RDKit

The primary Python library for cheminformatics. Molecular manipulation, descriptors, fingerprints, 3D generation, reactions, and more.

When to Use This Skill

• Reading/writing molecules from SMILES, SDF, MOL, PDB files
• Calculating molecular properties and drug-likeness filters (Ro5, QED)
• Computing and comparing molecular fingerprints (Morgan/ECFP, MACCS, RDKit FP)
• Generating 3D conformers (ETKDG, MMFF, UFF)
• Substructure searching and SMARTS queries
• Maximum Common Substructure (MCS) analysis
• Chemical reactions via SMARTS or RXN files
• Molecular fragmentation (BRICS, RECAP, Murcko scaffolds)
• Stereochemistry assignment and analysis
• Tautomer enumeration and molecule standardization
• Molecular visualization (2D SVG/PNG, similarity maps)

Quick Start

from rdkit import Chem
from rdkit.Chem import AllChem, Descriptors, Draw, rdMolDescriptors

# Load molecule
mol = Chem.MolFromSmiles('CC(=O)Oc1ccccc1C(=O)O')  # aspirin

# Basic properties
print(Descriptors.MolWt(mol))        # 180.16
print(Descriptors.MolLogP(mol))      # 1.31
print(rdMolDescriptors.CalcNumHBD(mol))  # 1
print(rdMolDescriptors.CalcNumHBA(mol))  # 4
print(rdMolDescriptors.CalcTPSA(mol))    # 63.6

# Morgan fingerprint (ECFP4-like)
fpgen = AllChem.GetMorganGenerator(radius=2)
fp = fpgen.GetFingerprint(mol)

# 2D image
img = Draw.MolToImage(mol, size=(300, 200))

Router — What to Read

Task	Reference
SMILES, SDF, MOL, PDB, SMARTS I/O, serialization	references/io-molecules.md
Descriptors, Lipinski Ro5, QED, ADME, drug filters	references/properties-descriptors.md
Morgan, MACCS, RDKit FP, atom pair, similarity, diversity	references/fingerprints-similarity.md
3D conformers (ETKDG), MMFF/UFF optimization, 3D descriptors	references/3d-conformers.md
Reactions (SMARTS), BRICS, RECAP, Murcko, tautomers, standardization	references/transformations.md
Substructure search (SMARTS), MCS, rings, stereochemistry, pharmacophores	references/analysis-search.md
Visualization: SVG/PNG, highlighting, similarity maps, grids	references/visualization.md

Key Modules

Module	Import	Role
Chem	from rdkit import Chem	Core molecule objects, I/O
AllChem	from rdkit.Chem import AllChem	3D, fingerprints, reactions
Descriptors	from rdkit.Chem import Descriptors	200+ 2D descriptors
rdMolDescriptors	from rdkit.Chem import rdMolDescriptors	Fast C++ descriptors
DataStructs	from rdkit import DataStructs	Fingerprint similarity
Draw	from rdkit.Chem import Draw	2D visualization
rdMolDraw2D	from rdkit.Chem.Draw import rdMolDraw2D	SVG/Cairo rendering
MACCSkeys	from rdkit.Chem import MACCSkeys	MACCS fingerprints
rdFMCS	from rdkit.Chem import rdFMCS	Maximum Common Substructure
BRICS	from rdkit.Chem import BRICS	BRICS fragmentation
Recap	from rdkit.Chem import Recap	RECAP fragmentation
MurckoScaffold	from rdkit.Chem.Scaffolds import MurckoScaffold	Scaffold extraction
rdMolStandardize	from rdkit.Chem.MolStandardize import rdMolStandardize	Tautomers, cleanup
rdChemReactions	from rdkit.Chem import rdChemReactions	Reaction handling

Installation

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

# pip (official wheel since 2022)
pip install rdkit

# verify
python -c "from rdkit import Chem; print(Chem.MolFromSmiles('c1ccccc1'))"

Related Skills

• deepchem — ML models on molecular datasets built on top of RDKit
• cheminformatics — SMILES notation, file formats, molecular representations
• nextflow — Pipeline execution for high-throughput molecular workflows