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[WIP] Fix for LPRMSD after mdtraj merge#427

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schwancr wants to merge 8 commits intomsmbuilder:masterfrom

schwancr:lprmsd_mdtraj

Commits on Jun 18, 2014

temporary(?) fix for LPRMSD extension. It was still trying to use RMSD.TheoData from msmbuilder.metrics, which no longer exists since we moved to mdtraj. I don't know what the permanent fix should …
schwancr
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added openmp check to lprmsd's setup.py
schwancr
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everything imports and no errors are thrown but I get a segfault when using lprmsd now...
schwancr
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i don't know where this is coming from
schwancr
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translated msmbuilder.metrics.positions to use mdtraj.lprmsd. This works now (I think)
schwancr
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code seems ok, but I think there's actually an issue in mdtraj's implementation of lprmsd...
schwancr
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My test cases that have a bunch of atoms on a single line keep getting messed up in theobald_rmsd... where the rotation matrix is not calculated correctly. Just calling md.lprmsd works. but trying …
schwancr
committed

Commits on Jul 9, 2014

added test for positions
schwancr
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