Good morning,
I am trying to manually set/change the stereochemistry of a chiral center
of a molecule, and I cant understand how to set the
CHI_TETRAHEDRAL_CW/CHI_TETRAHEDRAL_CCW tag on a certain atom. So far my
script does the following:
-----
from rdkit import Chem
from rdkit.Chem import AllChem
molecule='C[C@@H](C(=O)COc1c(F)c(F)cc(F)c1F)n1cc([C@
@H](NCc2ccc3c(c2)OCO3)c2ncc[nH]2)nn1'
molecule_smiles=Chem.MolFromSmiles(molecule)
chiralty=Chem.FindMolChiralCenters(molecule_smiles)
centers=len(chiralty)
for i in range(centers):
current_center=chiralty[i][1]
print(current_center)
center_to_change=chiralty[i][0]
print(center_to_change)
for a in molecule_smiles.GetAtoms():
print(a.GetChiralTag())
----
executing the above mentioned script I can see that the molecule has 2
chiral centers, the first one on index 1, which is S, and the second one,
with index 19, which is R. Both chiral tags are set to: CHI_TETRAHEDRAL_CW.
now, I want to manually change the configuration of index 19 to S, so I
want to change its tag to CHI_TETRAHEDRAL_CCW.
Which would be the command to set this tag and how is the index indicated?
thanks in advance for the help,
kind regards
Alfredo
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