[nathanmlim]

This PR adds in an analysis module I've been working on that automatically identify metastable ligand binding modes using tools from PyEMMA. Included is a juypter notebook that provides a brief walk through usage of the analysis modules, located in notebooks/example-id_bmodes.ipynb

The analysis modules can be accessed like blues.analysis import msm,cluster. Helper functions for these modules are located in tools.py

• msm submodule contains the ConstructMSM class:

ConstructMSM provides convenience functions for using PyEMMA.
This class assists in selecting the appropriate lagtime
through plots, TICA-transforms the input feature coordinates for
k-means clustering to discretize the trajectories, and constructs the MSM
for the purpose of identifying the metastable binding modes.

• cluster submodule contains the FindBindingModes class:

FindBindingModes provides functions to analyze and determine the number of
metastable modes from the resulting MSM data out of ConstructMSM() via
spectral clustering from PCCA.

• population submodule contains the BindingModeOccupancy class:

    BindingModeOccupancy provides functionality to calculate the occupancy
    of each defined binding mode, determined from FindBindingModes().

[nathanmlim]

This will need some changes with upcoming changes to our NCMC reporter.

[stevenayoub]

@davidlmobley

This PR looks quite useful—it adds a modular analysis toolkit (blues.analysis) for identifying metastable ligand binding modes using PyEMMA. It’s well-scoped and does not alter the core functionality of BLUES, making it a safe and valuable addition for post-simulation analysis.

For future development, it may be worth refactoring to support deeptime ( https://deeptime-ml.github.io/latest/index.html ) , given the deprecation of PyEMMA.

I did encounter some merge conflicts with the following files:
• Both added: .gitignore
• Both modified: .travis.yml
• Deleted by us: blues/version.py
• Both modified: setup.py

These are all straightforward and can be resolved by merging both sets of changes.