Dear Csongor,
as far as I know it is not well documented how you can access the python
objects and its methods or data structures created by the PyMOL API. For
many tasks one usually finds some information, often PyMOL or python
scripts. Concerning your example of the hydrogen bonds determined by the
distance command, the following python script may provide hints:
https://pymolwiki.org/index.php/Get_raw_distances
and:
https://pymol-users.narkive.com/zHPUseVG/pymol-is-there-a-way-to-count-hydrogen-bond-interactions
When working with the PyMOL distance command to determine hydrogen bonds
please note that the algorithm is very generous concerning non-linearity
of the D-H...A angles if you use the default parameters. In addition, it
will miss some perfect hydrogen bonds.
See
https://research.uni-leipzig.de/straeter/pymol/pymol_hbond.html
and
https://github.com/schrodinger/pymol-open-source/pull/374
Best wishes,
Norbert
Am 22.01.2025 um 15:21 schrieb Csongor MATYAS via PyMOL-users:
Hey everyone,
I am trying to use pymol from python to have some repetitive tasks
done. I've managed to get some basic functions running but I'm running
into walls frequently. I couldn't find a tutorial or documentation
about this. Am I missing something? I know it's under development but
I would assume that some basic instructions would be available
somewhere, otherwise the conda package isn't very useful.
I've managed to sort out the cmd.select() function for example but I
can't use the data, there is no object or output. All I can do is to
cmd.save() selection into a .pdb file. I've managed to select ligand,
and then residues around it, I've also been able to use
show_contacts() (from link below) between two selections, but I can't
access the pairs that suggest hydrogen bonding, it is only a visual
thing. Even from pymol, the software, if I do it manually, I don't
know how to save those (unless I save it as a pymol session file that
is not human readable).
https://wiki.pymol.org/index.php/Show_contacts
Please, if anyone has advice, anything is appreciated 😄
Csongor
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