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cmelab / polybinder

Initialization of thermoplastic polymer systems to simulate thermal welding
GNU General Public License v3.0
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Using mbuild's polymer class for building up molecules #42

Closed chrisjonesBSU closed 3 years ago

chrisjonesBSU commented 3 years ago

This PR gets rid of DeepSMILES and the polymer generation scheme I was using before. Now, it will use mbuild's polymer class to build up molecules from a SMILES string.

Addresses #41

It's working so far for PEEK, I still need to change the SMILES string for PEKK. Also, I want to make sure we're doing whatever is needed to be able to utilize infer_residues in the foyer atom typing step.

codecov[bot] commented 3 years ago

Codecov Report

Merging #42 (b75e561) into master (090acff) will increase coverage by 7.56%. The diff coverage is 100.00%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master      #42      +/-   ##
==========================================
+ Coverage   87.30%   94.86%   +7.56%     
==========================================
  Files           6        4       -2     
  Lines         441      370      -71     
==========================================
- Hits          385      351      -34     
+ Misses         56       19      -37
Impacted Files Coverage Δ
uli_init/simulate.py 94.29% <100.00%> (-0.11%) :arrow_down: