008 Document A786cd2e

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RDKit API Reference

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RDKit API Reference

This document provides a comprehensive reference for RDKit's Python API, organized by functionality.

Core Module: rdkit.Chem

The fundamental module for working with molecules.

Molecule I/O

Reading Molecules:

Chem.MolFromSmiles(smiles, sanitize=True) - Parse SMILES string
Chem.MolFromSmarts(smarts) - Parse SMARTS pattern
Chem.MolFromMolFile(filename, sanitize=True, removeHs=True) - Read MOL file
Chem.MolFromMolBlock(molblock, sanitize=True, removeHs=True) - Parse MOL block string
Chem.MolFromMol2File(filename, sanitize=True, removeHs=True) - Read MOL2 file
Chem.MolFromMol2Block(molblock, sanitize=True, removeHs=True) - Parse MOL2 block
Chem.MolFromPDBFile(filename, sanitize=True, removeHs=True) - Read PDB file
Chem.MolFromPDBBlock(pdbblock, sanitize=True, removeHs=True) - Parse PDB block
Chem.MolFromInchi(inchi, sanitize=True, removeHs=True) - Parse InChI string
Chem.MolFromSequence(seq, sanitize=True) - Create molecule from peptide sequence

Writing Molecules:

Chem.MolToSmiles(mol, isomericSmiles=True, canonical=True) - Convert to SMILES
Chem.MolToSmarts(mol, isomericSmarts=False) - Convert to SMARTS
Chem.MolToMolBlock(mol, includeStereo=True, confId=-1) - Convert to MOL block
Chem.MolToMolFile(mol, filename, includeStereo=True, confId=-1) - Write MOL file
Chem.MolToPDBBlock(mol, confId=-1) - Convert to PDB block
Chem.MolToPDBFile(mol, filename, confId=-1) - Write PDB file
Chem.MolToInchi(mol, options='') - Convert to InChI
Chem.MolToInchiKey(mol, options='') - Generate InChI key
Chem.MolToSequence(mol) - Convert to peptide sequence

Batch I/O:

Chem.SDMolSupplier(filename, sanitize=True, removeHs=True) - SDF file reader
Chem.ForwardSDMolSupplier(fileobj, sanitize=True, removeHs=True) - Forward-only SDF reader
Chem.MultithreadedSDMolSupplier(filename, numWriterThreads=1) - Parallel SDF reader
Chem.SmilesMolSupplier(filename, delimiter=' ', titleLine=True) - SMILES file reader
Chem.SDWriter(filename) - SDF file writer
Chem.SmilesWriter(filename, delimiter=' ', includeHeader=True) - SMILES file writer

Molecular Manipulation

Sanitization:

Chem.SanitizeMol(mol, sanitizeOps=SANITIZE_ALL, catchErrors=False) - Sanitize molecule
Chem.DetectChemistryProblems(mol, sanitizeOps=SANITIZE_ALL) - Detect sanitization issues
Chem.AssignStereochemistry(mol, cleanIt=True, force=False) - Assign stereochemistry
Chem.FindPotentialStereo(mol) - Find potential stereocenters
Chem.AssignStereochemistryFrom3D(mol, confId=-1) - Assign stereo from 3D coords

Hydrogen Management:

Chem.AddHs(mol, explicitOnly=False, addCoords=False) - Add explicit hydrogens
Chem.RemoveHs(mol, implicitOnly=False, updateExplicitCount=False) - Remove hydrogens
Chem.RemoveAllHs(mol) - Remove all hydrogens

Aromaticity:

Chem.SetAromaticity(mol, model=AROMATICITY_RDKIT) - Set aromaticity model
Chem.Kekulize(mol, clearAromaticFlags=False) - Kekulize aromatic bonds
Chem.SetConjugation(mol) - Set conjugation flags

Fragments:

Chem.GetMolFrags(mol, asMols=False, sanitizeFrags=True) - Get disconnected fragments
Chem.FragmentOnBonds(mol, bondIndices, addDummies=True) - Fragment on specific bonds
Chem.ReplaceSubstructs(mol, query, replacement, replaceAll=False) - Replace substructures
Chem.DeleteSubstructs(mol, query,> - Delete substructures


Stereochemistry:

Chem.FindMolChiralCenters(mol, includeUnassigned=False, useLegacyImplementation=False) - Find chiral centers
Chem.FindPotentialStereo(mol, cleanIt=True) - Find potential stereocenters

Substructure Searching
Basic Matching:

mol.HasSubstructMatch(query, useChirality=False) - Check for substructure match
mol.GetSubstructMatch(query, useChirality=False) - Get first match
mol.GetSubstructMatches(query, uniquify=True, useChirality=False) - Get all matches
mol.GetSubstructMatches(query, maxMatches=1000) - Limit number of matches

Molecular Properties
Atom Methods:

atom.GetSymbol() - Atomic symbol
atom.GetAtomicNum() - Atomic number
atom.GetDegree() - Number of bonds
atom.GetTotalDegree() - Including hydrogens
atom.GetFormalCharge() - Formal charge
atom.GetNumRadicalElectrons() - Radical electrons
atom.GetIsAromatic() - Aromaticity flag
atom.GetHybridization() - Hybridization (SP, SP2, SP3, etc.)
atom.GetIdx() - Atom index
atom.IsInRing() - In any ring
atom.IsInRingSize(size) - In ring of specific size
atom.GetChiralTag() - Chirality tag

Bond Methods:

bond.GetBondType() - Bond type (SINGLE, DOUBLE, TRIPLE, AROMATIC)
bond.GetBeginAtomIdx() - Starting atom index
bond.GetEndAtomIdx() - Ending atom index
bond.GetIsConjugated() - Conjugation flag
bond.GetIsAromatic() - Aromaticity flag
bond.IsInRing() - In any ring
bond.GetStereo() - Stereochemistry (STEREONONE, STEREOZ, STEREOE, etc.)

