Another thing, once you detect the chiral atom all you have to do is modify
the SMILES. For example in "CCC(B)(O)C" the third carbon is chiral, now if
you put it like "CC[C@](B)(O)C" and "CC[C@@](B)(O)C" you can separate the
compounds. It's just a matter of editing the SMILES
2018-01-18 9:47 GMT-03:00 Gonzalo Nuñez <nunezgonzal...@gmail.com>:
> For what I've read there isn't. But with pybel you can identify chiral
> molecules and chiral atoms. Afetar that probably all you have to do is come
> up with a way to alter the SMILES. Here's a page where someone describes
> how to identify chiral atoms with pybel:
> http://python.zirael.org/e-openbabel9.html
>
> 2018-01-18 2:21 GMT-03:00 murat keçeli <kec...@gmail.com>:
>
>> Thank you Fredrik. You are right, I wasn't careful. Is there any function
>> to generate stereoisomers for a given species in open babel?
>>
>> Murat
>>
>> On Wed, Jan 17, 2018 at 1:29 AM, Fredrik Wallner <fred...@wallner.nu>
>> wrote:
>>
>>> Hi,
>>>
>>> I would say that your problem is that the SMILES string that you input
>>> is not correct. The second ‘/‘ is at the wrong place. If you try with
>>> CC(=O)/C=C/O
>>> instead, it should work.
>>>
>>> I was a bit surprised that there was no error with the first version
>>> though.
>>>
>>> Kind regards,
>>> Fredrik
>>>
>>> On 16 jan. 2018 23:51 +0100, murat keçeli <kec...@gmail.com>, wrote:
>>>
>>> Hi,
>>>
>>> May I learn how I can keep stereo information in a canonical SMILES?
>>>
>>> >>> import pybel
>>> >>> mol = pybel.readstring('smi', 'CC(=O)/C=/CO')
>>>
>>> >>> print mol.write('can')
>>> CC(=O)C=CO
>>>
>>> >>> print mol.write('smi')
>>> CC(=O)C=CO
>>>
>>> >>> print mol.write('fix')
>>> CC(=O)C=CO
>>>
>>>
>>> Thank you
>>> Murat Keceli
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>>
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>
>
> --
> Gonzalo Núñez
>
--
Gonzalo Núñez
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