Here is a list of all files with brief descriptions:

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
ZMatrix.h
ZMatrixUtils.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
FiniteDifference.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
TemplateSmarts.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
BoundsMatrixBuilderDetails.h
Embedder.h
ZMatrixBuilder.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
torsionData
gaussTorsionPreferences_v4.h
gaussTorsionPreferences_v4_macrocycles.h
gaussTorsionPreferences_v4_smallrings.h
GaussianTorsionAngleContribs.h
PlanarityContribs.h
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
GaussianShape
GaussianShape.h
ShapeInput.h
ShapeOverlayOptions.h
SingleConformerAlignment.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
MolDraw2DSGroupData.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
SubstructDetails.h
SubstructMatch.h
SubstructUtils.h
SubstructLibrary
PatternFactory.h
SubstructLibrary.h
SubstructLibrarySerialization.h
SynthonSpaceSearch
MemoryMappedFileReader.h
ProgressBar.h
SearchResults.h
Synthon.h
SynthonSet.h
SynthonShapeInput.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
SynthonSpaceSearchHelpers.h
SynthonSpaceShapeSearcher.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
MacroAtomInfo.h	Defines atom-level macro atom information
MacroBondInfo.h	Defines bond-level macro bond information
MacroMol.h
MacroMolTemplate.h
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
BFGSOpt_SVE.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
boost_shared_ptr.h
import_array.h
pyint_api.h
PySequenceHolder.h
python.h
python_capsule_nb.h
python_streambuf.h
python_streambuf_nb.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