Molecule Methods:

mol.GetNumAtoms(onlyExplicit=True) - Number of atoms
mol.GetNumHeavyAtoms() - Number of heavy atoms
mol.GetNumBonds() - Number of bonds
mol.GetAtoms() - Iterator over atoms
mol.GetBonds() - Iterator over bonds
mol.GetAtomWithIdx(idx) - Get specific atom
mol.GetBondWithIdx(idx) - Get specific bond
mol.GetRingInfo() - Ring information object

Ring Information:

Chem.GetSymmSSSR(mol) - Get smallest set of smallest rings
Chem.GetSSSR(mol) - Alias for GetSymmSSSR
ring_info.NumRings() - Number of rings
ring_info.AtomRings() - Tuples of atom indices in rings
ring_info.BondRings() - Tuples of bond indices in rings

rdkit.Chem.AllChem
Extended chemistry functionality.
2D/3D Coordinate Generation

AllChem.Compute2DCoords(mol, canonOrient=True, clearConfs=True) - Generate 2D coordinates
AllChem.EmbedMolecule(mol, maxAttempts=0, randomSeed=-1, useRandomCoords=False) - Generate 3D conformer
AllChem.EmbedMultipleConfs(mol, numConfs=10, maxAttempts=0, randomSeed=-1) - Generate multiple conformers
AllChem.ConstrainedEmbed(mol, core, useTethers=True) - Constrained embedding
AllChem.GenerateDepictionMatching2DStructure(mol, reference, refPattern=None) - Align to template

Force Field Optimization

AllChem.UFFOptimizeMolecule(mol, maxIters=200, confId=-1) - UFF optimization
AllChem.MMFFOptimizeMolecule(mol, maxIters=200, confId=-1, mmffVariant='MMFF94') - MMFF optimization
AllChem.UFFGetMoleculeForceField(mol, confId=-1) - Get UFF force field object
AllChem.MMFFGetMoleculeForceField(mol, pyMMFFMolProperties, confId=-1) - Get MMFF force field

Conformer Analysis

AllChem.GetConformerRMS(mol, confId1, confId2, prealigned=False) - Calculate RMSD
AllChem.GetConformerRMSMatrix(mol, prealigned=False) - RMSD matrix
AllChem.AlignMol(prbMol, refMol, prbCid=-1, refCid=-1) - Align molecules
AllChem.AlignMolConformers(mol) - Align all conformers

Reactions

AllChem.ReactionFromSmarts(smarts, useSmiles=False) - Create reaction from SMARTS
reaction.RunReactants(reactants) - Apply reaction
reaction.RunReactant(reactant, reactionIdx) - Apply to specific reactant
AllChem.CreateDifferenceFingerprintForReaction(reaction) - Reaction fingerprint

Fingerprints

AllChem.GetMorganFingerprint(mol, radius, useFeatures=False) - Morgan fingerprint
AllChem.GetMorganFingerprintAsBitVect(mol, radius, nBits=2048) - Morgan bit vector
AllChem.GetHashedMorganFingerprint(mol, radius, nBits=2048) - Hashed Morgan
AllChem.GetErGFingerprint(mol) - ErG fingerprint

rdkit.Chem.Descriptors
Molecular descriptor calculations.
Common Descriptors

Descriptors.MolWt(mol) - Molecular weight
Descriptors.ExactMolWt(mol) - Exact molecular weight
Descriptors.HeavyAtomMolWt(mol) - Heavy atom molecular weight
Descriptors.MolLogP(mol) - LogP (lipophilicity)
Descriptors.MolMR(mol) - Molar refractivity
Descriptors.TPSA(mol) - Topological polar surface area
Descriptors.NumHDonors(mol) - Hydrogen bond donors
Descriptors.NumHAcceptors(mol) - Hydrogen bond acceptors
Descriptors.NumRotatableBonds(mol) - Rotatable bonds
Descriptors.NumAromaticRings(mol) - Aromatic rings
Descriptors.NumSaturatedRings(mol) - Saturated rings
Descriptors.NumAliphaticRings(mol) - Aliphatic rings
Descriptors.NumAromaticHeterocycles(mol) - Aromatic heterocycles
Descriptors.NumRadicalElectrons(mol) - Radical electrons
Descriptors.NumValenceElectrons(mol) - Valence electrons

Batch Calculation

Descriptors.CalcMolDescriptors(mol) - Calculate all descriptors as dictionary

Descriptor Lists

Descriptors._descList - List of (name, function) tuples for all descriptors

rdkit.Chem.Draw
Molecular visualization.
Image Generation

Draw.MolToImage(mol, size=(300,300), kekulize=True, wedgeBonds=True, highlightAtoms=None) - Generate PIL image
Draw.MolToFile(mol, filename, size=(300,300), kekulize=True, wedgeBonds=True) - Save to file
Draw.MolsToGridImage(mols, molsPerRow=3, subImgSize=(200,200), legends=None) - Grid of molecules
Draw.MolsMatrixToGridImage(mols, molsPerRow=3, subImgSize=(200,200), legends=None) - Nested grid
Draw.ReactionToImage(rxn, subImgSize=(200,200)) - Reaction image

