SimTk/msmbuilder — pull request #119 by kyleabeauchamp (2013-01-19 19:46:55+00:00)
Title: New mle code

Some notes:

1. I've left Lutz's code __hidden__ in MSMLib. We use his code as a reference in our nose tests.

2. The new code is called in exactly the same way as the old. Under the hood, however, I have a class that handles the optimization of the likelihood.

3. Merging will fix issues #118 and #16