Good evening, I am trying to superimpose a pair of conformers of the same molecule (files attached) using GetBestRMS. It does not seem to work if I keep the hydrogens.
m0 = Chem.MolFromMolFile('tgt.mol',removeHs=False)
m1 = Chem.MolFromMolFile('qry.mol',removeHs=False)
print AllChem.GetBestRMS(m0,m1)
f = open('WithH.mol','w')
f.write(Chem.MolToMolBlock(m1))
f.close()
However, if I don't use the "removeHs=False" option, it works fine.
Any idea?
Ling
qry.mol
Description: Binary data
tgt.mol
Description: Binary data
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