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jensengroup / propka

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
http://propka.org
GNU Lesser General Public License v2.1
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Convert parameter files to YAML or JSON? #94

Closed sobolevnrm closed 3 years ago

sobolevnrm commented 4 years ago

@speleo3 and @orbeckst -- what do you think about converting some of the parameter/configuration files to JSON, YAML, or some other human-readable but parseable format?

Thanks,

Nathan

speleo3 commented 4 years ago

You mean propka.cfg? The format looks pretty clean so for me it would not be urgent to change it, but in general it's a good idea to move away from custom parsers. So if someone has the bandwidth to spend time on coming up with a JSON or YAML replacement I wouldn't mind.

orbeckst commented 4 years ago

I agree with @speleo3 – good idea, not terribly urgent.

Are there any parameters that are still hard-coded and not inside files?

sobolevnrm commented 4 years ago

I agree. This isn't a high-priority item; however, we're making some similar changes in PDB2PQR and APBS so I thought I'd see if we could apply them here as well.