[Open Babel] How to set occupancy for a protein created from scratch

2018-07-26 Thread Lukas Pravda
Hi all, I’m creating protein structure from scratch (python using conda openbabel) I cant figure out what is the correct procedure how to set atom occupancy correctly. From The C++ PDB parser I extracted code the following: from openbabel import OBPairFloatingPoint def _set_ob_occupancy(

[Open Babel] Failed to kekulize aromatic bonds | structure building

2020-07-14 Thread Lukas Pravda
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

Re: [Open Babel] Failed to kekulize aromatic bonds | structure building

2020-07-14 Thread Lukas Pravda
data discrepancy downstream, so I wonder what can I do to find out what is wrong in my case. Best, Lukas From: Noel O'Boyle Date: Tuesday, 14 July 2020 at 15:13 To: Lukas Pravda Cc: "openbabel-discuss@lists.sourceforge.net" Subject: Re: [Open Babel] Failed to kekulize