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choderalab / brokenyank

YANK: GPU-accelerated calculation of ligand binding affinities
GNU Lesser General Public License v3.0
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Deprecate pyopenmm #5

Open kyleabeauchamp opened 11 years ago

kyleabeauchamp commented 11 years ago

The stuff in pyopenmm is pretty questionable. We should move the needed features to a separate repo and provide some sort of testing / quality control / docs.

jchodera commented 11 years ago

To be clear: Is this is a request to deprecate pyopenmm.py the more Pythonic pure-Python wrapper for OpenMM?

I agree that it's woefully out of date. Unfortunately, there is no simple way to provide the most important functionality, that of the overloaded addition (+) operator, without a similarly large and difficult-to-maintain piece of code to merge two System objects.

The plan for the first release of YANK will be to eliminate pyopenmm.py entirely and simply rely on the user to provide AMBER prmtop files for the protein, the ligand, and the complex.

Future releases may be able to avoid the need for something like the System + operator by relying entirely on OpenMM's Modeller and Forcefield classes, once some method of supporting small molecule parameterization is built in.

kyleabeauchamp commented 11 years ago

I'm mainly referring to the repository pyopenmm--any "production" features need to be put in a production repository. I'm agnostic as to which things you need to keep etc.