Hi all,
Is there any way to assign all bond directions (E/Z stereochemistry) to the
output SMILES string?
For example, here's a structure:
>>> mol = Chem.MolFromSmiles(r"F/C(Cl)=C(O)/N")
>>> Chem.MolToSmiles(mol)
'N/C(O)=C(/F)Cl'
It's a minimal definition, in that I could have specified the directions for
all of the bonds:
>>> mol = Chem.MolFromSmiles(r"F/C(/Cl)=C(\O)/N")
>>> Chem.MolToSmiles(mol)
'N/C(O)=C(/F)Cl'
Note that RDKit figured out which bond directions were minimal.
The underlying code checks for conflicting assignments:
>>> mol = Chem.MolFromSmiles(r"F/C(/Cl)=C(/O)/N")
[18:25:25] Conflicting single bond directions around double bond at index 2.
[18:25:25] BondStereo set to STEREONONE and single bond directions set to
NONE.
>>> Chem.MolToSmiles(mol)
'NC(O)=C(F)Cl'
What I want is some way to go from
N/C(O)=C(/F)Cl
to a fully specified
F/C(/Cl)=C(\O)/N
Andrew
da...@dalkescientific.com
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