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add --ignore_name_matching argument for all-to-all RMSD calculations #23

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add --ignore_name_matching argument for all-to-all RMSD calculations #23

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7765e3a
add --ignore_name_matching argument to all-to-all RMSD calculations
avnikonenko Jul 13, 2026
c96c2ef
add multiprocessing support
avnikonenko Jul 13, 2026
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139 changes: 92 additions & 47 deletions rmsd_rdkit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
import sys

from itertools import product
from multiprocessing import Pool, cpu_count

from rdkit import Chem
from rdkit.Chem import rdFMCS
Expand Down Expand Up @@ -75,7 +76,61 @@ def rmsd_calc(r_coord, m_coord):
return round(min_rmsd, 3)


def main_params(input_fnames, input_smi, output_fname, ref_name, refsmi, chirality, regex, align):
def calc_output_row(data):
if data[0] == 'line':
return data[1]

_, mol, mol_name, mol_idx, refmol, refmol_name, chirality, align = data
mol_rmsd = rmsd(mol, mol_name, refmol, chirality, align)
if refmol_name is None:
if mol_rmsd is not None:
return f'{mol_name}\t{mol_idx}\t{mol_rmsd}'
return f'{mol_name}\t{mol_idx}\tNo matches'
if mol_rmsd is not None:
return f'{mol_name}\t{mol_idx}\t{refmol_name}\t{mol_rmsd}'
return f'{mol_name}\t{mol_idx}\t{refmol_name}\tNo matches'


def write_output_rows(rows, pool):
if pool is None:
output_rows = map(calc_output_row, rows)
else:
output_rows = pool.imap(calc_output_row, rows)
for row in output_rows:
print(row)


def iter_output_row_data(in_fname, mols, ref, chirality, regex, align):
for i, mol in enumerate(mols, 1):
if mol is None:
yield 'line', f'{in_fname}\t{i}\tCannot read structure'
else:
# assign printed mol name from mol object or file name
mol_name = mol.GetProp('_Name')
if not mol_name:
if regex is not None:
mol_name = re.search(regex, os.path.basename(in_fname)).group()
else:
mol_name = os.path.basename(in_fname)
# assign ref mol object
if isinstance(ref, list):
for refmol_name, refmol in ref:
yield 'rmsd', mol, mol_name, i, refmol, refmol_name, chirality, align
elif isinstance(ref, dict):
try:
refmol = ref[mol.GetProp('_Name')]
except KeyError:
sys.stderr.write(f'Molecule with name {mol.GetProp("_Name")} is not available '
f'in the reference SDF file\n')
yield 'line', f'{mol_name}\t{i}\tNo matches'
else:
yield 'rmsd', mol, mol_name, i, refmol, None, chirality, align
else:
yield 'rmsd', mol, mol_name, i, ref, None, chirality, align


def main_params(input_fnames, input_smi, output_fname, ref_name, refsmi, chirality, regex, align,
ignore_name_matching, ncpu):

if ref_name.lower().endswith('.mol2'):
ref = Chem.MolFromMol2File(ref_name, removeHs=True)
Expand All @@ -84,7 +139,10 @@ def main_params(input_fnames, input_smi, output_fname, ref_name, refsmi, chirali
elif ref_name.lower().endswith('.mol'):
ref = Chem.MolFromMolFile(ref_name, removeHs=True)
elif ref_name.lower().endswith('.sdf'):
ref = {m.GetProp('_Name'): m for m in Chem.SDMolSupplier(ref_name) if m}
if ignore_name_matching:
ref = [(m.GetProp('_Name'), m) for m in Chem.SDMolSupplier(ref_name) if m]
else:
ref = {m.GetProp('_Name'): m for m in Chem.SDMolSupplier(ref_name) if m}
else:
sys.stderr.write('Wrong format of the reference file. Only MOL2, PDBQT and SDF files are allowed.\n')
raise ValueError
Expand All @@ -104,57 +162,38 @@ def main_params(input_fnames, input_smi, output_fname, ref_name, refsmi, chirali
sys.stderr.write(
f'Line "{line}" in input smiles does not have two fields - SMILES and mol name. Skipped.\n')

for in_fname in input_fnames:
nprocess = max(1, min(ncpu, cpu_count()))
pool = Pool(nprocess) if nprocess > 1 else None

