Type hinting and doc updating in tests

[andrewtarzia]

Requested Reviewers: @lukasturcani

This PR will be slow going, but I will occasionally do folders in tests and update their doc strings to Google and add TypeHints.

• Once this process is done, we can remove the exclusion of tests from ruff and mypy

[andrewtarzia]

Testing functions for this PR:

def test1():
    initial = stk.BuildingBlock(
        smiles="C1=C(C(=C(C(=C1Br)Br)Br)Br)Br",
        functional_groups=(stk.BromoFactory(),),
    )
    fgs = list(initial.get_functional_groups())
    print(len(fgs))

    rng = np.random.default_rng(seed=1000)

    chosen_fgs = rng.choice(
        fgs,
        size=3,
        replace=False,
    )
    print(len(chosen_fgs))

    temp_molecule = initial.with_functional_groups(chosen_fgs)
    # The fg_repr was not updating prior to this!
    print(temp_molecule)
    print(temp_molecule.get_num_functional_groups())


def get_disconnected_components(molecule):
    # Produce a graph from the molecule that does not include edges
    # where the bonds to be optimized are.
    mol_graph = nx.Graph()
    for atom in molecule.get_atoms():
        mol_graph.add_node(atom.get_id())

    # Add edges.
    for bond in molecule.get_bonds():
        pair_ids = (bond.get_atom1().get_id(), bond.get_atom2().get_id())
        mol_graph.add_edge(*pair_ids)

    # Get atom ids in disconnected subgraphs.
    components = {}
    for c in nx.connected_components(mol_graph):
        c_ids = sorted(c)
        molecule.write("temp_mol.mol", atom_ids=c_ids)
        num_atoms = len(c_ids)
        newbb = stk.BuildingBlock.init_from_file("temp_mol.mol")
        os.system("rm temp_mol.mol")

        components[num_atoms] = newbb

    return components


def extract_host(molecule):
    components = get_disconnected_components(molecule)
    return components[max(components.keys())]


def extract_guest(molecule):
    components = get_disconnected_components(molecule)
    return components[min(components.keys())]


def test2():
    host = stk.ConstructedMolecule(
        topology_graph=stk.cage.FourPlusSix(
            building_blocks=(
                stk.BuildingBlock(
                    smiles="NC1CCCCC1N",
                    functional_groups=[
                        stk.PrimaryAminoFactory(),
                    ],
                ),
                stk.BuildingBlock(
                    smiles="O=Cc1cc(C=O)cc(C=O)c1",
                    functional_groups=[stk.AldehydeFactory()],
                ),
            ),
            optimizer=stk.MCHammer(),
        ),
    ).with_centroid((0, 0, 0))
    print("host:", host.get_centroid())
    guest_bb = stk.BuildingBlock("C1=C(C(=C(C(=C1Br)Br)Br)Br)Br")
    guest = stk.host_guest.Guest(
        building_block=guest_bb,
        start_vector=guest_bb.get_direction(),
        end_vector=host.get_plane_normal(),
        displacement=(0, 0, 0),
    )
    hgcomplex = stk.ConstructedMolecule(
        topology_graph=stk.host_guest.Complex(
            host=stk.BuildingBlock.init_from_molecule(host),
            guests=guest,
        ),
    )
    hgcomplex.write("hg1.mol")
    print("host 1", extract_host(hgcomplex).get_centroid())
    extract_host(hgcomplex).write("eh_1.mol")
    print("guest 1", extract_guest(hgcomplex).get_centroid())
    extract_guest(hgcomplex).write("eg_1.mol")
    print("----")
    host = stk.ConstructedMolecule(
        topology_graph=stk.cage.FourPlusSix(
            building_blocks=(
                stk.BuildingBlock(
                    smiles="NC1CCCCC1N",
                    functional_groups=[
                        stk.PrimaryAminoFactory(),
                    ],
                ),
                stk.BuildingBlock(
                    smiles="O=Cc1cc(C=O)cc(C=O)c1",
                    functional_groups=[stk.AldehydeFactory()],
                ),
            ),
            optimizer=stk.MCHammer(),
        ),
    ).with_centroid((2, 3, 5))
    print("host:", host.get_centroid())
    guest = stk.host_guest.Guest(
        building_block=guest_bb,
        start_vector=guest_bb.get_direction(),
        end_vector=host.get_plane_normal(),
        displacement=host.get_centroid(),
    )
    hgcomplex = stk.ConstructedMolecule(
        topology_graph=stk.host_guest.Complex(
            host=stk.BuildingBlock.init_from_molecule(host),
            guests=guest,
        ),
    )
    hgcomplex.write("hg2.mol")
    print("host 2", extract_host(hgcomplex).get_centroid())
    print("guest 2", extract_guest(hgcomplex).get_centroid())
    extract_host(hgcomplex).write("eh_2.mol")
    extract_guest(hgcomplex).write("eg_2.mol")

    guest = stk.host_guest.Guest(
        building_block=guest_bb,
        start_vector=guest_bb.get_direction(),
        end_vector=host.get_plane_normal(),
    )
    hgcomplex = stk.ConstructedMolecule(
        topology_graph=stk.host_guest.Complex(
            host=stk.BuildingBlock.init_from_molecule(host),
            guests=guest,
        ),
    )
    hgcomplex.write("hg3.mol")
    print("host 3", extract_host(hgcomplex).get_centroid())
    print("guest 3", extract_guest(hgcomplex).get_centroid())
    extract_host(hgcomplex).write("eh_3.mol")
    extract_guest(hgcomplex).write("eg_3.mol")
    raise SystemExit

[andrewtarzia]

Some issue with rebasing! Tried again