cmelab / polybinder

Initialization of thermoplastic polymer systems to simulate thermal welding
GNU General Public License v3.0
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Add mol2 files for PEEK and PEKK #55

Closed chrisjonesBSU closed 3 years ago

chrisjonesBSU commented 3 years ago

I've noticed some issues with using the SMILES stricks to generate the monomers each time. I'm not exactly sure if it was caused by the change to RDkit in mbuild, of if the SMILES strings need tweaking, but I'm adding mol2 files for PEKK and PEEK (para and meta) as well as updated .JSON files that work with the .mol2 files. This should be more reproducible.

codecov[bot] commented 3 years ago

Codecov Report

Merging #55 (763b7b5) into master (d997cfe) will increase coverage by 0.80%. The diff coverage is 60.00%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master      #55      +/-   ##
==========================================
+ Coverage   93.95%   94.75%   +0.80%     
==========================================
  Files           6        6              
  Lines         480      477       -3     
==========================================
+ Hits          451      452       +1     
+ Misses         29       25       -4     
Impacted Files Coverage Δ
uli_init/system.py 94.16% <60.00%> (+1.47%) :arrow_up:
chrisjonesBSU commented 3 years ago

I tested this out with peek, pekk at different combinations of para and meta and it builds the molecules correctly.