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GilsonLabUCSD / pAPRika

Advanced toolkit for binding free energy calculations
BSD 3-Clause "New" or "Revised" License
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Refactor build-related modules into one common namespace? #156

Closed jeff231li closed 3 years ago

jeff231li commented 3 years ago

I'm thinking of grouping dummy.py, align.py, and tleap.py into a common namespace called like maybe build. So then we would call these functions like

from paprika.build.dummy import add_dummy
from paprika.build.tleap import System
from paprika.build.align import zalign

And perhaps change the class name in tleap.py to TLeapSystem. The reasoning is because I'm planning to implement a similar class for building CHARMM-based systems (PSFGen+Packmol/Solvate), and maybe call it PSFGenSystem to follow the same convention.

@slochower what do you think?

slochower commented 3 years ago

Yes, this is a great idea. I never liked that tleap got System, which sounds overly commanding.