Merge branch 'master' of github.com:SimTk/msmbuilder
Merge issues, when pulling from master. I really hope this is not pushing to master. I think I did it right though.
Bugfix in metrics.parsers.py introduced in merge. Only because I have 'layered' metrics now.
Bugfix in arglib which allows for tICA_train.py to actually run.
Bugfixes to metrics/parsers.py to adjust the layered metric to work with the new metrics layout
adding accessible surface area code; _asa is a C extention module, wrapped using f2py (crazy, I know), that implmenets the Shrake-Rupley algorithm. geometry/asa.py is a python wrapper that calls the code. No scripts are installed yet that actually call this code, but it does have tests
Bugfix in TestWrappers to asser the arrays are 'almost' equal as opposed to actually equal
Added a script which can compute Project distances (just like CalculateProjectRMSD.py). Also I modified the UnitTestReference/ProjectInfo.h5 to have the right directory. Also I cp'd native.pdb from new_tests/native.pdb to the Reference directory. At some point these two things should be together right?
Modifed description in CalculateProjectDistance as well as the old scripts to indicate that the old ones are deprecated. I also added a unit test for the new script, which checks RMSD and LPRMSD.
Bugfix in SavePDBs.py
Merge branch 'master' of github.com:SimTk/msmbuilder
Added TPT unit tests, fixed some TPT issues - TPT still broken
Merge branch 'master' of https://github.com/SimTk/msmbuilder

Conflicts:
	src/python/transition_path_theory.py
Added CalculateProjectSASA.py as well as unit tests for it. Though I used the script to generate the data... So I may want to re-work it to use the GMX data.
Merge branch 'master' of github.com:SimTk/msmbuilder
Merge branch 'master' of github.com:SimTk/msmbuilder into tICA
Merge branch 'master' of github.com:SimTk/msmbuilder into tICA
Merge branch 'tICA' of github.com:SimTk/msmbuilder into tICA
fixed some of TPT, added hub scores
fixed all names in TPT, moved tests to new_tests