Dear colleagues, Is there a way to make SDMolSupplier faithful to the input chirality? I mean, I would like to keep whatever info that is stored in the atom and bond blocks, avoiding deducing anything from the geometry.
When I read in the attached sdf, it assigns a chirality to the charged
nitrogen, while at the same time clears the stereo information of the C=N
double bond. The following are the possibilities I got when I did a
MolToSmiles on the molecules.
C[N@@H+]([13CH3])c1ccc(N=C2C(=O)Nc3ccccc32)cc1
C[N@H+]([13CH3])c1ccc(N=C2C(=O)Nc3ccccc32)cc1
I apologize if this has been raised in this forum before. I did try to
search for "SDMolSupplier chirality" but I got almost 1500 returns so I
cannot go through them.
Ling
================================================
from rdkit import Chem
for m in Chem.SDMolSupplier("ao4291.sdf"):
print (Chem.MolToSmiles(m))
ao4291.sdf
Description: application/vnd.openmolecules.sdf
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