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Fix AMBER FEP mappings #366

Merged
merged 15 commits into from
Nov 25, 2024
Merged

Fix AMBER FEP mappings #366

merged 15 commits into from
Nov 25, 2024

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lohedges
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This PR adds the missing mapping pruning functions from the Exscientia, which are required for stable mappings when using AMBER as the FEP engine. This functionality is tested within the sandpit. I've also tidied a few bits of the mapping code and made sure that sub-functions take kwargs so that we don't get bugs if the order of inputs changes in future.

  • I confirm that I have merged the latest version of devel into this branch before issuing this pull request (e.g. by running git pull origin devel): [y]
  • I confirm that I have permission to release this code under the GPL3 license: [y]

@lohedges lohedges added the bug Something isn't working label Nov 13, 2024
@lohedges lohedges requested a review from mb2055 November 13, 2024 13:47
@lohedges lohedges mentioned this pull request Nov 14, 2024
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The PR also includes edits that are required for @annamherz's RBFE pipeline code.

mb2055
mb2055 approved these changes Nov 20, 2024
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Looks good 👍

@lohedges lohedges merged commit 357beaf into devel Nov 25, 2024
@lohedges lohedges deleted the fix_amber_fep_mappings branch November 25, 2024 15:53
lohedges added a commit that referenced this pull request Nov 25, 2024
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Backport fixes from PR #366. [ci skip]
cb9814b
@lohedges lohedges mentioned this pull request Nov 25, 2024
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lohedges added a commit that referenced this pull request Dec 3, 2024
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Merge pull request #371 from OpenBioSim/backport_366
36fef25 
Backport fixes from PR #366
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