Questions tagged [openbabel]

Questions about or related to Open Babel.

Filter by
Sorted by
Tagged with
5
votes
0answers
50 views

How can I add double bonds to Triazine-derivatives for OpenBabel generation of pdbqt files?

The double bonds are initially present at the sdf file but disappear or are misplaced after .pdbqt conversion. I tried all kinds of combinations using renumbering ...
14
votes
2answers
265 views

What's the best quantum chemistry output parser for the command line?

This question is about tools like Open Babel. Are there any good command-line parsers for quantum chemistry program outputs? A good Python library could come in as a close second. I am interested e.g. ...
10
votes
2answers
130 views

How to canonicalize SMILES written with aromatic bond symbols (:)?

I am using a package called PySmiles and it is returning a dialect of SMILES for aromatic groups that uses aromatic bond symbols e.g. NC:1:N:N:C:[N]1N. RDKit does ...