Fix issue #134 #135
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Fix issue #134 #135
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This PR closes #134. To work around rounding issues with triclinic box vectors following conversion from dimensions and angles we now perform a pre lattice reduction using the internal OpenMM functionality. This isn't needed when using the native OpenMM AMBER format parsers, so can be removed once the fix related to this previous issue has made its way into a conda-forge release of OpenMM.
Note that a single test may fail for macOS py311. This is due to a precision issue, which has been adjusted in #132.
As before, the code duplication here is because the OpenMM protocols are currently (mostly) independent as we work out the best options for each. This will be refactored once we port to
BioSimSpace._Config. (We might just use the native Sire conversion, so do away with this entirely.)For reference, the native OpenMM parsers also appear to fail (with a different error) on macOS. I'll debug this if we have issues when removing the ParmEd workaround in future.
develinto this branch before issuing this pull request (e.g. by runninggit pull origin devel): [y]Suggested reviewers:
@chryswoods