[Chimera-users] Loop through hundreds of files and find HBonds

[Elaine Meng]

Dear Samuel,
First figure out interactively (by typing in the commands) what set of commands you need for each one.  Take a look at "addh" for adding hydrogens and "findhbond" for finding H-bonds.  Of course, you may also need other commands, like "open" "close" "select" etc.  See the commands index and click the links to see the detailed information for each command.
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>

Then here is some basic information on how to use python to loop through several input files, and how to save the log. 
<https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

The "findhbond" command also has an option to save information to a file if you wanted a separate output file for each docked ligand file.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 13, 2022, at 5:41 AM, Samuel Kyobe via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear Chimera (and ChimeraX) team
> 
> I have run a large docking experiment using several ligands to determine the best binders for further analysis in Molecular Dynamics studies and possible wetlab evaluation.
> 
> I need to find some python example or code snippet capable of looping over hundreds of files and find several .pdb poses from a docking run and find Hydrogen bonds in each one using one receptor. 
> 
> In the process of finding the H bonds, I would like to add Hydrogens, and the protonation state is unspecified. Then at FindHBond, I want to find intermodal Hbonds and write the results to a file.
> 
> Thanks
> 
> Samuel