> 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 calculated results change for each isomer. So we want to generate all isomers for each SMILES. As Gonzalo mentioned, one can generate cis/trans isomers or chiral isomers by editing SMILES. But the algorithm gets complicated if there are more than one double bond or chiral centers. There is actually a paper discussing about an algorithm https://arxiv.org/pdf/1303.1724.pdf. Thank you, Murat On Thu, Jan 18, 2018 at 7:30 AM, Noel O'Boyle <baoille...@gmail.com> wrote: > > 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 <kec...@gmail.com> 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? >> >> 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 >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> OpenBabel-discuss mailing list >>> OpenBabel-discuss@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> > ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