Fingerprint Visualization

Draw.DrawMorganBit(mol, bitId, bitInfo, whichExample=0) - Visualize Morgan bit
Draw.DrawMorganBits(bits, mol, bitInfo, molsPerRow=3) - Multiple Morgan bits
Draw.DrawRDKitBit(mol, bitId, bitInfo, whichExample=0) - Visualize RDKit bit

IPython Integration

Draw.IPythonConsole - Module for Jupyter integration
Draw.IPythonConsole.ipython_useSVG - Use SVG (True) or PNG (False)
Draw.IPythonConsole.molSize - Default molecule image size

Drawing Options

rdMolDraw2D.MolDrawOptions() - Get drawing options object
.addAtomIndices - Show atom indices
.addBondIndices - Show bond indices
.addStereoAnnotation - Show stereochemistry
.bondLineWidth - Line width
.highlightBondWidthMultiplier - Highlight width
.minFontSize - Minimum font size
.maxFontSize - Maximum font size



rdkit.Chem.rdMolDescriptors
Additional descriptor calculations.

rdMolDescriptors.CalcNumRings(mol) - Number of rings
rdMolDescriptors.CalcNumAromaticRings(mol) - Aromatic rings
rdMolDescriptors.CalcNumAliphaticRings(mol) - Aliphatic rings
rdMolDescriptors.CalcNumSaturatedRings(mol) - Saturated rings
rdMolDescriptors.CalcNumHeterocycles(mol) - Heterocycles
rdMolDescriptors.CalcNumAromaticHeterocycles(mol) - Aromatic heterocycles
rdMolDescriptors.CalcNumSpiroAtoms(mol) - Spiro atoms
rdMolDescriptors.CalcNumBridgeheadAtoms(mol) - Bridgehead atoms
rdMolDescriptors.CalcFractionCsp3(mol) - Fraction of sp3 carbons
rdMolDescriptors.CalcLabuteASA(mol) - Labute accessible surface area
rdMolDescriptors.CalcTPSA(mol) - TPSA
rdMolDescriptors.CalcMolFormula(mol) - Molecular formula

rdkit.Chem.Scaffolds
Scaffold analysis.
Murcko Scaffolds

MurckoScaffold.GetScaffoldForMol(mol) - Get Murcko scaffold
MurckoScaffold.MakeScaffoldGeneric(mol) - Generic scaffold
MurckoScaffold.MurckoDecompose(mol) - Decompose to scaffold and sidechains

rdkit.Chem.rdMolHash
Molecular hashing and standardization.

rdMolHash.MolHash(mol, hashFunction) - Generate hash
rdMolHash.HashFunction.AnonymousGraph - Anonymized structure
rdMolHash.HashFunction.CanonicalSmiles - Canonical SMILES
rdMolHash.HashFunction.ElementGraph - Element graph
rdMolHash.HashFunction.MurckoScaffold - Murcko scaffold
rdMolHash.HashFunction.Regioisomer - Regioisomer (no stereo)
rdMolHash.HashFunction.NetCharge - Net charge
rdMolHash.HashFunction.HetAtomProtomer - Heteroatom protomer
rdMolHash.HashFunction.HetAtomTautomer - Heteroatom tautomer



rdkit.Chem.MolStandardize
Molecule standardization.

rdMolStandardize.Normalize(mol) - Normalize functional groups
rdMolStandardize.Reionize(mol) - Fix ionization state
rdMolStandardize.RemoveFragments(mol) - Remove small fragments
rdMolStandardize.Cleanup(mol) - Full cleanup (normalize + reionize + remove)
rdMolStandardize.Uncharger() - Create uncharger object
.uncharge(mol) - Remove charges


rdMolStandardize.TautomerEnumerator() - Enumerate tautomers
.Enumerate(mol) - Generate tautomers
.Canonicalize(mol) - Get canonical tautomer



rdkit.DataStructs
Fingerprint similarity and operations.
Similarity Metrics

DataStructs.TanimotoSimilarity(fp1, fp2) - Tanimoto coefficient
DataStructs.DiceSimilarity(fp1, fp2) - Dice coefficient
DataStructs.CosineSimilarity(fp1, fp2) - Cosine similarity
DataStructs.SokalSimilarity(fp1, fp2) - Sokal similarity
DataStructs.KulczynskiSimilarity(fp1, fp2) - Kulczynski similarity
DataStructs.McConnaugheySimilarity(fp1, fp2) - McConnaughey similarity

Bulk Operations

DataStructs.BulkTanimotoSimilarity(fp, fps) - Tanimoto for list of fingerprints
DataStructs.BulkDiceSimilarity(fp, fps) - Dice for list
DataStructs.BulkCosineSimilarity(fp, fps) - Cosine for list

Distance Metrics

DataStructs.TanimotoDistance(fp1, fp2) - 1 - Tanimoto
DataStructs.DiceDistance(fp1, fp2) - 1 - Dice

rdkit.Chem.AtomPairs
Atom pair fingerprints.

Pairs.GetAtomPairFingerprint(mol, minLength=1, maxLength=30) - Atom pair fingerprint
Pairs.GetAtomPairFingerprintAsBitVect(mol, minLength=1, maxLength=30, nBits=2048) - As bit vector
Pairs.GetHashedAtomPairFingerprint(mol, nBits=2048, minLength=1, maxLength=30) - Hashed version

rdkit.Chem.Torsions
Topological torsion fingerprints.

