLibrary.MolHolderBase:
      - rdkit.Chem.rdSubstructLibrary.CachedMolHolder: Holds molecules in their binary representation.
      - rdkit.Chem.rdSubstructLibrary.CachedSmilesMolHolder: Holds molecules as smiles string This allows more molecules to be held in memory at a time AddMol(mol) -> adds a molecule to the molecule holder, returns index of molecule AddSmiles(smiles) -> adds a smiles string to the molecule holder, returns index of molecule The smiles is stored as-is, no checking is done for validity.
      - rdkit.Chem.rdSubstructLibrary.CachedTrustedSmilesMolHolder: Holds molecules as trusted smiles string This allows more molecules to be held in memory at a time and avoids RDKit sanitization overhead See: http://rdkit.blogspot.com/2016/09/avoiding-unnecessary-work-and.html AddMol(mol) -> adds a molecule to the molecule holder, returns index of molecule AddSmiles(smiles) -> adds a smiles string to the molecule holder, returns index of molecule The smiles is stored as-is, no checking is done for validity.
      - rdkit.Chem.rdSubstructLibrary.MolHolder: Holds raw in-memory molecules...
    - rdkit.Chem.rdfiltercatalog.MolList
    - rdkit.DataStructs.cDataStructs.MultiFPBReader: A class for reading and searching multiple FPB files from Andrew Dalke's chemfp.
    - rdkit.Chem.rdMolAlign.O3A: Open3DALIGN object
    - rdkit.Chem.rdmolfiles.PDBWriter: A class for writing molecules to PDB files.
    - 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.rdMolDescriptors.Properties: Property computation and registry system.
    - rdkit.Chem.rdMolDescriptors.PropertyFunctor: Property computation class stored in the property registry.
      - rdkit.Chem.rdMolDescriptors.PythonPropertyFunctor:
        - rdkit.Chem.Descriptors.PropertyFunctor: Creates a python based property function that can be added to the global property list.
    - rdkit.Chem.rdMolDescriptors.PropertyRangeQuery: Property Range Query for a molecule.
    - rdkit.Chem.rdRGroupDecomposition.RGroupDecomposition: RGroupDecompositionParameters controls how the RGroupDecomposition sets labelling and matches structures OPTIONS: - RGroupCoreAlignment: can be one of RGroupCoreAlignment.None or RGroupCoreAlignment.MCS If set to MCS, cores labels are mapped to each other using their Maximum common substructure overlap.
    - rdkit.Chem.rdRGroupDecomposition.RGroupDecompositionParameters: RGroupDecompositionParameters controls how the RGroupDecomposition sets labelling and matches structures OPTIONS: - RGroupCoreAlignment: can be one of RGroupCoreAlignment.None or RGroupCoreAlignment.MCS If set to MCS, cores labels are mapped to each other using their Maximum common substructure overlap.
    - rdkit.Chem.rdChemReactions.ROMolList
    - rdkit.Chem.rdChemReactions.ReactionFingerprintParams: A class for storing parameters to manipulate the calculation of fingerprints of chemical reactions.
    - rdkit.Chem.rdchem.ResonanceMolSupplier: A class which supplies resonance structures (as mols) from a mol.
    - 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.FastSDMolSupplier.FastSDMolSupplier
    - 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.SmilesParserParams: Parameters controlling SMILES Parsing
    - 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.rdStructChecker.StructChecker
    - rdkit.Chem.rdStructChecker.StructCheckerOptions
    - rdkit.Chem.rdSubstructLibrary.SubstructLibrary: SubstructLibrary: This provides a simple API for substructure searching large datasets The SubstructLibrary takes full advantage of available threads during the search operation.
