One more thing I would like to add here. I have also tried this one to
check the CIP code of the atoms of the molecule and again getting
Precondition violation. Am I missing anything very obvious?
for p in product:
...: for m in p:
...: print Chem.MolToSmiles(m, True)
...: Chem.AssignStereochemistry(m)
...: for a in m.GetAtoms():
...: if a.HasProp('_CIPCode'):
...: print a.GetProp('_CIPCode')
...:
CC[C@@H]1OS(=O)O[C@H]1C
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
<ipython-input-44-0a5b7fc9fb8b> in <module>()
2 for m in p:
3 print Chem.MolToSmiles(m, True)
----> 4 Chem.AssignStereochemistry(m)
5 for a in m.GetAtoms():
6 if a.HasProp('_CIPCode'):
RuntimeError: Pre-condition Violation
Thanks a lot for your help.
Bests
Sabrina
*Syeda Sabrina*
*Graduate Assistant*
*Department of Chemical Engineering, Penn State University*
*University Park, PA*
*
*
On Fri, Jul 19, 2013 at 11:52 AM, Syeda Sabrina <[email protected]> wrote:
> 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?
>>>>
>>>>
>>>>
>
------------------------------------------------------------------------------
See everything from the browser to the database with AppDynamics
Get end-to-end visibility with application monitoring from AppDynamics
Isolate bottlenecks and diagnose root cause in seconds.
Start your free trial of AppDynamics Pro today!
http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