Torsions.GetTopologicalTorsionFingerprint(mol, targetSize=4) - Torsion fingerprint
Torsions.GetTopologicalTorsionFingerprintAsIntVect(mol, targetSize=4) - As int vector
Torsions.GetHashedTopologicalTorsionFingerprint(mol, nBits=2048, targetSize=4) - Hashed version

rdkit.Chem.MACCSkeys
MACCS structural keys.

MACCSkeys.GenMACCSKeys(mol) - Generate 166-bit MACCS keys

rdkit.Chem.ChemicalFeatures
Pharmacophore features.

ChemicalFeatures.BuildFeatureFactory(featureFile) - Create feature factory
factory.GetFeaturesForMol(mol) - Get pharmacophore features
feature.GetFamily() - Feature family (Donor, Acceptor, etc.)
feature.GetType() - Feature type
feature.GetAtomIds() - Atoms involved in feature

rdkit.ML.Cluster.Butina
Clustering algorithms.

Butina.ClusterData(distances, nPts, distThresh, isDistData=True) - Butina clustering
Returns tuple of tuples with cluster members



rdkit.Chem.rdFingerprintGenerator
Modern fingerprint generation API (RDKit 2020.09+).

rdFingerprintGenerator.GetMorganGenerator(radius=2, fpSize=2048) - Morgan generator
rdFingerprintGenerator.GetRDKitFPGenerator(minPath=1, maxPath=7, fpSize=2048) - RDKit FP generator
rdFingerprintGenerator.GetAtomPairGenerator(minDistance=1, maxDistance=30) - Atom pair generator
generator.GetFingerprint(mol) - Generate fingerprint
generator.GetCountFingerprint(mol) - Count-based fingerprint

Common Parameters
Sanitization Operations

SANITIZE_NONE - No sanitization
SANITIZE_ALL - All operations (default)
SANITIZE_CLEANUP - Basic cleanup
SANITIZE_PROPERTIES - Calculate properties
SANITIZE_SYMMRINGS - Symmetrize rings
SANITIZE_KEKULIZE - Kekulize aromatic rings
SANITIZE_FINDRADICALS - Find radical electrons
SANITIZE_SETAROMATICITY - Set aromaticity
SANITIZE_SETCONJUGATION - Set conjugation
SANITIZE_SETHYBRIDIZATION - Set hybridization
SANITIZE_CLEANUPCHIRALITY - Cleanup chirality

Bond Types

BondType.SINGLE - Single bond
BondType.DOUBLE - Double bond
BondType.TRIPLE - Triple bond
BondType.AROMATIC - Aromatic bond
BondType.DATIVE - Dative bond
BondType.UNSPECIFIED - Unspecified

Hybridization

HybridizationType.S - S
HybridizationType.SP - SP
HybridizationType.SP2 - SP2
HybridizationType.SP3 - SP3
HybridizationType.SP3D - SP3D
HybridizationType.SP3D2 - SP3D2

Chirality

ChiralType.CHI_UNSPECIFIED - Unspecified
ChiralType.CHI_TETRAHEDRAL_CW - Clockwise
ChiralType.CHI_TETRAHEDRAL_CCW - Counter-clockwise

Installation
# Using conda (recommended)
conda install -c conda-forge rdkit

# Using pip
pip install rdkit-pypi

Importing
# Core functionality
from rdkit import Chem
from rdkit.Chem import AllChem

