def _reconstruct_mol_from_conformer(
mol: Molecule,
positions: unit.Quantity,
) -> Molecule:
mol = deepcopy(mol)
mol._conformers = None
mol.add_conformer(positions)
return mol
def _get_rms_two_conformers(mol: Molecule, positions1: unit.Quantity,
positions2: unit.Quantity) -> float:
"""Find the RMSD between two conformers of a molecule using RDKit"""
# TODO: Is it worth making Molecule.get_rmsd(), which operates
# through ToolkitWrapper methods?
from rdkit.Chem import rdMolAlign
mol_copy = Molecule(mol)
mol_copy._conformers = None
mol_copy.add_conformer(positions1)
mol_copy.add_conformer(positions2)
rdmol = mol_copy.to_rdkit()
rmslist: List = []
rdMolAlign.AlignMolConformers(rdmol, RMSlist=rmslist)
return rmslist[0]
