Hi all,
I have came across quite puzzling (at least for me) RDKit's behavior while
using SMILES with specified tetrahedral stereocenters.
Converting following SMILES 'F[C@H]1CCNSC1' seem to result in assignment of
the incorrect chiral tag to the tetrahedral stereocenter.
m = Chem.MolFromSmiles('F[C@H]1CCNSC1')
for a in m.GetAtoms():
print a.GetIdx(), a.GetSymbol(), a.GetChiralTag()
0 F CHI_UNSPECIFIED
1 C CHI_TETRAHEDRAL_CW
2 C CHI_UNSPECIFIED
3 C CHI_UNSPECIFIED
4 N CHI_UNSPECIFIED
5 S CHI_UNSPECIFIED
6 C CHI_UNSPECIFIED
Although the molecule still gives back the correct SMILES.
print Chem.MolToSmiles(m, isomericSmiles=True)
F[C@H]1CCNSC1
Problem seems to vanish if I use non-canonical version the original
input SMILES, e.g.:
m = Chem.MolFromSmiles('N1CC[C@H](F)CS1')
for a in m.GetAtoms():
print a.GetIdx(), a.GetSymbol(), a.GetChiralTag()
0 N CHI_UNSPECIFIED
1 C CHI_UNSPECIFIED
2 C CHI_UNSPECIFIED
3 C CHI_TETRAHEDRAL_CCW
4 F CHI_UNSPECIFIED
5 C CHI_UNSPECIFIED
6 S CHI_UNSPECIFIED
print Chem.MolToSmiles(m, isomericSmiles=True)
F[C@H]1CCNSC1
Am I missing something obvious? If yes, I will be grateful for any pointers.
I am using the latest stable release (2013_03_02) of RDKit.
Regards,
--
MikoĊaj Kowalik
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