RDKit: File List

| RDKit Open-source cheminformatics and machine learning.

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File List
Here is a list of all files with brief descriptions:
[detail level 1234]

► Catalogs |
Catalog.h |
CatalogEntry.h |
CatalogParams.h |
► ChemicalFeatures |
ChemicalFeature.h |
FreeChemicalFeature.h |
► DataManip |
► MetricMatrixCalc |
MetricFuncs.h |
MetricMatrixCalc.h |
► DataStructs |
base64.h | Functionality for base64 encoding/decoding
BitOps.h | Contains general bit-comparison and similarity operations
BitVect.h |
BitVects.h | Pulls in all the BitVect classes
BitVectUtils.h |
DatastructsException.h |
DatastructsStreamOps.h |
DiscreteDistMat.h |
DiscreteValueVect.h |
ExplicitBitVect.h |
FPBReader.h | Simple class for reading and searching FPB files
MultiFPBReader.h | Class for reading and searching collections of FPB files
RealValueVect.h |
SparseBitVect.h |
SparseIntVect.h |
► DistGeom |
BoundsMatrix.h |
ChiralSet.h |
ChiralViolationContribs.h |
DistGeomUtils.h |
DistViolationContribs.h |
FourthDimContribs.h |
TriangleSmooth.h |
► Features |
Feature.h |
► ForceField |
► MMFF |
AngleBend.h |
AngleConstraint.h |
BondStretch.h |
Contribs.h | This convenience include pulls in all the other MMFF include files
DistanceConstraint.h |
Nonbonded.h |
OopBend.h |
Params.h |
PositionConstraint.h |
StretchBend.h |
TorsionAngle.h |
TorsionConstraint.h |
► UFF |
AngleBend.h |
AngleConstraint.h |
BondStretch.h |
Contribs.h | This convenience include pulls in all the other UFF include files
DistanceConstraint.h |
Inversion.h |
Inversions.h |
Nonbonded.h |
Params.h |
PositionConstraint.h |
TorsionAngle.h |
TorsionConstraint.h |
Utils.h |
AngleConstraint.h |
AngleConstraints.h |
Contrib.h |
DistanceConstraint.h |
DistanceConstraints.h |
ForceField.h |
PositionConstraint.h |
TorsionConstraint.h |
► Geometry |
Grid3D.h |
GridUtils.h |
point.h |
Transform.h |
Transform2D.h |
Transform3D.h |
UniformGrid3D.h |
UniformRealValueGrid3D.h |
Utils.h |
► GraphMol |
► Abbreviations |
Abbreviations.h |
► ChemReactions |
► Enumerate |
CartesianProduct.h |
Enumerate.h | Contains the public API of the for the reaction enumeration engine
EnumerateBase.h |
EnumerateTypes.h |
EnumerationPickler.h |
EnumerationStrategyBase.h |
EvenSamplePairs.h |
RandomSample.h |
RandomSampleAllBBs.h |
PreprocessRxn.h |
Reaction.h |
ReactionFingerprints.h |
ReactionParser.h |
ReactionPickler.h |
ReactionRunner.h |
ReactionUtils.h |
SanitizeRxn.h |
► ChemTransforms |
ChemTransforms.h |
MolFragmenter.h |
MolFragmenterJSONParser.h |
► CIPLabeler |
► configs |
AtropisomerBond.h |
Configuration.h |
Sp2Bond.h |
Tetrahedral.h |
► rules |
Pairlist.h |
Rule1a.h |
Rule1b.h |
Rule2.h |
Rule3.h |
Rule4a.h |
Rule4b.h |
Rule4c.h |
Rule5.h |
Rule5New.h |
Rule6.h |
Rules.h |
SequenceRule.h |