# Descriptors
from rdkit.Chem import Descriptors

# Drawing
from rdkit.Chem import Draw

# Similarity
from rdkit import DataStructs

   1---2name: 008-document-a786cd2e3description: RDKit API Reference4---5# RDKit API Reference67This document provides a comprehensive reference for RDKit's Python API, organized by functionality.89## Core Module: rdkit.Chem1011The fundamental module for working with molecules.1213### Molecule I/O1415**Reading Molecules:**1617- `Chem.MolFromSmiles(smiles, sanitize=True)` - Parse SMILES string18- `Chem.MolFromSmarts(smarts)` - Parse SMARTS pattern19- `Chem.MolFromMolFile(filename, sanitize=True, removeHs=True)` - Read MOL file20- `Chem.MolFromMolBlock(molblock, sanitize=True, removeHs=True)` - Parse MOL block string21- `Chem.MolFromMol2File(filename, sanitize=True, removeHs=True)` - Read MOL2 file22- `Chem.MolFromMol2Block(molblock, sanitize=True, removeHs=True)` - Parse MOL2 block23- `Chem.MolFromPDBFile(filename, sanitize=True, removeHs=True)` - Read PDB file24- `Chem.MolFromPDBBlock(pdbblock, sanitize=True, removeHs=True)` - Parse PDB block25- `Chem.MolFromInchi(inchi, sanitize=True, removeHs=True)` - Parse InChI string26- `Chem.MolFromSequence(seq, sanitize=True)` - Create molecule from peptide sequence2728**Writing Molecules:**2930- `Chem.MolToSmiles(mol, isomericSmiles=True, canonical=True)` - Convert to SMILES31- `Chem.MolToSmarts(mol, isomericSmarts=False)` - Convert to SMARTS32- `Chem.MolToMolBlock(mol, includeStereo=True, confId=-1)` - Convert to MOL block33- `Chem.MolToMolFile(mol, filename, includeStereo=True, confId=-1)` - Write MOL file34- `Chem.MolToPDBBlock(mol, confId=-1)` - Convert to PDB block35- `Chem.MolToPDBFile(mol, filename, confId=-1)` - Write PDB file36- `Chem.MolToInchi(mol, options='')` - Convert to InChI37- `Chem.MolToInchiKey(mol, options='')` - Generate InChI key38- `Chem.MolToSequence(mol)` - Convert to peptide sequence3940**Batch I/O:**4142- `Chem.SDMolSupplier(filename, sanitize=True, removeHs=True)` - SDF file reader43- `Chem.ForwardSDMolSupplier(fileobj, sanitize=True, removeHs=True)` - Forward-only SDF reader44- `Chem.MultithreadedSDMolSupplier(filename, numWriterThreads=1)` - Parallel SDF reader45- `Chem.SmilesMolSupplier(filename, delimiter=' ', titleLine=True)` - SMILES file reader46- `Chem.SDWriter(filename)` - SDF file writer47- `Chem.SmilesWriter(filename, delimiter=' ', includeHeader=True)` - SMILES file writer4849### Molecular Manipulation5051**Sanitization:**5253- `Chem.SanitizeMol(mol, sanitizeOps=SANITIZE_ALL, catchErrors=False)` - Sanitize molecule54- `Chem.DetectChemistryProblems(mol, sanitizeOps=SANITIZE_ALL)` - Detect sanitization issues55- `Chem.AssignStereochemistry(mol, cleanIt=True, force=False)` - Assign stereochemistry56- `Chem.FindPotentialStereo(mol)` - Find potential stereocenters57- `Chem.AssignStereochemistryFrom3D(mol, confId=-1)` - Assign stereo from 3D coords5859**Hydrogen Management:**6061- `Chem.AddHs(mol, explicitOnly=False, addCoords=False)` - Add explicit hydrogens62- `Chem.RemoveHs(mol, implicitOnly=False, updateExplicitCount=False)` - Remove hydrogens63- `Chem.RemoveAllHs(mol)` - Remove all hydrogens6465**Aromaticity:**6667- `Chem.SetAromaticity(mol, model=AROMATICITY_RDKIT)` - Set aromaticity model68- `Chem.Kekulize(mol, clearAromaticFlags=False)` - Kekulize aromatic bonds69- `Chem.SetConjugation(mol)` - Set conjugation flags7071**Fragments:**7273- `Chem.GetMolFrags(mol, asMols=False, sanitizeFrags=True)` - Get disconnected fragments74- `Chem.FragmentOnBonds(mol, bondIndices, addDummies=True)` - Fragment on specific bonds75- `Chem.ReplaceSubstructs(mol, query, replacement, replaceAll=False)` - Replace substructures76- `Chem.DeleteSubstructs(mol, query, onlyFrags=False)` - Delete substructures7778**Stereochemistry:**7980- `Chem.FindMolChiralCenters(mol, includeUnassigned=False, useLegacyImplementation=False)` - Find chiral centers81- `Chem.FindPotentialStereo(mol, cleanIt=True)` - Find potential stereocenters8283### Substructure Searching8485**Basic Matching:**8687- `mol.HasSubstructMatch(query, useChirality=False)` - Check for substructure match88- `mol.GetSubstructMatch(query, useChirality=False)` - Get first match89- `mol.GetSubstructMatches(query, uniquify=True, useChirality=False)` - Get all matches90- `mol.GetSubstructMatches(query, maxMatches=1000)` - Limit number of matches9192### Molecular Properties9394**Atom Methods:**9596- `atom.GetSymbol()` - Atomic symbol97- `atom.GetAtomicNum()` - Atomic number98- `atom.GetDegree()` - Number of bonds99- `atom.GetTotalDegree()` - Including hydrogens100- `atom.GetFormalCharge()` - Formal charge101- `atom.GetNumRadicalElectrons()` - Radical electrons102- `atom.GetIsAromatic()` - Aromaticity flag103- `atom.GetHybridization()` - Hybridization (SP, SP2, SP3, etc.)104- `atom.GetIdx()` - Atom index105- `atom.IsInRing()` - In any ring106- `atom.IsInRingSize(size)` - In ring of specific size107- `atom.GetChiralTag()` - Chirality tag108109**Bond Methods:**110111- `bond.GetBondType()` - Bond type (SINGLE, DOUBLE, TRIPLE, AROMATIC)112- `bond.GetBeginAtomIdx()` - Starting atom index113- `bond.GetEndAtomIdx()` - Ending atom index114- `bond.GetIsConjugated()` - Conjugation flag115- `bond.GetIsAromatic()` - Aromaticity flag116- `bond.IsInRing()` - In any ring117- `bond.GetStereo()` - Stereochemistry (STEREONONE, STEREOZ, STEREOE, etc.)118119**Molecule Methods:**120121- `mol.GetNumAtoms(onlyExplicit=True)` - Number of atoms122- `mol.GetNumHeavyAtoms()` - Number of heavy atoms123- `mol.GetNumBonds()` - Number of bonds124- `mol.GetAtoms()` - Iterator over atoms125- `mol.GetBonds()` - Iterator over bonds126- `mol.GetAtomWithIdx(idx)` - Get specific atom127- `mol.GetBondWithIdx(idx)` - Get specific bond128- `mol.GetRingInfo()` - Ring information object129130**Ring Information:**131132- `Chem.GetSymmSSSR(mol)` - Get smallest set of smallest rings133- `Chem.GetSSSR(mol)` - Alias for