Modify bond graph to include independent particle

[daico007]

PR Summary:

Currently, compound bond graph only include bonded particles. This PR modify mb.Compound so that its bond graph also include independent/non-bonded particle.

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 ✅

Project coverage is 90.39%. Comparing base (a7ff062) to head (1da0474).
Report is 157 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #1036   +/-   ##
=======================================
  Coverage   90.38%   90.39%           
=======================================
  Files          64       64           
  Lines        9029     9027    -2     
=======================================
- Hits         8161     8160    -1     
+ Misses        868      867    -1     

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[bc118]

This PR seems to be passing all the existing MOSDEF-GOMC-GMSO tests if you add the other PRs data to the compound.py file:

def group_by_molecules(self):
    """Create a restructured compound where each molecule is grouped together.

    This top down method looks through the children in a compound and identifies
    individual molecules looking until is_independent() returns False. Then,
    the parent of that child is added to a list of molecule and grouped into one
    master compound.

    Parameters
    ----------
    compound : mbuild.Compound with molecules in the hierarchy

    Returns
    -------
    grouped_compound : mb.Compound where each child are the uniquely named
    independent molecules in the syste,

    See Also
    --------
    mbuild.compound.Compound._recursive_id_molecules

    Examples
    --------
    Creating a per molecule compound:

    >>> import mbuild as mb
    >>> cpd1 = mb.load("CCCC", smiles=True)
    >>> cpd1.name = "Butane"
    >>> cpd2 = mb.load("CCCCO", smiles=True)
    >>> cpd2.name = "Butanol"
    >>> box = mb.packing.solvate(
        solvent = cpd1,
        solute = cpd2,
        box = mb.Box([5,5,5]),
        n_solvent = 100,
    )
    >>> box2 = mb.packing.fill_box(cpd1, box=mb.Box([5,5,5]), n_compounds=100)
    >>> box2.translate([5,0,0])
    >>> box.add(box2)
    >>> partitioned_box = box.group_by_molecules()
    >>> print(child.name for child in partitioned_box.children)
    Output
    ["Butane", "Butanol"]

    """
    grouped_compound = Compound()
    grouped_compound.box = self.box
    molecule_list = self._recursive_id_molecules()
    if molecule_list:
        subtops = {}
        for molecule in molecule_list:
            if subtops.get(molecule.name):
                subtops[molecule.name].add(clone(molecule))
            else:
                subtops[molecule.name] = Compound(name=molecule.name)
                subtops[molecule.name].add(clone(molecule))
        for subtop in subtops.values():
            grouped_compound.add(subtop)
        return grouped_compound
    else:
        msg = f"""No molecules were found in {self.name}. Return molecule as is."""
        warn(msg)
        return mb.clone(self)

def _recursive_id_molecules(self, molecule_list=None):
    """Iterate through the compound top down to identify independent structures."""
    if not molecule_list:
        molecule_list = []

    # Handle the case where self is a lone particle
    if not self.children and self.is_independent():
        molecule_list.append(self)
        return molecule_list

    for child in self.children:
        if not child.is_independent():
            molecule_list.append(self)
            return molecule_list
        else:
            molecule_list = child._recursive_id_molecules(
                molecule_list=molecule_list
            )

    return molecule_list