Add some topology slicing methods.

[chrisjonesBSU]

PR Summary:

This is ultimately an effort to help out @JAGarcia03 with his project, but it should be a useful addition in general.

utils.py gets new slicing methods where the goal is to create a new topology object that contains a subset of another topology's molecules or residues. This should live in utils.py as we have been wanting to reduce the amount of methods and code in general within Topology, and this file will be a good place to add other, more creative slicing methods.

This also adds the ability to filter by number in addition to tag within iter_sites_by_molecule and iter_sites_by_residue.

For example, if you want to get just the sites belonging to the 0th "Benzene" (instead of all of them) you can now do:

for site in topology.iter_sites_by_molecule(molecule_tag="Benzene", molecule_number=0)

A quick example:

import mbuild as mb
import gmso
from gmso.core.topology import Topology
from gmso.utils.slicing import slice_topology_by_molecule

benzene = mb.load("c1ccccc1", smiles=True)
benzene.name = "Benzene"
ethane = mb.load("CC", smiles=True)
ethane.name = "Ethane"

system = mb.fill_box(compound=[benzene, ethane], n_compounds=[2, 2], box=[2,2,2])
topology = system.to_gmso()
topology.identify_connections()

single_benzene_top = slice_topology_by_molecule(topology=topology, molecule_tag="Benzene", molecule_number=0)

all_benzene_top = slice_topology_by_molecule(topology=topology, molecule_tag="Benzene", molecule_number=None)

I still need to make the slicing tests more thorough, and add new tests for the changes to iter_sites_by_*

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

❌ Patch coverage is 41.46341% with 48 lines in your changes missing coverage. Please review.
✅ Project coverage is 92.88%. Comparing base (3720cd0) to head (d7b0755).

Files with missing lines	Patch %	Lines
gmso/external/convert_openmm.py	8.69%	21 Missing ⚠️
gmso/core/topology.py	51.72%	14 Missing ⚠️
gmso/utils/charges.py	0.00%	13 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #961      +/-   ##
==========================================
- Coverage   93.42%   92.88%   -0.55%     
==========================================
  Files          67       69       +2     
  Lines        8020     8096      +76     
==========================================
+ Hits         7493     7520      +27     
- Misses        527      576      +49     

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