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Datamol for molecular manipulation, SMILES processing, and cheminformatics
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| name | datamol |
| description | Datamol for molecular manipulation, SMILES processing, and cheminformatics |
Datamol is a lightweight Python library built on top of RDKit that simplifies molecular manipulation. It provides a clean API for SMILES parsing, standardization, fingerprints, scaffolds, and visualization.
import datamol as dm
# Parse and standardize SMILES
mol = dm.to_mol("CC(=O)Oc1ccccc1C(=O)O")
std_mol = dm.standardize_mol(mol)
smiles = dm.to_smiles(std_mol, canonical=True)
# Fix and sanitize
mol = dm.to_mol("bad_smiles", ordered=True) # returns None if invalid
fixed = dm.fix_mol(mol)
sanitized = dm.sanitize_mol(fixed)
# Molecular properties
dm.descriptors.mw(mol) # molecular weight
dm.descriptors.logp(mol) # cLogP
dm.descriptors.tpsa(mol) # topological polar surface area
dm.descriptors.n_hba(mol) # H-bond acceptors
dm.descriptors.n_hbd(mol) # H-bond donors
# Fingerprints
fp = dm.to_fp(mol, fp_type="ecfp", n_bits=2048) # numpy array
dm.to_scaffold_murcko(mol), dm.fragment.brics(mol).None inputs (return None).dm.to_smiles returns canonical SMILES by default.dm.to_mol(["CCO", "c1ccccc1"]) accepts lists.dm.cluster.cluster_mols(mols, cutoff=0.7).pip install datamol.