CIPLabeler.h |
CIPMol.h |
Descriptor.h |
Digraph.h |
Edge.h |
Mancude.h |
Node.h |
Priority.h |
Sort.h |
TooManyNodesException.h |
► Depictor |
DepictUtils.h |
EmbeddedFrag.h |
RDDepictor.h |
Templates.h |
TemplateSmiles.h |
► Deprotect |
Deprotect.h |
► Descriptors |
AtomFeat.h |
AUTOCORR2D.h |
AUTOCORR3D.h |
BCUT.h |
ConnectivityDescriptors.h | Use MolDescriptors.h in client code
CoulombMat.h |
Crippen.h | Use MolDescriptors.h in client code
Data3Ddescriptors.h |
DCLV.h |
DCLV_dots.h |
EEM.h |
GETAWAY.h |
Lipinski.h | Contains Lipinski and Lipinski-like descriptors. Use MolDescriptors.h in client code
MolData3Ddescriptors.h |
MolDescriptors.h |
MolDescriptors3D.h |
MolSurf.h | Use MolDescriptors.h in client code
MORSE.h |
MQN.h | Use MolDescriptors.h in client code
OxidationNumbers.h |
PBF.h |
PMI.h |
Property.h |
RDF.h |
RegisterDescriptor.h |
USRDescriptor.h | Contains the USR descriptor. Use MolDescriptors.h in client code
WHIM.h |
► DetermineBonds |
DetermineBonds.h |
► DistGeomHelpers |
BoundsMatrixBuilder.h |
Embedder.h |
► EnumerateStereoisomers |
EnumerateStereoisomers.h |
Flippers.h |
► FileParsers |
CDXMLParser.h |
FileParsers.h |
FileParserUtils.h |
FileWriters.h |
GeneralFileReader.h |
MaestroProperties.h |
MolFileStereochem.h |
MolSGroupParsing.h |
MolSGroupWriting.h |
MolSupplier.h |
MolSupplier.v1API.h |
MolWriters.h |
MultithreadedMolSupplier.h |
MultithreadedSDMolSupplier.h |
MultithreadedSmilesMolSupplier.h |
PNGParser.h |
ProximityBonds.h |
SequenceParsers.h |
SequenceWriters.h |
► FilterCatalog |
FilterCatalog.h |
FilterCatalogEntry.h |
FilterMatcherBase.h |
FilterMatchers.h |
Filters.h |
FunctionalGroupHierarchy.h |
► Fingerprints |
AtomPairGenerator.h |
AtomPairs.h |
FingerprintGenerator.h |
Fingerprints.h |
FingerprintUtil.h |
MACCS.h |
MHFP.h |
MorganFingerprints.h |
MorganGenerator.h |
RDKitFPGenerator.h |
TopologicalTorsionGenerator.h |
► FMCS |
Composition2N.h |
DebugTrace.h |
DuplicatedSeedCache.h |
FMCS.h |
Graph.h |
MatchTable.h |
MaximumCommonSubgraph.h |
Seed.h |
SeedSet.h |
SubstructMatchCustom.h |
SubstructureCache.h |
Target.h |
TargetMatch.h |
► ForceFieldHelpers |
► CrystalFF |
TorsionAngleContribs.h |
TorsionAngleM6.h |
TorsionPreferences.h |
► MMFF |
AtomTyper.h |
Builder.h |
MMFF.h |
► UFF |
AtomTyper.h |
Builder.h |
UFF.h |
FFConvenience.h |
► FragCatalog |
FragCatalogEntry.h |
FragCatalogUtils.h |
FragCatGenerator.h |
FragCatParams.h |
FragFPGenerator.h |
► GeneralizedSubstruct |
XQMol.h |
► GenericGroups |
GenericGroups.h |
► MarvinParse |
MarvinDefs.h |
MarvinParser.h |
► MMPA |
MMPA.h |
► MolAlign |
AlignMolecules.h |
O3AAlignMolecules.h |
► MolCatalog |
MolCatalog.h |
MolCatalogEntry.h |
MolCatalogParams.h |
► MolChemicalFeatures |
FeatureParser.h |
MolChemicalFeature.h |
MolChemicalFeatureDef.h |
