Dear JP,
On Mon, Apr 4, 2011 at 6:53 PM, JP <[email protected]> wrote:
> 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
The difference is that the conformation-generation code isn't using
the best RMSD, as your code does, instead it's just using the standard
RMSD. You can see this by printing an additional value in your code:
#-------------------------------------
# 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.AlignMol(mol_h, mol_h, 0, i)
bestrms = AllChem.GetBestRMS(mol_h, mol_h, 0, i)
print(rms,bestrms)
#-------------------------------------
The output from this is:
$ python script.py
(0.0, 0.0)
(1.3379167659438125, 0.60362436042913903)
(1.1782030519271443, 0.59622250108412145)
(1.2243862716355582, 0.30392328812710512)
(1.1984592787588044, 0.55143501013497576)
(1.0641915526094825, 0.68902440786535935)
Best,
-greg
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