    - 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.rdfiltercatalog.VectFilterMatch
    - rdkit.Chem.rdChemReactions.VectMolVect
    - rdkit.Chem.rdChemReactions.VectSizeT
    - rdkit.Chem.rdChemReactions.VectorOfStringVectors
    - 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._ROQAtomSeq: Read-only sequence of atoms matching a query, 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
    - rdkit.Chem.Draw.rdMolDraw2D.map_indexing_suite_IntStringMap_entry
    - rdkit.rdBase.std_ostream
      - rdkit.rdBase.ostream
    - rdkit.rdBase.streambuf
  - int: int(x=0) -> int or long int(x, base=10) -> int or long
    - unreachable.enum
      - rdkit.Chem.rdmolops.AdjustQueryWhichFlags
      - rdkit.Chem.rdmolops.AromaticityModel
      - rdkit.Chem.rdFMCS.AtomCompare
      - rdkit.Chem.rdchem.AtomMonomerType
      - rdkit.Chem.rdFMCS.BondCompare
      - rdkit.Chem.rdchem.BondDir
      - rdkit.Chem.rdchem.BondStereo
      - rdkit.Chem.rdchem.BondType
      - rdkit.Chem.rdchem.ChiralType
      - rdkit.SimDivFilters.rdSimDivPickers.ClusterMethod
      - rdkit.Chem.rdchem.CompositeQueryType
      - rdkit.DataStructs.cDataStructs.DiscreteValueType
      - rdkit.Chem.rdfiltercatalog.FilterCatalogParams.FilterCatalogs
      - rdkit.Chem.rdChemReactions.FingerprintType
      - rdkit.Chem.rdchem.HybridizationType
      - rdkit.ML.InfoTheory.rdInfoTheory.InfoType
      - rdkit.Chem.rdMolDescriptors.NumRotatableBondsOptions: Options for generating rotatble bonds...
      - rdkit.Chem.rdchem.PropertyPickleOptions
      - rdkit.Chem.rdRGroupDecomposition.RGroupCoreAlignment
      - rdkit.Chem.rdRGroupDecomposition.RGroupLabelling
      - rdkit.Chem.rdRGroupDecomposition.RGroupLabels
      - rdkit.Chem.rdRGroupDecomposition.RGroupMatching
      - rdkit.Chem.rdchem.ResonanceFlags
      - rdkit.Chem.rdmolops.SanitizeFlags
      - rdkit.Chem.rdChemReactions.SanitizeFlags
      - rdkit.Avalon.pyAvalonTools.StruChkFlag
      - rdkit.Avalon.pyAvalonTools.StruChkResult
      - rdkit.Chem.rdStructChecker.StructureFlags
  - rdkit.Chem.fmcs.fmcs'.starting_from
  - tuple: tuple() -> empty tuple tuple(iterable) -> tuple initialized from iterable's items
    - rdkit.Chem.QED.ADSparameter: ADSparameter(A, B, C, D, E, F, DMAX)
    - rdkit.Chem.fmcs.fmcs'.Atom: Atom(real_atom, atom_smarts, bond_indices, is_in_ring)
    - rdkit.Chem.fmcs.fmcs'.Bond: Bond(real_bond, bond_smarts, canonical_bondtype, atom_indices, is_in_ring)
    - rdkit.Chem.fmcs.fmcs'.DirectedEdge: DirectedEdge(bond_index, end_atom_index)
    - rdkit.Chem.fmcs.fmcs'.EnumerationMolecule: Molecule(rdmol, atoms, bonds, directed_edges)
    - rdkit.Chem.MolKey.MolKey.InchiResult: InchiResult(error, inchi, fixed_ctab)
    - rdkit.Chem.MolKey.MolKey.MolKeyResult: MolKeyResult(mol_key, error, inchi, fixed_ctab, stereo_code, stereo_comment)
    - rdkit.Chem.fmcs.fmcs'.OutgoingEdge: OutgoingEdge(from_atom_index, bond_index, bond_smarts, other_node_idx, other_node)
    - rdkit.Chem.QED.QEDproperties: QEDproperties(MW, ALOGP, HBA, HBD, PSA, ROTB, AROM, ALERTS)
    - rdkit.Chem.fmcs.fmcs'.Subgraph: Subgraph(atom_indices, bond_indices)