Energy decomposition function, native contacts by configurational state

[cwalker7]

Description

Some assorted fixes and updates:

1. Applies the conformational state decomposition for native contact expectations. This is done in a similar way as the 'partial' heat capacity contributions by manually summing the relevant MBAR weights. This is intended for systems with more than 2 configurational states, where we want the Q vs T expectation curves within each state.
2. Compute the number of effective samples for the configurational state partial heat capacities - these weights would be the same for the configurational state native contact expectations, so don't need to also compute there.
3. Fixes a bug in the native contacts end-to-end symmetry check, which occurred for the case of a linear homopolymer with 2 identical backbone beads in 1 residue.
4. New energy decomposition function - read in cgmodel and coordinate file, and return OpenMM total energy and contributions from bonds, angles, torsions, nonbonded force groups.

Todos

• Tests for configurational state native contact expectations
• Make the end-to-end symmetry check for native contacts more robust
• Tests for energy decomposition
• Fix import statement issues with OpenMM 7.6/7.7

Status

• Ready to go

[codecov]

Codecov Report

Merging #144 (411a9d9) into master (266bcf0) will increase coverage by 1.01%.
The diff coverage is 86.22%.