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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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Attempt to standardize data and parameter file formats #5

Open sobolevnrm opened 4 years ago

sobolevnrm commented 4 years ago

Too many data/parameter files in APBS/PDB2PQR use their own bespoke format, generating code bloat for parsing. It would be good to standardize on a readable (e.g., not XML) format that has simple support through Python. Possibilities include JSON (https://docs.python.org/3/library/json.html) or Python config format (https://docs.python.org/3/library/configparser.html). Comments are a bit more straightforward in the latter.

intendo commented 4 years ago

The ConfigParser allows comments which is great. The JSON config files do not allow comments or you have to parse them out before you read them.

sobolevnrm commented 4 years ago

YAML also allows comments and seems to be something we're looking at for other parts of the software.

@intendo What do you think about using YAML for this?

intendo commented 4 years ago

@sobolevnrm I like YAML. This seems pretty simple: https://martin-thoma.com/configuration-files-in-python/#yaml