Major changes to linear-programming RMSD calculation
Added 'ligand' RMSD functionality where alignment is performed
with one set of indices and RMSD is calculated using another
LPW Pre-Cleanup Commit
cleaned up ambiguous error message in ContinuousContact
faster version of RenumberStates
removed useless stuff in simple_assign
Major cleanup of permutation-invariant RMSD code
Variables renamed, code documented, much shorter
Preparation stage has been optimized
Tested against normal RMSD, and for Lee-Ping and Morgan's systems
More testing is welcome :)
Even more documentation, I'm sure you're tired of hearing me talk by now
RebuildProject imports Emsmbuilder rather than msmbuilder
Bugfixes, added NewPCCAPlus
moved normalizelefteigenvectors to newpcca+
tjl added in situ project generation
Updated lockslide
Remove redundant oldcorrelation import
Minor fixes in PCCA+
Minor fixes in PCCA+
more cleanup of lumping
minor flux PCCA+ change
Added omega angle capability to dihedral.py
Fixed a typo in contact.py xyzlist.float32(xyzlist) -> np.float32(xyzlist)
fixed typo in metrics.py