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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