Minor improvements to PolymerProposalEngine

[zhang-ivy]

Description

Here, I am adding the following improvements to PolymerProposalEngine:

1. For protein mutations, do not map sidechain atoms (CB atoms and beyond)
2. Speed up the execution of construct_atom_map
3. Handle ring amino acids

Motivation and context

Changes:

1. We don't want to map sidechain atoms for protein mutations because of the sidechain rotamer sampling problem. We can use REST to enhance sampling if we do not map sidechain atoms.
2. We can speed up the execution of construct_atom_map by removing one of the nested for loops.
3. We need to set allow_ring_breaking=False for ring amino acids.

How has this been tested?

As long as the tests in test_topology_proposal.py run ok, we should be fine.

Change log

[codecov]

Codecov Report

Merging #841 (27dd44f) into master (45e1092) will increase coverage by 0.00%.
The diff coverage is 100.00%.