Thanks a lot Greg.
*Syeda Sabrina*
*Graduate Assistant*
*Department of Chemical Engineering, Penn State University*
*University Park, PA*
*
*
On Wed, Jul 17, 2013 at 12:55 PM, Greg Landrum <[email protected]>wrote:
> Hi Syeda,
>
> On Wed, Jul 17, 2013 at 12:45 PM, Syeda Sabrina <[email protected]>wrote:
>
>> Hi everyone,
>>
>> I must be missing it, but is there any way to check the CIP codes of
>> atoms by some function or fixing them? I am trying to compare two
>> molecules' stereochemistry and want to see what are the differences between
>> them. I have already compared the the atoms and bonds with GetChiralTag,
>> GetBondDir and GetStereo (on bonds). Is there any way to check the R/S of
>> atoms just like I checked E/Z on bonds by GetStereo?
>>
>>
> They are stored in an atom property called "_CIPCode":
> In [2]: m = Chem.MolFromSmiles('F[C@H](Cl)CCC[C@H](F)Br')
>
> In [3]: m.GetAtomWithIdx(1).GetProp('_CIPCode')
> Out[3]: 'R'
>
> In [4]: m.GetAtomWithIdx(6).GetProp('_CIPCode')
> Out[4]: 'R'
>
> In [5]: m.GetAtomWithIdx(4).GetProp('_CIPCode')
> ---------------------------------------------------------------------------
> KeyError Traceback (most recent call last)
> <ipython-input-5-a3860799f0c0> in <module>()
> ----> 1 m.GetAtomWithIdx(4).GetProp('_CIPCode')
>
> KeyError: '_CIPCode'
>
>
> -greg
>
>
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