Update mol2 files, add axis rotations of chains

[chrisjonesBSU]

This PR makes 2 improvements:

1. The individual molecule files contained a better relaxed/optimization structure

• The PPS mol2 file now contains 4 monomers instead of a single phenyl ring + sulfur linkage

3. The polymer chains are rotated to run along, and parallel to the z-axis.

The primary motivation for this PR was to improve system initialization using the crystal function in system.Initializer

The hoomd version in the yml files was bumped up from 3.1 to 3.2

[codecov[bot]]

Codecov Report

Merging #81 (386d6bc) into master (9ddab07) will increase coverage by 0.09%. The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master      #81      +/-   ##
==========================================
+ Coverage   91.08%   91.17%   +0.09%     
==========================================
  Files           7        7              
  Lines         673      680       +7     
==========================================
+ Hits          613      620       +7     
  Misses         60       60              

Impacted Files	Coverage Δ
polybinder/system.py	91.68% <100.00%> (+0.16%)	:arrow_up: