Version Compatibility

Reference examples tested with: RDKit 2024.03+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Molecular I/O

"Load my chemical library into Python" → Parse molecular file formats (SMILES, SDF, MOL2, PDB) into RDKit molecule objects for programmatic access, standardization, and format conversion.

• Python: Chem.MolFromSmiles(), Chem.SDMolSupplier() (RDKit)

Read, write, and convert molecular file formats with structure standardization.

Supported Formats

Format	Extension	Use Case
SMILES	.smi	Text representation, databases
SDF/MOL	.sdf, .mol	3D structures, compound libraries
MOL2	.mol2	Docking, force field atoms
PDB	.pdb	Protein-ligand complexes

Reading Molecules

Goal: Load molecules from SMILES strings, SDF files, or SMILES files into RDKit molecule objects.

Approach: Use Chem.MolFromSmiles for individual SMILES, SDMolSupplier for multi-molecule SDF files, and file iteration for SMILES files, filtering out parse failures.

from rdkit import Chem
from rdkit.Chem import AllChem

# From SMILES
mol = Chem.MolFromSmiles('CCO')

# From SDF file (single molecule)
mol = Chem.MolFromMolFile('molecule.mol')

# From SDF file (multiple molecules)
supplier = Chem.SDMolSupplier('library.sdf')
molecules = [mol for mol in supplier if mol is not None]
print(f'Loaded {len(molecules)} molecules')

# From SMILES file
with open('compounds.smi') as f:
    molecules = []
    for line in f:
        parts = line.strip().split()
        if parts:
            mol = Chem.MolFromSmiles(parts[0])
            if mol:
                mol.SetProp('_Name', parts[1] if len(parts) > 1 else '')
                molecules.append(mol)