File Formats & Conversion

Format conversion lets you move molecules between SMILES, SDF, and PDB so each stage of a workflow gets the representation it expects. Careful parsing — checking for None, sanitizing, and preserving provenance — is what most affects whether a batch runs clean or silently drops records.

Parse molecules

from rdkit import Chem

mol = Chem.MolFromSmiles("CC(=O)Oc1ccccc1C(=O)O")
if mol is None:
    raise ValueError("Invalid SMILES")

mol = Chem.AddHs(mol)
Chem.SanitizeMol(mol)

SDF to SMILES

from rdkit.Chem import SDMolSupplier

supplier = SDMolSupplier("input.sdf", removeHs=False)
smiles: list[str] = []
for mol in supplier:
    if mol is None:
        continue
    smiles.append(Chem.MolToSmiles(Chem.RemoveHs(mol)))

SMILES to SDF

from rdkit.Chem import SDWriter

writer = SDWriter("/workspace/outputs/library.sdf")
for s in smiles:
    mol = Chem.MolFromSmiles(s)
    if mol is None:
        continue
    Chem.SanitizeMol(mol)
    writer.write(Chem.AddHs(mol))
writer.close()

PDB hygiene

• Use Chem.MolFromPDBFile("structure.pdb", removeHs=False, sanitize=True).
• Strip waters/ions before minimization if they are not needed.
• Ensure residue/atom names are preserved before exporting back to PDB.

Validation tips

• Always check for None after parsing; skip invalid records rather than crashing the batch.
• Normalize tautomers if your downstream model expects a canonical form.
• Record provenance: store the source file path in mol.SetProp("source", path).