Fix mismatched gmso residue name when molecule is loaded from mol2

[marjanalbooyeh]

This PR fixes the gmso topology parameterization issue caused by name mismatch in mbuild compound.
For a Molecule loaded from a mol2 file, if we change the mbuild compound name, the name of its children does not change accordingly. When the forcefield dictionary with keys similar to the compound name is being applied to the system, the gmso topology is not parameterized because of this naming mismach.

As a quick fix, this PR makes sure that the name is assigned to every child of the mbuild compound. However, more investigation needs to be done on gmso's behavior when converting an mbuild compound to a topology. (see the example in the comments).

[chrisjonesBSU]

LGTM, Thanks!

[marjanalbooyeh]

Here is the example that shows this inconsistency in gmso's from_mbuild behavior based on how that mbuild compound is being loaded:

import mbuild as mb
from mbuild.lib.molecules import Ethane
from gmso.parameterization import apply
from gmso.external.convert_mbuild import from_mbuild
import forcefield_utilities as ffutils

opls = ffutils.FoyerFFs().load(ffname="oplsaa").to_gmso_ff()

ethane = Ethane()
ethane.save("ethane.mol2", overwrite=True)
ethane_mol2 = mb.load("ethane.mol2")
ethane_mol2.name = "Ethane"

ethane_top = from_mbuild(ethane)
ethane_top.identify_connections()

ethane_mol2_top = from_mbuild(ethane_mol2)
ethane_mol2_top.identify_connections()

apply(
    ethane_top,
    {"Ethane": opls},
)

apply(
    ethane_mol2_top,
    {"Ethane": opls},
)

for site in ethane_top.sites:
    print(site.atom_type.parameters)

for site in ethane_mol2_top.sites:
    print(site.atom_type.parameters)

In this example, the ethane_mol2_top is not parameterized.

[codecov]

Codecov Report

Merging #37 (d1a9e87) into main (165fc3f) will increase coverage by 0.01%.
The diff coverage is 100.00%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #37      +/-   ##
==========================================
+ Coverage   92.23%   92.24%   +0.01%     
==========================================
  Files          18       18              
  Lines        1326     1328       +2     
==========================================
+ Hits         1223     1225       +2     
  Misses        103      103              

Files Changed	Coverage Δ
hoomd_organics/base/molecule.py	96.62% <100.00%> (+0.02%)	⬆️