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nlesc-nano / auto-FOX

A library for analyzing potential energy surfaces (PESs) and using the resulting PES descriptors for constructing forcefield parameters.
GNU Lesser General Public License v3.0
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ENH: Add the `TOPContainer.generate_pairs` method for generation 1,4-pairs #297

Closed BvB93 closed 1 year ago

BvB93 commented 1 year ago

xref https://github.com/nlesc-nano/auto-FOX/issues/293

Adds the new TOPContainer.generate_pairs method that generates and populates the pairs directive with all 1,4-pairs as defined by the bonds directive. 1,4-pairs are generated automatically in the create_top recipe.

codecov[bot] commented 1 year ago

Codecov Report

Merging #297 (64fe2b5) into master (5eed054) will increase coverage by 0.00%. The diff coverage is 87.23%.

@@           Coverage Diff           @@
##           master     #297   +/-   ##
=======================================
  Coverage   74.85%   74.86%           
=======================================
  Files          70       70           
  Lines        7923     7949   +26     
  Branches     1678     1682    +4     
=======================================
+ Hits         5931     5951   +20     
- Misses       1570     1573    +3     
- Partials      422      425    +3
Impacted Files Coverage Δ
FOX/ff/degree_of_separation.py 85.96% <81.81%> (-2.72%) :arrow_down:
FOX/io/_read_top.py 79.68% <87.87%> (+0.02%) :arrow_up:
FOX/recipes/top.py 75.00% <100.00%> (+0.45%) :arrow_up: