Prepared molecules

PrepareMol(...) pays the RDKit preparation cost once and returns an opaque PreparedMol.

Use it when the same molecule will be decoded, enumerated, inventoried, or checked more than once. It is also the storage path when you want to load a prepared molecule later without touching RDKit again.

from rdkit import Chem
import grimace

mol = Chem.MolFromSmiles("CCO")
prepared = grimace.PrepareMol(mol, isomericSmiles=False)

payload = prepared.to_bytes()
restored = grimace.PreparedMol.from_bytes(payload)

PreparedMol is accepted anywhere the public runtime accepts a molecule:

• MolToSmilesEnum(...)
• MolToSmilesDecoder(...)
• MolToSmilesDeterminizedDecoder(...)
• MolToSmilesDeviation(...)
• MolToSmilesTokenInventory(...)
• MolToSmilesTokenInventorySuperset(...)

Writer-surface flags passed to PrepareMol(...) are baked into the prepared object. Runtime calls with conflicting writer flags raise ValueError. rootedAtAtom, canonical, and doRandom remain runtime options.

FLAGS = dict(canonical=False, doRandom=True)

all_smiles = tuple(
    grimace.MolToSmilesEnum(
        restored,
        rootedAtAtom=-1,
        isomericSmiles=False,
        **FLAGS,
    )
)

PreparedMol.to_bytes() returns a versioned binary payload owned by the Rust core. Treat the bytes as opaque.

For the supported writer flags, see Runtime.