mol_getter

Build RDKit molecules from a TS .xyz file (and optional SMILES), providing different strategies for topology inference.

MolGetterSMILES

Combines one or more SMILES (as separate fragments) and maps atoms to the .xyz structure to transfer bond orders where applicable.

Choosing quickly

  • Have SMILES? Use smiles.
  • No SMILES but you know the charge? Pick bonds.

MolGetterBonds

Reads the .xyz, then uses rdDetermineBonds.DetermineBonds to infer bonding (needs charge). These arguments are passed on to the DetermineBonds algorithm: - assignBonds: bool = True - allowChargedFragments: bool = True

MolGetterConnectivity

Reads the .xyz and uses RDKit's rdDetermineBonds.DetermineConnectivity (sets connectivity without bond orders), sanitizes (hybridization, aromaticity, conjugation, symmetric rings), and assigns stereochemistry from 3D.