Compute optimal RMSD between two molecular structures

rmsd.py

#!/usr/bin/env python3

from rdkit.Chem.rdmolfiles import MolFromMol2File
from rdkit.Chem.rdMolAlign import AlignMol

import argparse

if __name__ == "__main__":
    PARSER = argparse.ArgumentParser(
        description="""Compute optimal RMSD of two structures.
Atom order is not changed, and no matching is attempted. For details refer to:

https://www.rdkit.org/docs/source/rdkit.Chem.rdMolAlign.html#module-rdkit.Chem.rdMolAlign
""",
        formatter_class=argparse.RawDescriptionHelpFormatter,
    )
    PARSER.add_argument(
        "file_a",
        metavar="PATH_A",
        help="path to the first structure in TRIPOS mol2 format",
    )
    PARSER.add_argument(
        "file_b",
        metavar="PATH_B",
        help="path to the second structure in TRIPOS mol2 format",
    )
    args = PARSER.parse_args()

    a = MolFromMol2File(args.file_a)
    b = MolFromMol2File(args.file_b)
    res = AlignMol(a, b)
    print(res)