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Electrostatics / pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
http://www.poissonboltzmann.org/
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Cyclic peptide support #307

Closed stefdoerr closed 2 years ago

stefdoerr commented 2 years ago

pdb2pqr was adding terminals to cyclic peptides. I fixed it by checking if the distance between the two terminal N/C are smaller than the amide distance. If that's the case it skips the adding of termini. I added a test for 5VAV PDB https://www.rcsb.org/structure/5vav which is a nice small cyclic peptide, also with a disulfide CYX/CYX bond. Closes https://github.com/Electrostatics/pdb2pqr/issues/306

I also added a fix for supporting modified backbone residues like: https://www.rcsb.org/ligand/33X Before the code was checking just if the residue was a proline but the same rule should apply to any N atom which has more than two heavy atom bonds (counted as 1 here since we don't count the peptide bond to the next residue).

Finally there is also a tiny improvement for my last PR where I was not checking NEUTRAL-N/C{RES} names for keeping the protonation state.

stefdoerr commented 2 years ago

I do have a question though about optimization. If you look at the resulting pqr file it seems like pdb2pqr modifies the backbone dihedrals a lot (and the side chains). I'm a bit preoccupied if your optimization algorithm has issues with cyclic peptide backbones.

codecov[bot] commented 2 years ago

Codecov Report

Merging #307 (4fa2c1f) into master (82f02e5) will increase coverage by 0.01%. The diff coverage is 81.81%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #307      +/-   ##
==========================================
+ Coverage   65.38%   65.40%   +0.01%     
==========================================
  Files          30       30              
  Lines        7783     7792       +9     
==========================================
+ Hits         5089     5096       +7     
- Misses       2694     2696       +2
Impacted Files Coverage Δ
pdb2pqr/biomolecule.py 75.86% <81.81%> (+0.02%) :arrow_up:

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