Can anyone explain why the conformer RMS values which are printed out
are all smaller than 1.0?
I am pruning using the pruneRmsThresh (=1.0) variable in
EmbedMultipleConfs method so I was expecting this would not happen.
I am expecting to see values > 1.0 since they should be at least this
distance from the first conformer so not to be pruned
# usual imports
from rdkit import Chem
from rdkit.Chem import AllChem
# generate a mol
mol = Chem.MolFromSmiles('O=CCC=O')
# add hydrogens
mol_h = AllChem.AddHs(mol)
# notice the prune threshold - set to 1.0 RMS...
conformation_ids = AllChem.EmbedMultipleConfs(mol_h, numConfs=50,
pruneRmsThresh=1.0)
for i in range(mol_h.GetNumConformers()):
# match the first (original) conformer to the rest
rms = AllChem.GetBestRMS(mol_h, mol_h, 0, i)
# why are these all smaller than the 1.0 I set earlier??!!
print(rms)
Where am I wrong?
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