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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, isomericSmiles=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, onlyFrags=False) - 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

• Prefer rdFingerprintGenerator.GetMorganGenerator() for new Morgan fingerprint code
• AllChem.GetMorganFingerprint(mol, radius, useFeatures=False) - Legacy Morgan fingerprint helper
• AllChem.GetMorganFingerprintAsBitVect(mol, radius, nBits=2048) - Legacy Morgan bit vector helper
• AllChem.GetHashedMorganFingerprint(mol, radius, nBits=2048) - Legacy hashed Morgan helper
• 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.

Import the current standardization implementation from rdkit.Chem.MolStandardize:

from rdkit.Chem.MolStandardize import rdMolStandardize

• 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. Prefer this over legacy AllChem.GetMorganFingerprint* helpers for new code.

• 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
• rdFingerprintGenerator.GetTopologicalTorsionGenerator(fpSize=2048) - Topological torsion generator
• generator.GetFingerprint(mol) - Generate fingerprint
• generator.GetCountFingerprint(mol) - Count-based fingerprint
• rdFingerprintGenerator.AdditionalOutput() - Collect bit information for visualization and explanations

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

# Existing uv/pip environment
uv pip install rdkit

# Fresh conda-forge environment (upstream recommendation)
conda create -c conda-forge -n my-rdkit-env rdkit

The PyPI package is now rdkit; rdkit-pypi is the legacy name for older releases.

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