Fix AMBER FEP mappings #366
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The PR also includes edits that are required for @annamherz's RBFE pipeline code. |
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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.
develinto this branch before issuing this pull request (e.g. by runninggit pull origin devel): [y]