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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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PDB2PQR should not crash when reading malformed PDB headers #210

Closed sobolevnrm closed 3 years ago

sobolevnrm commented 3 years ago

The code should be more tolerant of the odd REMARK and similar headers that some files generate.

sobolevnrm commented 3 years ago

For example:

REMARK    GENERATED BY TRJCONV
REMARK    THIS IS A SIMULATION BOX
Eo300 commented 3 years ago

From what I found, this appears to be already be addressed in the master branch in pdb.py: https://github.com/Electrostatics/pdb2pqr/blob/1264a73e7a62f747af4b8cd09fa0dba02ddb1473/pdb2pqr/pdb.py#L2581-L2590

Where it's eventually detected in io.py: https://github.com/Electrostatics/pdb2pqr/blob/1264a73e7a62f747af4b8cd09fa0dba02ddb1473/pdb2pqr/io.py#L462-L467

However, the former snippet was added after v3.1.0 was released, hence the latest release crashing on malformed REMARKS

sobolevnrm commented 3 years ago

Fixed in 8c810ca64e6a6fb4c39c2394f3da28d317fc6350