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msmbuilder / msmbuilder-legacy

Legacy release of MSMBuilder
http://msmbuilder.org
GNU General Public License v2.0
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Use MDTraj instead of LPRMSD in msmb.metrics.Positions #367

Open kyleabeauchamp opened 10 years ago

kyleabeauchamp commented 10 years ago

I forget, but is our MDTraj RMSD stuff now sufficiently general to stop using LPRMSD here?

I guess the key factor is aligning to a subset of atoms, then calculating RMSD based on a possibly different subset.

leeping commented 10 years ago

I think that particular usage of LPRMSD was easy enough that MDTraj should be able to easily replace it. A couple of considerations:

1) LPRMSD shouldn't be eliminated completely because it currently is the only way to permute groups of indistinguishable particles before calculating RMSD (though this may change in the future.)

2) Not sure but I think LPRMSD is currently used in SaveStructures, because it aligns the structures prior to saving. Just need to make sure to do a complete replacement.

kyleabeauchamp commented 10 years ago

Agree

rmcgibbo commented 10 years ago

This should be easy now.