Fix issues caught by BioSimSpaceTutorials #128
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[ref OpenBioSim/BioSimSpaceTutorials#32]
[closes OpenBioSim/BioSimSpaceTutorials#36]
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chryswoods
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Looks good - could I have some tests that show the difference in the rmsd calculated by sire. I am pretty sure the code is correct - it will be different definitions of reference or subsets of atoms being calculated I think. It would be good to debug to find a way to produce an equivalent rmsd.
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Yes, no problem, I'll try to dig out the code that I wrote. It was off for a single frame and I tried with-and-without molecular wrapping. I imagine it will be very easy to fix once we work out why we're getting a difference. |
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This PR fixes some issues that were caught by the BioSimSpaceTutorials suite. (Why some of these weren't caught by the previous run through, I don't know.)
Changes are:
Allow the user to specify a trajectory backend when calling
process.getTrajectory. This is required since the default Sire backend can't (yet) compute the RMSD correctly. I've also updated the example notebook indemosto specify a backend.Fix the PLUMED version check required for determining whether and auxiliary file is needed to enable funnel metadynamics simulations.
Pass the
process._work_dirattribute to theProcess.Plumedconstructor as a string withinProcess.OpenMM. Previously, the_Utils.WorkDirobject was being passed, so a type check was failing.I confirm that I have merged the latest version of
develinto this branch before issuing this pull request (e.g. by runninggit pull origin devel): [y]I confirm that I have permission to release this code under the GPL3 license: [y]
Suggested reviewers:
@chryswoods