Electrostatics / pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
http://www.poissonboltzmann.org/
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Missing heavy atoms error erroring #299

Closed stefdoerr closed 2 years ago

stefdoerr commented 2 years ago

Fixes this error when not enough heavy atoms exist

File ~/miniconda3/envs/htmd3.9/lib/python3.9/site-packages/pdb2pqr/main.py:465, in is_repairable(biomolecule, has_ligand)
    463 if miss_frac > REPAIR_LIMIT:
    464     error = f"This PDB file is missing too many ({num_missing} out of "
--> 465     error += f"{num_heavy:i}, {miss_frac:g}) "
    466     error += "heavy atoms to accurately repair the file."
    467     error += f"The current repair limit is set at {REPAIR_LIMIT:g}. "

ValueError: Unknown format code 'i' for object of type 'int'
codecov[bot] commented 2 years ago

Codecov Report

Merging #299 (a5ddcc3) into master (d30def3) will not change coverage. The diff coverage is 0.00%.

Impacted file tree graph

@@           Coverage Diff           @@
##           master     #299   +/-   ##
=======================================
  Coverage   65.29%   65.29%           
=======================================
  Files          30       30           
  Lines        7779     7779           
=======================================
  Hits         5079     5079           
  Misses       2700     2700           
Impacted Files Coverage Δ
pdb2pqr/main.py 79.38% <0.00%> (ø)

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