Thanks! This is silly how could I miss that!
Anyways, Thanks again.
Bests
Sabrina
*Syeda Sabrina*
*Graduate Assistant*
*25, Fenske Laboratory*
*Department of Chemical Engineering, Penn State University*
*University Park, PA*
*
*
On Wed, May 8, 2013 at 2:45 AM, Greg Landrum <[email protected]> wrote:
> Hi,
>
> That carbon is only three-coordinate, so the rdkit is removing the chiral
> flag.
>
> If you add the missing H you will get the desired chirality:
> [2]>>> Chem.CanonSmiles('O=C1C[C@H](O)[C@@]1S')
> [2]: 'O=C1C[C@H](O)[C]1S'
>
> [3]>>> Chem.CanonSmiles('O=C1C[C@H](O)[C@@H]1S')
> [3]: 'O=C1C[C@H](O)[C@@H]1S'
>
> -greg
>
> On Tuesday, May 7, 2013, Syeda Sabrina wrote:
>
>> 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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