Speed up json loader

[daico007]

PR Summary:

Address #1162. Add some workaround to the ind particle bond graph before adding to the main compound and speed up the loader in general.

import mbuild as mb#
eth = mb.load("CC", smiles=True)
eth.name = "Ethane"
eth_box = mb.packing.fill_box(
    compound=eth,
    n_compounds=1000,
    box=[5, 5, 5]
)
eth_box.name = "EthaneBox"
eth_box.save("eth_box1000.json", overwrite=True)

comp = mb.load("eth_box1000.json") # This now takes a few second. 

PR Checklist

---

• [ ] Includes appropriate unit test(s)
• [ ] Appropriate docstring(s) are added/updated
• [ ] Code is (approximately) PEP8 compliant
• [ ] Issue(s) raised/addressed?

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Comparison is base (9d20e3d) 87.18% compared to head (0908345) 87.27%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #1163 +/- ## ========================================== + Coverage 87.18% 87.27% +0.09% ========================================== Files 62 62 Lines 6492 6499 +7 ========================================== + Hits 5660 5672 +12 + Misses 832 827 -5 ```

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