Internal updates due to Sire API fixes #203
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This PR applies some internal updates due to Sire changes introduced via OpenBioSim/sire#119 and OpenBioSim/sire#120. For the
cursor.rotateupdate I've chosen (for now) to userotate_velocities=Falseand manually rotate the velocities using the property map, i.e. adjusting whatcoordinatesis mapped to. This is so the user can rename things how they like. I also manually apply a rotation for both end states when perturbable molecules are present. By addingrotate_velocities=FalseI'm simply making sure that I don't perform a double rotation. (Note that I could use the end state linking functionality, but this is simpler for now.)develinto this branch before issuing this pull request (e.g. by runninggit pull origin devel): [y]Suggested reviewers:
@chryswoods