If you would like to enumerate stereoisomers (for any reason) I would do it on
the SMILES string level byt pure text handling. I put together a short python
function to do this to get you started. It’s not tested or guaranteed to work
in all cases, but can be found at
https://gist.github.com/fr
Or for example I use pybel and autodock vina through python, so when
docking trying all conformers is something important
2018-01-18 20:59 GMT-03:00 Dimitri Maziuk :
> On 01/18/2018 07:30 AM, Noel O'Boyle wrote:
> > This question has come up before. Can I ask why you would find this
> useful?
>
>
On 01/18/2018 07:30 AM, Noel O'Boyle wrote:
> This question has come up before. Can I ask why you would find this useful?
E.g. in a mixture of isomers NMR can show multiple peaks for "same"
atom. Knowing how many peaks you might get beforehand could be useful.
ICBW, IANA NMR spectroscopist (I jus
> This question has come up before. Can I ask why you would find this useful?
> As in, what are trying to do?
Given a list of SMILES, we compute thermochemical parameters,
enthalpy, entropy etc. This list is generated by a code that cannot
distinguish cis/trans or chiral isomers but the calculate
This question has come up before. Can I ask why you would find this useful?
As in, what are trying to do?
On 18 January 2018 at 05:21, murat keçeli wrote:
> Thank you Fredrik. You are right, I wasn't careful. Is there any function
> to generate stereoisomers for a given species in open babel?
>
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-0
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.
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 wrote:
> Hi,
>
> I would say that your problem is that the SMILES string that you input is
> not correct.
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.
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
---
10 matches
Mail list logo