GetSymmSSSR134- `ring_info.NumRings()` - Number of rings135- `ring_info.AtomRings()` - Tuples of atom indices in rings136- `ring_info.BondRings()` - Tuples of bond indices in rings137138## rdkit.Chem.AllChem139140Extended chemistry functionality.141142### 2D/3D Coordinate Generation143144- `AllChem.Compute2DCoords(mol, canonOrient=True, clearConfs=True)` - Generate 2D coordinates145- `AllChem.EmbedMolecule(mol, maxAttempts=0, randomSeed=-1, useRandomCoords=False)` - Generate 3D conformer146- `AllChem.EmbedMultipleConfs(mol, numConfs=10, maxAttempts=0, randomSeed=-1)` - Generate multiple conformers147- `AllChem.ConstrainedEmbed(mol, core, useTethers=True)` - Constrained embedding148- `AllChem.GenerateDepictionMatching2DStructure(mol, reference, refPattern=None)` - Align to template149150### Force Field Optimization151152- `AllChem.UFFOptimizeMolecule(mol, maxIters=200, confId=-1)` - UFF optimization153- `AllChem.MMFFOptimizeMolecule(mol, maxIters=200, confId=-1, mmffVariant='MMFF94')` - MMFF optimization154- `AllChem.UFFGetMoleculeForceField(mol, confId=-1)` - Get UFF force field object155- `AllChem.MMFFGetMoleculeForceField(mol, pyMMFFMolProperties, confId=-1)` - Get MMFF force field156157### Conformer Analysis158159- `AllChem.GetConformerRMS(mol, confId1, confId2, prealigned=False)` - Calculate RMSD160- `AllChem.GetConformerRMSMatrix(mol, prealigned=False)` - RMSD matrix161- `AllChem.AlignMol(prbMol, refMol, prbCid=-1, refCid=-1)` - Align molecules162- `AllChem.AlignMolConformers(mol)` - Align all conformers163164### Reactions165166- `AllChem.ReactionFromSmarts(smarts, useSmiles=False)` - Create reaction from SMARTS167- `reaction.RunReactants(reactants)` - Apply reaction168- `reaction.RunReactant(reactant, reactionIdx)` - Apply to specific reactant169- `AllChem.CreateDifferenceFingerprintForReaction(reaction)` - Reaction fingerprint170171### Fingerprints172173- `AllChem.GetMorganFingerprint(mol, radius, useFeatures=False)` - Morgan fingerprint174- `AllChem.GetMorganFingerprintAsBitVect(mol, radius, nBits=2048)` - Morgan bit vector175- `AllChem.GetHashedMorganFingerprint(mol, radius, nBits=2048)` - Hashed Morgan176- `AllChem.GetErGFingerprint(mol)` - ErG fingerprint177178## rdkit.Chem.Descriptors179180Molecular descriptor calculations.181182### Common Descriptors183184- `Descriptors.MolWt(mol)` - Molecular weight185- `Descriptors.ExactMolWt(mol)` - Exact molecular weight186- `Descriptors.HeavyAtomMolWt(mol)` - Heavy atom molecular weight187- `Descriptors.MolLogP(mol)` - LogP (lipophilicity)188- `Descriptors.MolMR(mol)` - Molar refractivity189- `Descriptors.TPSA(mol)` - Topological polar surface area190- `Descriptors.NumHDonors(mol)` - Hydrogen bond donors191- `Descriptors.NumHAcceptors(mol)` - Hydrogen bond acceptors192- `Descriptors.NumRotatableBonds(mol)` - Rotatable bonds193- `Descriptors.NumAromaticRings(mol)` - Aromatic rings194- `Descriptors.NumSaturatedRings(mol)` - Saturated rings195- `Descriptors.NumAliphaticRings(mol)` - Aliphatic rings196- `Descriptors.NumAromaticHeterocycles(mol)` - Aromatic heterocycles197- `Descriptors.NumRadicalElectrons(mol)` - Radical electrons198- `Descriptors.NumValenceElectrons(mol)` - Valence electrons199200### Batch Calculation201202- `Descriptors.CalcMolDescriptors(mol)` - Calculate all descriptors as dictionary203204### Descriptor Lists205206- `Descriptors._descList` - List of (name, function) tuples for all descriptors207208## rdkit.Chem.Draw209210Molecular visualization.211212### Image Generation213214- `Draw.MolToImage(mol, size=(300,300), kekulize=True, wedgeBonds=True, highlightAtoms=None)` - Generate PIL image215- `Draw.MolToFile(mol, filename, size=(300,300), kekulize=True, wedgeBonds=True)` - Save to file216- `Draw.MolsToGridImage(mols, molsPerRow=3, subImgSize=(200,200), legends=None)` - Grid of molecules217- `Draw.MolsMatrixToGridImage(mols, molsPerRow=3, subImgSize=(200,200), legends=None)` - Nested grid218- `Draw.ReactionToImage(rxn, subImgSize=(200,200))` - Reaction image219220### Fingerprint Visualization221222- `Draw.DrawMorganBit(mol, bitId, bitInfo, whichExample=0)` - Visualize Morgan bit223- `Draw.DrawMorganBits(bits, mol, bitInfo, molsPerRow=3)` - Multiple Morgan bits224- `Draw.DrawRDKitBit(mol, bitId, bitInfo, whichExample=0)` - Visualize RDKit bit225226### IPython Integration227228- `Draw.IPythonConsole` - Module for Jupyter integration229- `Draw.IPythonConsole.ipython_useSVG` - Use SVG (True) or PNG (False)230- `Draw.IPythonConsole.molSize` - Default molecule image size231232### Drawing Options233234- `rdMolDraw2D.MolDrawOptions()` - Get drawing options object235  - `.addAtomIndices` - Show atom indices236  - `.addBondIndices` - Show bond indices237  - `.addStereoAnnotation` - Show stereochemistry238  - `.bondLineWidth` - Line width239  - `.highlightBondWidthMultiplier` - Highlight width240  - `.minFontSize` - Minimum font size241  - `.maxFontSize` - Maximum font size242243## rdkit.Chem.rdMolDescriptors244245Additional descriptor calculations.246247- `rdMolDescriptors.CalcNumRings(mol)` - Number of rings248- `rdMolDescriptors.CalcNumAromaticRings(mol)` - Aromatic rings249- `rdMolDescriptors.CalcNumAliphaticRings(mol)` - Aliphatic rings250- `rdMolDescriptors.CalcNumSaturatedRings(mol)` - Saturated rings251- `rdMolDescriptors.CalcNumHeterocycles(mol)` - Heterocycles252- `rdMolDescriptors.CalcNumAromaticHeterocycles(mol)` - Aromatic heterocycles253- `rdMolDescriptors.CalcNumSpiroAtoms(mol)` - Spiro atoms254- `rdMolDescriptors.CalcNumBridgeheadAtoms(mol)` - Bridgehead atoms255- `rdMolDescriptors.CalcFractionCsp3(mol)` - Fraction of sp3 carbons256- `rdMolDescriptors.CalcLabuteASA(mol)` - Labute accessible surface area257- `rdMolDescriptors.CalcTPSA(mol)` - TPSA258- `rdMolDescriptors.CalcMolFormula(mol)` - Molecular formula259260## rdkit.Chem.Scaffolds261262Scaffold analysis.263264### Murcko Scaffolds265266- `MurckoScaffold.GetScaffoldForMol(mol)` - Get