If they are protonated by Chimera that means you should have the bonds and
bond orders for everything. In which case, you shouldn't need to do any of
this, just get Chimera to export the structure including this information.
- Noel
On Tue, 14 Jul 2020 at 14:58, Lukas Pravda wrote:
> Hi Noel,
>
Hi Noel,
Thanks for a prompt reply. The structures I use are actually protonated using
ChimeraX so all the hydrogens are explicit. If I understand you correctly the
3.0 version should work better in my case, however I’m getting this warning and
quite possibly because of that there is a data
Before 3.0, aromaticity perception was performed as if the position of the
hydrogens were unknown, and the hydrogens were inferred afterwards. This
makes sense for structures from the PDB, but not for anything else (e.g.
SMILES) where there were occasional errors and it was much slower than
necessa
Dear all,
I’m maintaining a package to perceive molecular interactions that depends on
openbabel functionality using python. Historically it used openbabel 2.4.1, but
recently I’ve learned that there is a version 3.x so I wanted to give it a go
(newer should be better right? 😊). I made few
