rdkit_utilities.rdMolAlign

rdkit_utilities.rdMolAlign.GetBestConformerRMS(mol, heavyAtomsOnly=False, confIds=None)[source]

Get square array of conformer-to-conformer symmetric RMS

Parameters

  • mol (rdkit.Chem.Mol) – Molecule of interest

  • heavyAtomsOnly (bool) – If True, all hydrogens are removed before calculating RMS. This is done on a copy to avoid changing the molecule

  • confIds (Optional[List[int]]) – If given, the RMS calculation is limited to these conformer IDs. If not, all conformers are used.

Returns

rms – Square array of RMS from each conformer to each other. This is ordered by the input confIds if given, or by the order of the conformers on the molecule if confIds=None.

Return type

numpy.ndarray

Parameters

  • mol (Mol) –

  • heavyAtomsOnly (bool) –

  • confIds (Optional[List[int]]) –