[Open Babel] Help with generation of atom names in mol2 format

Hello all, I'm a newby in obabel and I need a bit of help. I use obabel to convert a file from sdf to mol2 format because another program requires such conversion. The conversion is fine, and I get something like this (I only show the ATOM block): @ATOM   1 C   0.5825   -1.4943   

Re: [Open Babel] Canonical smiles for cis/trans species

> 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

Re: [Open Babel] Canonical smiles for cis/trans species

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

Re: [Open Babel] Canonical smiles for cis/trans species

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

Re: [Open Babel] Canonical smiles for cis/trans species

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: