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AMBER FEP parser #42

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orbeckst opened this issue Nov 28, 2017 · 2 comments
Closed
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AMBER FEP parser #42

orbeckst opened this issue Nov 28, 2017 · 2 comments
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@shuail @brycestx
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parsers
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release 0.2.0

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@orbeckst
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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:

  • Extracting reduced potentials u_nk from 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.
@orbeckst
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orbeckst commented Jan 8, 2018

@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

@brycestx brycestx mentioned this issue Jan 11, 2018
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@orbeckst orbeckst added this to the release 0.2.0 milestone Jan 16, 2018
orbeckst pushed a commit that referenced this issue Jan 17, 2018
@orbeckst
add u_nk MBAR parser for Amber
9117cc6 
- 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`.
orbeckst added a commit that referenced this issue Jan 17, 2018
@orbeckst
Merge pull request #51 from alchemistry/amber-mbar-parse
ab1b657 
add Amber u_nk MBAR parser (#42)
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