Hi Greg,
Thanks. What I meant by tetrahedral chirality is say I have a molecule, I
print out the smiles and can see the @/@@ in the smiles and no cis/trans,
now after that when I set the type of bond in the same molecule and after
that again print out the smiles I can see the @/@@ signs are changed. As
suggested by you rather than depending on the GetChiralTags() I was trying
to use the following for checking chiral centers but getting Pre-condition
violation error.
rxn =
AllChem.ReactionFromSmarts('[C:2]\[CH1:3]=[CH1:4]\[C:5].[O:8]=[S:9]=[O:7].[C:13][O:12][P:11](=[O:10])([O:16][C:17])[O:14][C:15]>>[C:2][C@
@H:3]1[O:7][S:9](=[O:10])[O:8][C@H
:4]1[C:5].[C:13][O:12][P:11]([O:16][C:17])[O:14][C:15]')
reactants = [Chem.MolFromSmiles('CC\C=C\C'), Chem.MolFromSmiles('O=S=O'),
Chem.MolFromSmiles('COP(=O)(OC)OC')]
product = rxn.RunReactants(tuple(reactants))
for p in product:
...: for m in p:
...: print Chem.MolToSmiles(m,True),
Chem.FindMolChiralCenters(m)
The error message I get says:
RuntimeError Traceback (most recent call last)
<ipython-input-38-d8d31541346d> in <module>()
1 for p in product:
2 for m in p:
----> 3 print Chem.MolToSmiles(m,True), Chem.FindMolChiralCenters(m)
4
/usr/lib/python2.7/site-packages/rdkit/Chem/__init__.py in
FindMolChiralCenters(mol, force, includeUnassigned)
89
90 """
---> 91 AssignStereochemistry(mol,force=force,
flagPossibleStereoCenters=includeUnassigned)
92 centers = []
93 for atom in mol.GetAtoms():
RuntimeError: Pre-condition Violation
Any thoughts?
*Syeda Sabrina*
*Graduate Assistant*
*Department of Chemical Engineering, Penn State University*
*University Park, PA*
*
*
On Fri, Jul 19, 2013 at 4:09 AM, Greg Landrum <[email protected]>wrote:
> That depends on what you mean by tetrahedral chirality?
>
> If you're talking about the result returned by the atom.GetChiralTag()
> method, then no. Making changes to bond directions or types should not
> affect it. The one caveat here is that if you change a bond in such a way
> that you remove the chirality of the center and then re-perceive chirality,
> the chiral tag on the atom will be removed.
>
> If you mean the R or S label of an atom, then this kind of change can
> absolutely make a difference. Here's an example:
> In [3]: AllChem.FindMolChiralCenters(Chem.MolFromSmiles('C[C@H
> ](/C=C/Cl)/C=C\\Cl'))
> Out[3]: [(1, 'R')]
>
> In [4]: AllChem.FindMolChiralCenters(Chem.MolFromSmiles('C[C@H
> ](/C=C/Cl)/C=C/Cl'))
> Out[4]: []
>
> In [5]: AllChem.FindMolChiralCenters(Chem.MolFromSmiles('C[C@H
> ](/C=C\\Cl)/C=C/Cl'))
> Out[5]: [(1, 'S')]
>
> Note that you would have to re-perceive chirality after making the change
> to see the effect.
>
> -greg
>
>
>
> On Thu, Jul 18, 2013 at 10:19 PM, Syeda Sabrina <[email protected]>wrote:
>
>> Also, can SetBondType() can affect the tetrahedral chirality of atom?
>>
>> *Syeda Sabrina*
>> *Graduate Assistant*
>> *Department of Chemical Engineering, Penn State University*
>> *University Park, PA*
>> *
>> *
>>
>>
>> On Thu, Jul 18, 2013 at 10:11 PM, Syeda Sabrina <[email protected]>wrote:
>>
>>> Hi everyone,
>>>
>>> Is there any reason that setting bond directions of a molecule using
>>> SetBondDir() for each bond in the molecule can affect tetrahedral
>>> chirality of its atom?
>>>
>>>
>>>
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