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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 ability to specify custom .top atomtypes #298

Closed BvB93 closed 1 year ago

BvB93 commented 1 year ago

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

Adds a new set of TOPContainer.concatenate.... methods that can be used for adding new entries to the specified GROMACS .top directive. As of the moment the following 4 directives are supported:

Examples

>>> import FOX

>>> top: FOX.TOPContainer = ...
>>> top.concatenate.atomtypes(atnum=[6, 6, 7], sigma=[1.5, 1.2, 5.0], charge=0)
codecov[bot] commented 1 year ago

Codecov Report

Merging #298 (1e29376) into master (cbbe023) will decrease coverage by 0.22%. The diff coverage is 64.19%.

@@            Coverage Diff             @@
##           master     #298      +/-   ##
==========================================
- Coverage   74.86%   74.65%   -0.22%     
==========================================
  Files          70       71       +1     
  Lines        7949     8111     +162     
  Branches     1682     1719      +37     
==========================================
+ Hits         5951     6055     +104     
- Misses       1573     1614      +41     
- Partials      425      442      +17
Impacted Files Coverage Δ
FOX/io/_top_concat.py 63.05% <63.05%> (ø)
FOX/io/_read_top.py 80.00% <100.00%> (+0.31%) :arrow_up: