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Symmetry-corrected RMSD calculations in Python
"""
if __name__ == "__main__":
import argparse as ap
import importlib.util
import sys
from spyrmsd import io
from spyrmsd.rmsd import rmsdwrapper
parser = ap.ArgumentParser(
prog="python -m spyrmsd",
description="Symmetry-corrected RMSD calculations in Python.",
)
parser.add_argument("reference", type=str, help="Reference file")
parser.add_argument("molecules", type=str, nargs="+", help="Input file(s)")
parser.add_argument("-m", "--minimize", action="store_true", help="Minimize (fit)")
parser.add_argument(
"-c", "--center", action="store_true", help="Center molecules at origin"
)
parser.add_argument("--hydrogens", action="store_true", help="Keep hydrogen atoms")
parser.add_argument(
"-n", "--nosymm", action="store_false", help="No graph isomorphism"
)
args = parser.parse_args()
if (
importlib.util.find_spec("openbabel") is None
and importlib.util.find_spec("rdkit") is None
):
raise ImportError(
"OpenBabel or RDKit not found. Please install OpenBabel or RDKit to use sPyRMSD as a standalone tool."
)
try:
ref = io.loadmol(args.reference)
except OSError:
print("ERROR: Reference file not found.", file=sys.stderr)
exit(-1)
# Load all molecules
try:
mols = [mol for molfile in args.molecules for mol in io.loadallmols(molfile)]
except OSError:
print("ERROR: Molecule file(s) not found.", file=sys.stderr)
exit(-1)
# Loop over molecules within fil
RMSDlist = rmsdwrapper(
ref,
mols,
symmetry=args.nosymm, # args.nosymm store False
center=args.center,
minimize=args.minimize,
strip=not args.hydrogens,
)
for RMSD in RMSDlist:
print(f"{RMSD:.5f}")
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