Murcko scaffold267- `MurckoScaffold.MakeScaffoldGeneric(mol)` - Generic scaffold268- `MurckoScaffold.MurckoDecompose(mol)` - Decompose to scaffold and sidechains269270## rdkit.Chem.rdMolHash271272Molecular hashing and standardization.273274- `rdMolHash.MolHash(mol, hashFunction)` - Generate hash275  - `rdMolHash.HashFunction.AnonymousGraph` - Anonymized structure276  - `rdMolHash.HashFunction.CanonicalSmiles` - Canonical SMILES277  - `rdMolHash.HashFunction.ElementGraph` - Element graph278  - `rdMolHash.HashFunction.MurckoScaffold` - Murcko scaffold279  - `rdMolHash.HashFunction.Regioisomer` - Regioisomer (no stereo)280  - `rdMolHash.HashFunction.NetCharge` - Net charge281  - `rdMolHash.HashFunction.HetAtomProtomer` - Heteroatom protomer282  - `rdMolHash.HashFunction.HetAtomTautomer` - Heteroatom tautomer283284## rdkit.Chem.MolStandardize285286Molecule standardization.287288- `rdMolStandardize.Normalize(mol)` - Normalize functional groups289- `rdMolStandardize.Reionize(mol)` - Fix ionization state290- `rdMolStandardize.RemoveFragments(mol)` - Remove small fragments291- `rdMolStandardize.Cleanup(mol)` - Full cleanup (normalize + reionize + remove)292- `rdMolStandardize.Uncharger()` - Create uncharger object293  - `.uncharge(mol)` - Remove charges294- `rdMolStandardize.TautomerEnumerator()` - Enumerate tautomers295  - `.Enumerate(mol)` - Generate tautomers296  - `.Canonicalize(mol)` - Get canonical tautomer297298## rdkit.DataStructs299300Fingerprint similarity and operations.301302### Similarity Metrics303304- `DataStructs.TanimotoSimilarity(fp1, fp2)` - Tanimoto coefficient305- `DataStructs.DiceSimilarity(fp1, fp2)` - Dice coefficient306- `DataStructs.CosineSimilarity(fp1, fp2)` - Cosine similarity307- `DataStructs.SokalSimilarity(fp1, fp2)` - Sokal similarity308- `DataStructs.KulczynskiSimilarity(fp1, fp2)` - Kulczynski similarity309- `DataStructs.McConnaugheySimilarity(fp1, fp2)` - McConnaughey similarity310311### Bulk Operations312313- `DataStructs.BulkTanimotoSimilarity(fp, fps)` - Tanimoto for list of fingerprints314- `DataStructs.BulkDiceSimilarity(fp, fps)` - Dice for list315- `DataStructs.BulkCosineSimilarity(fp, fps)` - Cosine for list316317### Distance Metrics318319- `DataStructs.TanimotoDistance(fp1, fp2)` - 1 - Tanimoto320- `DataStructs.DiceDistance(fp1, fp2)` - 1 - Dice321322## rdkit.Chem.AtomPairs323324Atom pair fingerprints.325326- `Pairs.GetAtomPairFingerprint(mol, minLength=1, maxLength=30)` - Atom pair fingerprint327- `Pairs.GetAtomPairFingerprintAsBitVect(mol, minLength=1, maxLength=30, nBits=2048)` - As bit vector328- `Pairs.GetHashedAtomPairFingerprint(mol, nBits=2048, minLength=1, maxLength=30)` - Hashed version329330## rdkit.Chem.Torsions331332Topological torsion fingerprints.333334- `Torsions.GetTopologicalTorsionFingerprint(mol, targetSize=4)` - Torsion fingerprint335- `Torsions.GetTopologicalTorsionFingerprintAsIntVect(mol, targetSize=4)` - As int vector336- `Torsions.GetHashedTopologicalTorsionFingerprint(mol, nBits=2048, targetSize=4)` - Hashed version337338## rdkit.Chem.MACCSkeys339340MACCS structural keys.341342- `MACCSkeys.GenMACCSKeys(mol)` - Generate 166-bit MACCS keys343344## rdkit.Chem.ChemicalFeatures345346Pharmacophore features.347348- `ChemicalFeatures.BuildFeatureFactory(featureFile)` - Create feature factory349- `factory.GetFeaturesForMol(mol)` - Get pharmacophore features350- `feature.GetFamily()` - Feature family (Donor, Acceptor, etc.)351- `feature.GetType()` - Feature type352- `feature.GetAtomIds()` - Atoms involved in feature353354## rdkit.ML.Cluster.Butina355356Clustering algorithms.357358- `Butina.ClusterData(distances, nPts, distThresh, isDistData=True)` - Butina clustering359  - Returns tuple of tuples with cluster members360361## rdkit.Chem.rdFingerprintGenerator362363Modern fingerprint generation API (RDKit 2020.09+).364365- `rdFingerprintGenerator.GetMorganGenerator(radius=2, fpSize=2048)` - Morgan generator366- `rdFingerprintGenerator.GetRDKitFPGenerator(minPath=1, maxPath=7, fpSize=2048)` - RDKit FP generator367- `rdFingerprintGenerator.GetAtomPairGenerator(minDistance=1, maxDistance=30)` - Atom pair generator368- `generator.GetFingerprint(mol)` - Generate fingerprint369- `generator.GetCountFingerprint(mol)` - Count-based fingerprint370371## Common Parameters372373### Sanitization Operations374375- `SANITIZE_NONE` - No sanitization376- `SANITIZE_ALL` - All operations (default)377- `SANITIZE_CLEANUP` - Basic cleanup378- `SANITIZE_PROPERTIES` - Calculate properties379- `SANITIZE_SYMMRINGS` - Symmetrize rings380- `SANITIZE_KEKULIZE` - Kekulize aromatic rings381- `SANITIZE_FINDRADICALS` - Find radical electrons382- `SANITIZE_SETAROMATICITY` - Set aromaticity383- `SANITIZE_SETCONJUGATION` - Set conjugation384- `SANITIZE_SETHYBRIDIZATION` - Set hybridization385- `SANITIZE_CLEANUPCHIRALITY` - Cleanup chirality386387### Bond Types388389- `BondType.SINGLE` - Single bond390- `BondType.DOUBLE` - Double bond391- `BondType.TRIPLE` - Triple bond392- `BondType.AROMATIC` - Aromatic bond393- `BondType.DATIVE` - Dative bond394- `BondType.UNSPECIFIED` - Unspecified395396### Hybridization397398- `HybridizationType.S` - S399- `HybridizationType.SP` - SP400- `HybridizationType.SP2` - SP2401- `HybridizationType.SP3` - SP3402- `HybridizationType.SP3D` - SP3D403- `HybridizationType.SP3D2` - SP3D2404405### Chirality406407- `ChiralType.CHI_UNSPECIFIED` - Unspecified408- `ChiralType.CHI_TETRAHEDRAL_CW` - Clockwise409- `ChiralType.CHI_TETRAHEDRAL_CCW` - Counter-clockwise410411## Installation412413```bash414# Using conda (recommended)415conda install -c conda-forge rdkit416417# Using pip418pip install rdkit-pypi419```420421## Importing422423```python424# Core functionality425from rdkit import Chem426from rdkit.Chem import AllChem427428# Descriptors429from rdkit.Chem import Descriptors430431# Drawing432from rdkit.Chem import Draw433434# Similarity435from rdkit import DataStructs436```

