Florian Kaiser

Currently all but the first alternative location are discarded, unless you specify `--altlocation`. Then all atoms will be processed. There is no way to select a specific alternative location at...

Hi, PLIP pre-processes and, if necessary, protonates the input. This could change the atom numbering. Did PLIP generate a `plipfixed` PDB file? And what was the exact command line call...

Thanks for the detailed report! Single protonated states are obviously not considered during detection at the moment. The decision has to be implemented in these lines of code: https://github.com/pharmai/plip/blob/99df154d831cea92900ff7daf0e3e38f689ec89a/plip/structure/preparation.py#L936

Rather then bundling a micro service directly into the existing Docker container, a new one should be derived from `pharmai/plip` that stacks an API on top. This is a very...

Dear @snbolz, thanks for reporting this. Inter-Ligand interactions are indeed not considered so far. This could be a feature for a future release.

Thanks for the issue, we should investigate this. Would it be possible for you to provide the specific example PDB file, PLIP commands and PyMol commands that you used? It...

Thanks for detailing! We will consider this, but we are very limited in capacity, so any pull requests from your end are welcome :smiley:

Hi fabioatuib, the atom numbering issue is a "feature" of processing the molecule with OpenBabel. Have you tried to run PLIP wirh `config.NOFIX = True`? I think a crucial line...

This is an interesting feature request and is certainly interesting. However, we will not integrate `mdtraj` as third party dependency. For now the easiest option would be to split your...

Hi @snbolz, thanks for reporting that issue! It is hard to recognize all polymer types for PLIP, but we will have a look. Migration to mmCIF would solve this issue.