Fix #208 #210
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Fix #208 #210
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This PR closes #208 by fixing the
renumberoption inBioSImSpace._SireWrappers.Molecule.extract. The idea behind this was to allow the user to extract a partial molecule then update the same original molecule in a system in one step, rather than needing to remove the old molecule and add the new one, which would (potentially) change the order. (There are ways to preserve this, i.e. you can update by index.)Since this option was already broken, and hasn't seemed to cause any issue, perhaps it's better to remove it entirely and just deal with a different number, e.g. updating by index as suggested above. (There is code to do this and preserve the existing molecular order, i.e. you just replace the molecule in its existing position in the system.)
I've also added a quick fix that closes #213 by using the
sire.legacy.IO.GroTopparser to reconstruct the intrascale matrices for the end states when loading a perturbable system from file. This has been tested viasomd2.develinto this branch before issuing this pull request (e.g. by runninggit pull origin devel): [y]Suggested reviewers:
@chryswoods