rdkit.Chem.ChemUtils.AlignDepict module — The RDKit 2025.09.6 documentation

# rdkit.Chem.ChemUtils.AlignDepict module

rdkit.Chem.ChemUtils.AlignDepict.AlignDepict(mol, core, corePattern=None, acceptFailure=False)
  Parameters:

    - mol (-) – the molecule to be aligned, this will come back with a single conformer.

    - core (-) – a molecule with the core atoms to align to; this should have a depiction.

    - corePattern (-) – (optional) an optional molecule to be used to generate the atom mapping between the molecule and the core.

rdkit.Chem.ChemUtils.AlignDepict.initParser()

  Initialize the parser

rdkit.Chem.ChemUtils.AlignDepict.main()

  Main application

rdkit.Chem.ChemUtils.AlignDepict.processArgs(args)