AMBER FEP parser #42
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@shuail @brycestx is this issue something that you're actively working on or are committed to doing? (Which would be great!) If not then it's ok to un-assign yourselves to make clear that really anyone can grab the issue and work on it. |
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First pass located at #51 |
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orbeckst
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Jan 17, 2018
- fixes #42 - Added functions to extract u_nk mbar energies from Amber files if they exist. - added test to determine if file was parsed correctly. ix test_amber.py to conform to new load_bace_example added to alchemtest. - small formatting adjustments. - Adding another test "load_bace_improper" to increase coverage - Adding support for exception thrown by improper clambda value for test case. - removed untested portion of amber parser from coverage The "file_validation(outfile)" step in extract_dHdl() is not covered by our tests. I am flagging the "not tested" status explicitly in the code with `#pragma: no cover`.
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In line with the overall API proposal, we want to have parsers for each of the major MD engines, and eventually have coverage for all of those in use. For Amber we already have a TI parser (#10), we still need an "MBAR/FEP" parser:
u_nkfrom output files (for FEP).This issue is the nexus for discussion for such parsers for the AMBER package. If you have existing parsing code for this package, comment below and we can begin adapting it into the parsers outlined above in a PR.
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