Bug fix

[ajfriedman22]

Description

Fix topology parsing error to generalize default conformational swapping function to more systems. Also fix issue when restarting from checkpoint in MT-REXEE.

Type of Change

• Bug fix

Todos

Notable points that this PR has either accomplished or will accomplish.

• Fix topology parsing error
• Prevent attempted repeat swap when restarting from checkpoint file

Checklist

Starting from PR #62, external PRs must keep the following checklist in the PR.

• I have read the contributing guidelines.
• My code follows the project’s coding style and is free from linting errors examined by flake8.
• My code comes with docstrings that follow the NumPy docstrings standard.
• I have updated the documentation in the docs directory if my changes affect the project's functionality or usage.
• I have added new tests for new features or changes to existing features. The code coverage is at least 90%.
• My code passes all unit tests and CI tests on CircleCI.

[codecov]

Codecov Report

Attention: Patch coverage is 82.52427% with 18 lines in your changes missing coverage. Please review.

Project coverage is 95.13%. Comparing base (4ffcb5c) to head (5088d7b).
Report is 23 commits behind head on master.

Files with missing lines	Patch %	Lines
ensemble_md/utils/coordinate_swap.py	80.43%	18 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master      #70      +/-   ##
==========================================
- Coverage   96.01%   95.13%   -0.88%     
==========================================
  Files          11       11              
  Lines        2583     2610      +27     
==========================================
+ Hits         2480     2483       +3     
- Misses        103      127      +24     

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