Change coarse-graining process to work on mbuild compounds instead of GSD files

[chrisjonesBSU]

Coarse-graining large systems is prohibitively slow. This PR makes the coarse graining process (via polybinerCG) work while staying in mBuild space, rather than creating a GSD file, and should speed up the process.

The way this new coarse-graining process works requires a pretty big change to the API in the Initializer class. Ultimately, I think we should remove the Initializer class and move all of the builder functions back into the System class, but I'll do this in a separate PR.

[codecov[bot]]

Codecov Report

Merging #103 (5deee15) into master (0d3fbfa) will increase coverage by 0.16%. The diff coverage is 86.59%.

Additional details and impacted files

[](https://codecov.io/gh/cmelab/polybinder/pull/103?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cmelab) ```diff @@ Coverage Diff @@ ## master #103 +/- ## ========================================== + Coverage 91.64% 91.80% +0.16% ========================================== Files 7 7 Lines 778 781 +3 ========================================== + Hits 713 717 +4 + Misses 65 64 -1 ``` | [Impacted Files](https://codecov.io/gh/cmelab/polybinder/pull/103?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cmelab) | Coverage Δ | | |---|---|---| | [polybinder/simulate.py](https://codecov.io/gh/cmelab/polybinder/pull/103/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cmelab#diff-cG9seWJpbmRlci9zaW11bGF0ZS5weQ==) | `87.26% <82.75%> (+0.65%)` | :arrow_up: | | [polybinder/system.py](https://codecov.io/gh/cmelab/polybinder/pull/103/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cmelab#diff-cG9seWJpbmRlci9zeXN0ZW0ucHk=) | `94.32% <88.23%> (-0.07%)` | :arrow_down: |

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