chemistry-rdkit
RDKit Cheminformatics Best Practice
Molecular I/O
- Create molecules from SMILES:
mol = Chem.MolFromSmiles('CCO') - Always check for None:
MolFromSmilesreturns None on invalid input - Convert to canonical SMILES:
Chem.MolToSmiles(mol) - Read SDF files:
suppl = Chem.SDMolSupplier('file.sdf') - Read SMILES files:
suppl = Chem.SmilesMolSupplier('file.smi') - Write molecules:
writer = Chem.SDWriter('output.sdf')
Molecular Descriptors
- Molecular weight:
Descriptors.MolWt(mol) - LogP (lipophilicity):
Descriptors.MolLogP(mol) - TPSA (polar surface area):
Descriptors.TPSA(mol) - H-bond donors/acceptors:
Descriptors.NumHDonors(mol),Descriptors.NumHAcceptors(mol) - Rotatable bonds:
Descriptors.NumRotatableBonds(mol) - Lipinski Rule of 5: MW <= 500, LogP <= 5, HBD <= 5, HBA <= 10
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