MolChemicalFeatureFactory.h |
► MolDraw2D |
► Fonts |
roboto_regular.h |
telex_regular.h |
► Qt |
DrawTextFTQt.h |
DrawTextQt.h |
MolDraw2DQt.h |
AtomSymbol.h |
DrawAnnotation.h |
DrawMol.h |
DrawMolMCH.h |
DrawMolMCHCircleAndLine.h |
DrawMolMCHLasso.h |
DrawShape.h |
DrawText.h |
DrawTextCairo.h |
DrawTextFT.h |
DrawTextFTCairo.h |
DrawTextFTJS.h |
DrawTextFTSVG.h |
DrawTextJS.h |
DrawTextNotFT.h |
DrawTextSVG.h |
MolDraw2D.h |
MolDraw2DCairo.h |
MolDraw2DDetails.h |
MolDraw2DHelpers.h |
MolDraw2DJS.h |
MolDraw2DSVG.h |
MolDraw2DUtils.h |
MolDraw2Dwx.h |
StringRect.h |
► MolEnumerator |
LinkNode.h |
MolEnumerator.h |
► MolHash |
mf.h |
MolHash.h |
nmmolhash.h |
► MolInteractionFields |
MIFDescriptors.h | Code for generating molecular interaction field (MIF) descriptors
► MolInterchange |
details.h |
MolInterchange.h | Contains the public API for the convertors to/from the commonchem interchange format
► MolProcessing |
MolProcessing.h |
► MolStandardize |
► AcidBaseCatalog |
AcidBaseCatalogEntry.h |
AcidBaseCatalogParams.h |
AcidBaseCatalogUtils.h |
► FragmentCatalog |
FragmentCatalogEntry.h |
FragmentCatalogParams.h |
FragmentCatalogUtils.h |
► TautomerCatalog |
TautomerCatalogEntry.h |
TautomerCatalogParams.h |
TautomerCatalogUtils.h |
► TransformCatalog |
TransformCatalogEntry.h |
TransformCatalogParams.h |
TransformCatalogUtils.h |
Charge.h | Defines the Reionizer class and Uncharger class
Fragment.h |
Metal.h | Defines the MetalDisconnector class
MolStandardize.h | Defines the CleanupParameters and some convenience functions
Normalize.h | Defines the Normalizer class
Pipeline.h |
Tautomer.h |
Validate.h |
► MolTransforms |
MolTransforms.h |
► PartialCharges |
GasteigerCharges.h |
GasteigerParams.h |
► RascalMCES |
PartitionSet.h |
RascalClusterOptions.h |
RascalDetails.h |
RascalMCES.h |
RascalOptions.h |
RascalResult.h |
► ReducedGraphs |
ReducedGraphs.h |
► RGroupDecomposition |
RGroupCore.h |
RGroupData.h |
RGroupDecomp.h |
RGroupDecompData.h |
RGroupDecompJSONParsers.h |
RGroupDecompParams.h |
RGroupFingerprintScore.h |
RGroupGa.h |
RGroupMatch.h |
RGroupScore.h |
RGroupUtils.h |
► ScaffoldNetwork |
detail.h |
ScaffoldNetwork.h |
► ShapeHelpers |
ShapeEncoder.h |
ShapeUtils.h |
► SLNParse |
SLNAttribs.h |
SLNParse.h |
SLNParseOps.h |
► SmilesParse |
CanonicalizeStereoGroups.h |
SmartsWrite.h |
SmilesJSONParsers.h |
SmilesParse.h |
SmilesParseOps.h |
SmilesWrite.h |
► StructChecker |
Pattern.h |
ReCharge.h |
Stereo.h |
StripSmallFragments.h |
StructChecker.h | Contains the public API of the StructChecker
StructCheckerOptions.h |
Tautomer.h |
Utilites.h |
► Subgraphs |
Subgraphs.h | Functionality for finding subgraphs and paths in molecules
SubgraphUtils.h |
► Substruct |
SubstructMatch.h |
SubstructUtils.h |
► SubstructLibrary |
PatternFactory.h |
SubstructLibrary.h |
