Salt Bridge recognised although it should not

[i2nico]

Hello,

Describe the bug currently I was analysing a protein-small ligand complex and recognised that a salt bridge was detected even thought it should not.

In particular, the compound (carboxylate group) is forming a salt bridge with residue H440 (see attached PDB file), however, this residue is single protonated and thus should not form a salt bridge.

To Reproduce I used both the webserver and the command-line tool. Regarding the command-line tool I used the following command:

sudo docker run --rm -v ${PWD}:/results -w /results -u $(id -u ${USER}):$(id -g ${USER}) pharmai/plip:latest -f <inputfiles.pdb> -tvy --nohydro --maxthreads 20

Expected behavior In this example, I would expect a hydrogen bond. However, as described by PLIP either a hydrogen bond or a salt bridge is reported. Therefore, I am suggesting that once the problem is fixed, a hydrogen bond would be detected.

Desktop (please complete the following information):

• OS: Ubuntu 18 (command-line was executed on this machine)

Thanks in advance!

I used the subsequent PDB-file: 6kb3_GitHub.txt

[fkaiserbio]

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