psize seems broken - Githubissues

Electrostatics / pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.

http://www.poissonboltzmann.org/

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psize seems broken #181

Closed rokdev closed 2 years ago

rokdev commented 3 years ago

When running psize on any .pqr file I get No ATOM entries in file!. This is the latest pdb2qpr from git:

$ pdb2pqr30 --version
pdb2pqr30 3.4.0

$ pdb2pqr30 --ff=PARSE 1LYZ 1LYZ.pqr
INFO:PDB2PQR v3.1.0+11.g5662cf6: biomolecular structure conversion software.
...

$ psize -h
...
PDB2PQR v3.1.0+11.g5662cf6: biomolecular structure conversion software. psize:
figuring out the size of electrostatics calculations since (at least) 2002.

$ psize 1LYZ.pqr
No ATOM entries in file!

sobolevnrm commented 3 years ago

We're moving psize to APBS eventually but I will try to fix this in the interim.

rokdev commented 3 years ago

Hi Nathan,

I think this can wait until psize is in APBS.

Thanks!

sobolevnrm commented 2 years ago

I'm going to remove the command-line version of this code from PDB2PQR in lieu of the version in APBS.