Correctly set the mass when creating mb.Compound from a Snapshot; add mass_scale parameter

[chrisjonesBSU]

I was getting some errors when trying to create a CG trajecotry of PPS. Ultimately, I think the errors resulted from a change in how mass is handled in mBuild. This PR sets the particle mass from the snapshot particle mass, and includes a mass_scale parameter for converting from reduced mass to real mass (similar to what was being done with length)

[codecov]

Codecov Report

Merging #49 (7549f13) into main (9a5dc8d) will increase coverage by 0.01%.
The diff coverage is 100.00%.

❗ Current head 7549f13 differs from pull request most recent head b2e8b72. Consider uploading reports for the commit b2e8b72 to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #49      +/-   ##
==========================================
+ Coverage   96.62%   96.64%   +0.01%     
==========================================
  Files           4        4              
  Lines         385      387       +2     
==========================================
+ Hits          372      374       +2     
  Misses         13       13              

Files Changed	Coverage Δ
grits/coarsegrain.py	98.20% <100.00%> (+<0.01%)	⬆️
grits/utils.py	96.77% <100.00%> (+0.03%)	⬆️

[RainierBarrett]

It looks like we are getting the SMARTS strings wrong in this test, or borking the search somewhere. Running on the p3ht.gsd included in the repo gives this warning:

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is Compound)

/Users/cmelab/repos/grits/grits/coarsegrain.py:139: UserWarning: c1cscc1 not found in compound!
  warn(f"{smart_str} not found in compound!")
/Users/cmelab/repos/grits/grits/coarsegrain.py:139: UserWarning: CCC not found in compound!
  warn(f"{smart_str} not found in compound!")```

[RainierBarrett]

Looks like it might be openbabel version updates causing the hiccup

[RainierBarrett]

It looks like we are getting the SMARTS strings wrong in this test, or borking the search somewhere. Running on the p3ht.gsd included in the repo gives this warning:

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is Compound)

/Users/cmelab/repos/grits/grits/coarsegrain.py:139: UserWarning: c1cscc1 not found in compound!
  warn(f"{smart_str} not found in compound!")
/Users/cmelab/repos/grits/grits/coarsegrain.py:139: UserWarning: CCC not found in compound!
  warn(f"{smart_str} not found in compound!")```

This was happening because of us removing hydrogens erroneously before invoking grits, and without using the proper flag in the CG_System call. False alarm!

[chrisjonesBSU]

Merging this for now since it is needed for #51 , we'll address the failing unit tests after this overhaul in finished up.