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Fix AMBER FEP mappings #366

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Fix AMBER FEP mappings #366

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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.

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@mb2055 mb2055 Awaiting requested review from mb2055

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