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Published 20 hours ago • verified publisher icon Electrostatics

Need refactoring and testing for inputgen and psize

Open sobolevnrm opened this issue 4 years ago • 6 comments

I think inputgen.py and psize.py are still important for the web server version of PDB2PQR. However, we appear to have no test coverage of these modules.

sobolevnrm avatar Apr 29 '20 03:04 sobolevnrm

Apparently, we built lots of PQR parsing routines for PDB2PQR and still parse PQR files manually in psize.py... why???

sobolevnrm avatar May 02 '20 01:05 sobolevnrm

The psize command-line tool has been removed. Should we do the same for inputgen? I don't think there are many use cases for it.

sobolevnrm avatar Jan 01 '22 00:01 sobolevnrm

@Eo300 isn't inputgen used by the apbs-web to generate the apbs input file after running pdb2pqr?

intendo avatar Jan 03 '22 19:01 intendo

I was referring to removing the command-line part -- not the entire module.

sobolevnrm avatar Jan 03 '22 20:01 sobolevnrm

We're not using the inputgen command-line for website operations, it ought to only be used as part of the pdb2pqr process itself

Eo300 avatar Jan 03 '22 20:01 Eo300

OK, so we can delete the inputgen command line code.

intendo avatar Jan 03 '22 22:01 intendo