chemistry-rdkit

RDKit Cheminformatics Best Practice

Molecular I/O

1. Create molecules from SMILES: mol = Chem.MolFromSmiles('CCO')
2. Always check for None: MolFromSmiles returns None on invalid input
3. Convert to canonical SMILES: Chem.MolToSmiles(mol)
4. Read SDF files: suppl = Chem.SDMolSupplier('file.sdf')
5. Read SMILES files: suppl = Chem.SmilesMolSupplier('file.smi')
6. Write molecules: writer = Chem.SDWriter('output.sdf')

Molecular Descriptors

1. Molecular weight: Descriptors.MolWt(mol)
2. LogP (lipophilicity): Descriptors.MolLogP(mol)
3. TPSA (polar surface area): Descriptors.TPSA(mol)
4. H-bond donors/acceptors: Descriptors.NumHDonors(mol), Descriptors.NumHAcceptors(mol)
5. Rotatable bonds: Descriptors.NumRotatableBonds(mol)
6. Lipinski Rule of 5: MW <= 500, LogP <= 5, HBD <= 5, HBA <= 10