Use when working with RDKit for cheminformatics in Python. Covers molecular I/O, property calculation, Lipinski filters, fingerprints, similarity, 3D conformer generation, reactions, fragmentation, substructure search, MCS, stereochemistry, and tautomers.
The primary Python library for cheminformatics. Molecular manipulation, descriptors, fingerprints, 3D generation, reactions, and more.
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))
| 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 |
| 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 |
# 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'))"
deepchem — ML models on molecular datasets built on top of RDKitcheminformatics — SMILES notation, file formats, molecular representationsnextflow — Pipeline execution for high-throughput molecular workflows