Upgrade input/output methods

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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Upgrade input/output methods #57

Open sobolevnrm opened 4 years ago

sobolevnrm commented 4 years ago

[ ] Convert read/write file manipulation to context managers
[ ] Allow for StringIO and related file-like classes

orbeckst commented 4 years ago

Excellent idea.

Some of this already works. We use run.single() https://github.com/jensengroup/propka-3.1/blob/0cb470fbdbc9e57c4487e421b9110975d21799ce/propka/run.py#L28 with a StreamIO in propkatraj namely https://github.com/Becksteinlab/propkatraj/blob/2abd91fca33a5e980a2b8d8c6e18a2d192fda2c3/propkatraj/propkatraj.py#L73-L96

sobolevnrm commented 4 years ago

Excellent; thank you!

orbeckst commented 4 years ago

As @IAlibay found out and noted in #83: StringIO does not work any longer so my https://github.com/jensengroup/propka/issues/57#issuecomment-646302417 is not true anymore.

orbeckst commented 4 years ago

With #83 and #82 fixed, StreamIO (EDIT: for a single input PDB) should be working again (with a cleaner API, too, mainly thanks to @speleo3 's suggestions in PR #84 ).