  tools-only/X-Skills/tree/main/data-analysis/008-document_a786cd2e commit 86fd4fce82 
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008 Document A786cd2e

File contents

RDKit API Reference

Core Module: rdkit.Chem

Molecule I/O

Molecular Manipulation

Substructure Searching

Molecular Properties

rdkit.Chem.AllChem

2D/3D Coordinate Generation

Force Field Optimization

Conformer Analysis

Reactions

Fingerprints

rdkit.Chem.Descriptors

Common Descriptors

Batch Calculation

Descriptor Lists

rdkit.Chem.Draw

Image Generation

Fingerprint Visualization

IPython Integration

Drawing Options

rdkit.Chem.rdMolDescriptors

rdkit.Chem.Scaffolds

Murcko Scaffolds

rdkit.Chem.rdMolHash

rdkit.Chem.MolStandardize

rdkit.DataStructs

Similarity Metrics

Bulk Operations

Distance Metrics

rdkit.Chem.AtomPairs

rdkit.Chem.Torsions

rdkit.Chem.MACCSkeys

rdkit.Chem.ChemicalFeatures

rdkit.ML.Cluster.Butina

rdkit.Chem.rdFingerprintGenerator

Common Parameters

Sanitization Operations

Bond Types

Hybridization

Chirality

Installation

Importing

Related skills

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