Hi
I'm using GetBestRMS to score conformers in an sdf relative to a pdb
extracted sdf ligand using the snippet below. I get odd behaviour when the
molecule includes a carboxylic acid. depending on whether the charge is
explicitly defined in the sdf or not I get a different RMS which seems to
be that the symmetry of the carboxyl is not considered by GetBestRMS is
that so? And if not can anyone suggest a workaround. (FWIW I have
examples which "work" when the charge is supplied and "fail" if not as well
as vice versa)
import sys
from rdkit import Chem
from rdkit.Chem import AllChem, rdMolAlign
# The ensemble sdf conformations with hydrogens
suppl = Chem.SDMolSupplier(sys.argv[2],sanitize=False)
count=0
#compare them to ref pdb extract no hydrogens
for molh in suppl:
count=count+1
mol1 = Chem.MolFromMolFile(sys.argv[1])
mol = Chem.RemoveHs(molh)
mol = AllChem.AssignBondOrdersFromTemplate(mol1, mol)
rms = AllChem.GetBestRMS(mol1, mol)
print(rms)
*Thanks*
Dr. Martin Watson
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