SubstructLibrarySerialization.h |
► SynthonSpaceSearch |
MemoryMappedFileReader.h |
SearchResults.h |
Synthon.h |
SynthonSet.h |
SynthonSpace.h | Class for searching combinatorial libraries in Synthon format such as Enamine REAL
SynthonSpaceFingerprintSearcher.h |
SynthonSpaceHitSet.h |
SynthonSpaceRascalSearcher.h |
SynthonSpaceSearch_details.h |
SynthonSpaceSearcher.h |
SynthonSpaceSubstructureSearcher.h |
► TautomerQuery |
TautomerQuery.h |
► Trajectory |
Snapshot.h |
Trajectory.h |
Atom.h | Defines the Atom class and associated typedefs
atomic_data.h | No user-serviceable parts inside
AtomIterators.h | Various tools for iterating over a molecule's Atoms
Atropisomers.h |
Bond.h |
BondIterators.h | Various tools for iterating over a molecule's Bonds
Canon.h |
Chirality.h |
Conformer.h |
details.h |
GraphMol.h | Pulls in RWMol and ROMol
MolBundle.h | Defines a class for managing bundles of molecules
MolOps.h |
MolPickler.h |
MonomerInfo.h | Defines Monomer information classes
new_canon.h |
PeriodicTable.h |
QueryAtom.h |
QueryBond.h |
QueryOps.h |
RDKitBase.h | Pulls in the core `RDKit` functionality
RDKitQueries.h | Pulls in the `RDKit` Query functionality
Resonance.h |
RingInfo.h |
Rings.h | Utility functionality for working with ring systems
ROMol.h | Defines the primary molecule class `ROMol` as well as associated typedefs
RWMol.h | Defines the editable molecule class `RWMol`
SanitException.h |
StereoGroup.h | Defines the class StereoGroup which stores relationships between the absolute configurations of atoms within a structure
Subset.h |
SubstanceGroup.h | Defines the SubstanceGroup class
► ML |
► InfoTheory |
CorrMatGenerator.h |
InfoBitRanker.h |
InfoGainFuncs.h |
► Numerics |
► Alignment |
AlignPoints.h |
► EigenSolvers |
PowerEigenSolver.h |
► Optimizer |
BFGSOpt.h |
Conrec.h |
Matrix.h |
SquareMatrix.h |
SymmMatrix.h |
Vector.h |
► Query |
AndQuery.h |
EqualityQuery.h |
GreaterEqualQuery.h |
GreaterQuery.h |
LessEqualQuery.h |
LessQuery.h |
NullQueryAlgebra.h |
OrQuery.h |
Query.h |
QueryObjects.h | Pulls in all the query types
RangeQuery.h |
SetQuery.h |
XOrQuery.h |
► RDBoost |
boost_numpy.h |
import_array.h |
pyint_api.h |
PySequenceHolder.h |
python.h |
python_streambuf.h |
► RDGeneral |
BadFileException.h |
BetterEnums.h |
BoostEndInclude.h |
BoostStartInclude.h |
ConcurrentQueue.h |
ControlCHandler.h |
Dict.h | Defines the Dict class
enum.h |
Exceptions.h |
export.h |
FileParseException.h |
hanoiSort.h |
Invariant.h |
JSONHelpers.h |
LocaleSwitcher.h |
Ranking.h |
RDAny.h |
RDConfig.h |
RDExportMacros.h |
RDLog.h |
RDProps.h |
RDThreads.h |
RDValue-doublemagic.h |
RDValue-taggedunion.h |
RDValue.h |
StreamOps.h |
types.h |
utils.h |
versions.h |
► SimDivPickers |
DistPicker.h |
HierarchicalClusterPicker.h |
LeaderPicker.h |
MaxMinPicker.h |