Fix issue with wrong pkas assigned to terminal residues

[stefdoerr]

Solves https://github.com/Electrostatics/pdb2pqr/issues/245

I'm not 1000% sure this is the best way to solve it but I checked a few PDBs and it seems like the group_type matches the res_name when you want to get the pKa of the sidechain.

[codecov[bot]]

Codecov Report

Merging #258 (bde74be) into master (b5c3c3b) will decrease coverage by 0.03%. The diff coverage is n/a.

@@            Coverage Diff             @@
##           master     #258      +/-   ##
==========================================
- Coverage   64.11%   64.07%   -0.04%     
==========================================
  Files          30       30              
  Lines        7753     7753              
==========================================
- Hits         4971     4968       -3     
- Misses       2782     2785       +3     

Impacted Files	Coverage Δ
pdb2pqr/main.py	78.81% <ø> (ø)
pdb2pqr/biomolecule.py	70.29% <0.00%> (-0.43%)	:arrow_down:

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[stefdoerr]

for example for 5VBL PDB I get:

for row in pkas:
      print(f"{row['res_name']} {row['group_type']} {row['res_name'] == row['group_type']}")

LYS N+ False
LYS LYS True
ARG ARG True
ARG ARG True
ARG ARG True
GLU COO False
HIS HIS True
LYS LYS True
LYS LYS True
A00 COO False
CYS N+ False
CYS CYS True
GLU COO False
TYR TYR True
ASP COO False
LYS LYS True
TYR TYR True
ARG ARG True
ARG ARG True
GLU COO False
LYS LYS True
ARG ARG True
ARG ARG True
ASP COO False
ASP COO False
TYR TYR True
TYR TYR True
ARG ARG True
ASP COO False
TYR TYR True
ASP COO False
CYS CYS True
LYS LYS True
TYR TYR True
TYR TYR True
CYS CYS True
ASP COO False
ARG ARG True
TYR TYR True
ARG ARG True
ARG ARG True
ARG ARG True
ARG ARG True
ARG ARG True
ASP COO False
GLU COO False
LYS LYS True
CYS CYS True
TYR TYR True
ASP COO False
TYR TYR True
GLU COO False
GLU COO False
CYS CYS True
TYR TYR True
LYS LYS True
LYS LYS True
TYR TYR True
CYS CYS True
CYS CYS True
TYR TYR True
TYR TYR True
GLU COO False
ASP COO False
ASP COO False
ASP COO False
ASP COO False
LYS LYS True
ASP COO False
ASP COO False
ASP COO False
CYS CYS True
CYS CYS True
LYS LYS True
ASP COO False
GLU COO False
GLU COO False
GLU COO False
GLU COO False
ARG ARG True
ARG ARG True
ARG ARG True
CYS CYS True
LYS LYS True
TYR TYR True
HIS HIS True
LYS LYS True
TYR TYR True
HIS HIS True
CYS CYS True
ASP COO False
ASP COO False
TYR TYR True
CYS CYS True
CYS CYS True
TYR TYR True
CYS CYS True
TYR TYR True
ASP COO False
ARG ARG True
ARG ARG True
CYS CYS True
ARG ARG True
ARG COO False

[stefdoerr]

No sorry, this creates issues with protonating ASP residues because they get reported as COO group. Maybe a better solution is the following check:

if row["group_label"].startswith(row["res_name"])

LYS N+ False
LYS LYS True
ARG ARG True
ARG ARG True
ARG ARG True
GLU COO True
HIS HIS True
LYS LYS True
LYS LYS True
A00 COO False
CYS N+ False
CYS CYS True
GLU COO True
TYR TYR True
ASP COO True
LYS LYS True
TYR TYR True
ARG ARG True
ARG ARG True
GLU COO True
LYS LYS True
ARG ARG True
ARG ARG True
ASP COO True
ASP COO True
TYR TYR True
TYR TYR True
ARG ARG True
ASP COO True
TYR TYR True
ASP COO True
CYS CYS True
LYS LYS True
TYR TYR True
TYR TYR True
CYS CYS True
ASP COO True
ARG ARG True
TYR TYR True
ARG ARG True
ARG ARG True
ARG ARG True
ARG ARG True
ARG ARG True
ASP COO True
GLU COO True
LYS LYS True
CYS CYS True
TYR TYR True
ASP COO True
TYR TYR True
GLU COO True
GLU COO True
CYS CYS True
TYR TYR True
LYS LYS True
LYS LYS True
TYR TYR True
CYS CYS True
CYS CYS True
TYR TYR True
TYR TYR True
GLU COO True
ASP COO True
ASP COO True
ASP COO True
ASP COO True
LYS LYS True
ASP COO True
ASP COO True
ASP COO True
CYS CYS True
CYS CYS True
LYS LYS True
ASP COO True
GLU COO True
GLU COO True
GLU COO True
GLU COO True
ARG ARG True
ARG ARG True
ARG ARG True
CYS CYS True
LYS LYS True
TYR TYR True
HIS HIS True
LYS LYS True
TYR TYR True
HIS HIS True
CYS CYS True
ASP COO True
ASP COO True
TYR TYR True
CYS CYS True
CYS CYS True
TYR TYR True
CYS CYS True
TYR TYR True
ASP COO True
ARG ARG True
ARG ARG True
CYS CYS True
ARG ARG True
ARG COO False