if in_fname.lower().endswith('.mol2'):
mols = [Chem.MolFromMol2File(in_fname)]
elif in_fname.lower().endswith('.pdbqt') or in_fname.endswith('.pdbqt_out'):
if regex is not None:
mols = read_pdbqt(in_fname, smis[re.search(regex, os.path.basename(in_fname)).group()], removeHs=True)
else:
mols = read_pdbqt(in_fname, smis[os.path.splitext(os.path.basename(in_fname))[0]], removeHs=True)
elif in_fname.lower().endswith('.sdf'):
mols = [mol for mol, mol_name in read_input(in_fname)]
else:
sys.stderr.write(f'Wrong format of the input file - {in_fname}. '
f'Only MOL2, PDBQT and SDF files are allowed.\n')
raise ValueError
try:
for in_fname in input_fnames:

for i, mol in enumerate(mols, 1):
if mol is None:
print(f'{in_fname}\t{i}\tCannot read structure')
else:
# assign printed mol name from mol object or file name
mol_name = mol.GetProp('_Name')
if not mol_name:
if regex is not None:
mol_name = re.search(regex, os.path.basename(in_fname)).group()
else:
mol_name = os.path.basename(in_fname)
# assign ref mol object
if isinstance(ref, dict):
try:
refmol = ref[mol.GetProp('_Name')]
except KeyError:
sys.stderr.write(f'Molecule with name {mol.GetProp("_Name")} is not available '
f'in the reference SDF file\n')
print(f'{mol_name}\t{i}\tNo matches')
refmol = None
if in_fname.lower().endswith('.mol2'):
mols = [Chem.MolFromMol2File(in_fname)]
elif in_fname.lower().endswith('.pdbqt') or in_fname.endswith('.pdbqt_out'):
if regex is not None:
mols = read_pdbqt(in_fname, smis[re.search(regex, os.path.basename(in_fname)).group()], removeHs=True)
else:
refmol = ref
mols = read_pdbqt(in_fname, smis[os.path.splitext(os.path.basename(in_fname))[0]], removeHs=True)
elif in_fname.lower().endswith('.sdf'):
mols = [mol for mol, mol_name in read_input(in_fname)]
else:
sys.stderr.write(f'Wrong format of the input file - {in_fname}. '
f'Only MOL2, PDBQT and SDF files are allowed.\n')
raise ValueError

if refmol is not None:
mol_rmsd = rmsd(mol, mol_name, refmol, chirality, align)
if mol_rmsd is not None:
print(f'{mol_name}\t{i}\t{mol_rmsd}')
else:
print(f'{mol_name}\t{i}\tNo matches')
write_output_rows(iter_output_row_data(in_fname, mols, ref, chirality, regex, align), pool)
finally:
if pool is not None:
pool.close()
pool.join()


def main():
parser = argparse.ArgumentParser(description='''Calc RMSD between a reference molecule and docked poses.
If reference molecule is not substructure of the docked molecule
maximum common substructure is used.''')
parser = argparse.ArgumentParser(description='''Calc RMSD between a reference molecule and an input molecule (docked poses).
If reference molecule is not substructure of the input molecule
maximum common substructure is used. SDF references can also be
compared all-to-all with input molecules.''')
parser.add_argument('-i', '--input', metavar='FILENAME', required=True, nargs='*',
help='input MOL2/PDBQT/SDF file(s) to compare with a reference molecule or molecules.')
parser.add_argument('--input_smi', metavar='FILENAME', required=False, default=None,
Expand Down Expand Up @@ -182,6 +221,11 @@ def main():
parser.add_argument('-x', '--nochirality', action='store_true', default=False,
help='choose this option if you want to omit matching chirality in substructure search. '
'By default chirality is considered.')
parser.add_argument('--ignore_name_matching', action='store_true', default=False,
help='for SDF reference files, compare each input molecule to each reference molecule '
'instead of matching molecules by name.')
parser.add_argument('-c', '--ncpu', metavar='INTEGER', required=False, default=1, type=int,
help='number of cpus to use for calculation. Default: 1.')

args = parser.parse_args()
if (args.refsmi is not None) and (args.refsmi.lower().endswith('.smi') or args.refsmi.lower().endswith('.smiles')):
Expand All @@ -190,7 +234,8 @@ def main():
else:
refsmi = args.refsmi

main_params(args.input, args.input_smi, args.output, args.reference, refsmi, not args.nochirality, args.regex, args.align)
main_params(args.input, args.input_smi, args.output, args.reference, refsmi, not args.nochirality, args.regex,
args.align, args.ignore_name_matching, args.ncpu)


if __name__ == '__main__':
Expand Down