Hi Greg,
At some point of my script I figured out that in the output SMILES of a
molecule, one desired chirality is missing.
So,
Desired SMILES: O=C1C[C@H](O)[C@@]1S
but I was getting,
Actual SMILES: O=C1C[C@H](O)[C]1S
So I did the following check on that molecule, I tried to check each atom's
chiral tag in the molecule. Although the chirality information was in the
atoms, but it did not appear in the smiles. And thus later on, when I
converted it back into moelcule chiral information one of the atom was
lost. I thought it might be a bug since it's not a usual case in other
molecules.
code:
try:
Chem.SanitizeMol(rdmol)
for atomIdx, atom in enumerate(rdmol.GetAtoms()):
print atomIdx, atom.GetAtomicNum(), atom.GetChiralTag(),
'before'
print Chem.MolToSmiles(rdmol, isomericSmiles = True)
m = Chem.MolFromSmiles(Chem.MolToSmiles(rdmol, isomericSmiles =
True))
for atomIdx, atom in enumerate(m.GetAtoms()):
print atomIdx, atom.GetAtomicNum(), atom.GetChiralTag(), 'after'
except:
Output:
0 8 CHI_UNSPECIFIED before
1 6 CHI_TETRAHEDRAL_CW before
2 6 CHI_UNSPECIFIED before
3 6 CHI_UNSPECIFIED before
4 8 CHI_UNSPECIFIED before
5 6 CHI_TETRAHEDRAL_CCW before
6 16 CHI_UNSPECIFIED before
[1OH][2C@H]1[3CH2][4C](=[5O])[6C]1[7SH]
0 8 CHI_UNSPECIFIED after
1 6 CHI_TETRAHEDRAL_CW after
2 6 CHI_UNSPECIFIED after
3 6 CHI_UNSPECIFIED after
4 8 CHI_UNSPECIFIED after
5 6 CHI_UNSPECIFIED after
6 16 CHI_UNSPECIFIED after
*Thanks,*
*Syeda Sabrina*
*Graduate Assistant*
*Penn State University*
*University Park, PA*
*
*
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