Added an optional 'mask' functionality to get_count_matrix_from_assignments and get_counts_from_traj in MSMLib.py

Added some code to include a 'mask' argument that allows separation of cis and trans conformers of CheY during count matrix construction, based on the proline dihedral angle. There are additional small edits in msm_analysis.py and CalculateImpliedTimescales.py. My goal is to set it up such that 'mask' is completely optional, so if not explicitly specified, all code should run as usual.