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]

Codecov Report

All modified and coverable lines are covered by tests ✅

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

Additional details and impacted files

@@            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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[CalCraven]

I this exact change looks fine. I would modify the Compound.save function to go along with this though. The argument "include_port" doesn't make a lot of sense to me while saving. I think the argument should be changed to include_port.

My suggestion is here, and includes changing the default behavior.

        include_ports : bool, optional, default=True
            When saving out with .json extension, be sure to include any `Compound.ports`