Modified tICA to use outer products rather than a sum of inner products
Changed project.__init__'s validate kwarg to default to False.
Cleaning up the tICA library and adding docstring with the hope of finally pulling this into MSMBuilder...
Mergest SimTk/msmbuilder into my forked tICA branch. Surprisingly few merge conflicts\!
Merge branch 'cluster_args' of github.com:SimTk/msmbuilder into tICA
Cleaned up tICA_train.py so that it conforms better with the msmbuilder standard. Added a tICA_train test in tests/test_wrappers.py, but currently the tests do not pass on my machine, but it's the Cluster ones that don't pass...
Merge branch 'cluster_args' of github.com:SimTk/msmbuilder into tICA
Typos in tICA.CovarianceMatrix.__init__ docstring. Also added a note that procs is not implemented in that method.
Began the cleanup of tica:msmbuilder.metrics.projection by removing the lprmsd components. We don't want to encourage people to use tica with atomic positions since there are some major issues with trying that...
Added os.mkdir(args.output_dir) to Assign.py. I think this is a bug in the master branch too, but no one runs into it because they save the assignments in the same directory as Gens.lh5.
Added fix for a bug in numpy that does not do a += a.T correctly if a is bigger than 91 x 91. I changed it to a = a + a.T.
I don't know what this commit did... should have committed a week ago. See diff.
added the MLE estimate of C and Sigma and \mu... Hopefully this helps?
bugfix in MLE estimate.
Added bugfix for a project builder issue when pdb filename does not exist. The builder actually assumed that the error was a corrupt xtc file, and so it was stuck in an infinite loop trying to throw away the last frame in the xtc.
merge conflict
Merge branch 'master' of github.com:SimTk/msmbuilder into tica_mle
first attempts at getting the project builder to update the file. This is harder than I thought it would be ...
Merge branch 'proj_builder' of github.com:schwancr/msmbuilder into proj_builder
small fix in ProjectBuilder docstring