Angled vertex

[andrewtarzia]

Related Issues: #156
Requested Reviewers: @lukasturcani
Note for Reviewers: If you accept the review request add a 👍 to this post

Using a set for placer ids, required to solve #156, lead to badly formed structures for M3L3Triangle and M4L4Square. I determined this to be because the LinearVertex was on an "orthogonal" position, so a new Vertex is required.

Most source changes in:

• src/stk/molecular/topology_graphs/cage/vertices.py: New vertex implemented.

Added new vertex test and new structure tests for the M3L3 Triangle - new position matrices needed.

[andrewtarzia]

A test case:

import stk

metal_atom = stk.BuildingBlock(
    smiles='[Pd+2]',
    functional_groups=(
        stk.SingleAtom(stk.Pd(0, charge=2))
        for i in range(4)
    ),
    position_matrix=[[0., 0., 0.]],
)

ligand = stk.BuildingBlock(
    smiles='NCCN',
    functional_groups=[
        stk.SmartsFunctionalGroupFactory(
            smarts='[#7]~[#6]',
            bonders=(0, ),
            deleters=(),
        ),
    ]
)

metal_complex = stk.ConstructedMolecule(
    stk.metal_complex.CisProtectedSquarePlanar(
        metals=metal_atom,
        ligands=ligand,
    )
)

metal_complex = stk.BuildingBlock.init_from_molecule(
    molecule=metal_complex,
    functional_groups=[
        stk.SmartsFunctionalGroupFactory(
            smarts='[Pd]~[#7]',
            bonders=(0, ),
            deleters=(),
            # The nitrogen atom will be different
            # for each functional group.
            placers=(0, 1),
        ),
    ],
)

linker = stk.BuildingBlock(
    smiles='C1=NC=CC(C2=CC=NC=C2)=C1',
    functional_groups=[
        stk.SmartsFunctionalGroupFactory(
            smarts='[#6]~[#7X2]~[#6]',
            bonders=(1, ),
            deleters=(),
        ),
    ]
)

print(metal_complex)
print(linker)
cage = stk.ConstructedMolecule(
    stk.cage.M3L3Triangle(
        corners=metal_complex,
        linkers=linker,
        reaction_factory=stk.DativeReactionFactory(
            stk.GenericReactionFactory(
                bond_orders={
                    frozenset({
                        stk.GenericFunctionalGroup,
                        stk.GenericFunctionalGroup,
                    }): 9
                }
            )
        ),
    )
)

cage.write('test33.mol')

cage = stk.ConstructedMolecule(
    stk.cage.M4L4Square(
        corners=metal_complex,
        linkers=linker,
        reaction_factory=stk.DativeReactionFactory(
            stk.GenericReactionFactory(
                bond_orders={
                    frozenset({
                        stk.GenericFunctionalGroup,
                        stk.GenericFunctionalGroup,
                    }): 9
                }
            )
        ),
    )
)

cage.write('test44.mol')