Addition of the MOFs core M6L8L12

docs/source/cage.rst

@@ -47,6 +47,7 @@ Metal-Organic
   M4L8 <_autosummary/stk.cage.M4L8>
   M6L2L3 Prism <_autosummary/stk.cage.M6L2L3Prism>
   M6L12 Cube <_autosummary/stk.cage.M6L12Cube>
+  M6L8L12 Cuboctahedron <_autosummary/stk.cage.M6L8L12Cuboctahedron>
   M8L6 Cube <_autosummary/stk.cage.M8L6Cube>
   M12L24 <_autosummary/stk.cage.M12L24>
   M24L48 <_autosummary/stk.cage.M24L48>

src/stk/_internal/topology_graphs/cage/m6l8l12_cuboctahedron.py

@@ -0,0 +1,215 @@
+import numpy as np
+
+from stk._internal.topology_graphs.edge import Edge
+
+from .cage import Cage
+from .vertices import LinearVertex, NonLinearVertex
+
+
+class M6L8L12Cuboctahedron(Cage):
+    """
+    Represents a cage topology graph.
+
+    Unoptimized construction
+
+    .. moldoc::
+
+        import moldoc.molecule as molecule
+        import stk
+
+        m1 = stk.BuildingBlock('[Ti](Br)(Br)(Br)(Br)(Br)(Br)(Br)(Br)', functional_groups=[stk.BromoFactory()])
+
+        bb1 = stk.BuildingBlock('C(OBr)=[O+]Br', functional_groups=[stk.BromoFactory()])
+
+        bb2 = stk.BuildingBlock('[O+](Br)(Br)(Br)', functional_groups=[stk.BromoFactory()])
+
+        cage = stk.ConstructedMolecule(
+            topology_graph = stk.cage.M6L8L12Cuboctahedron(
+                building_blocks = {
+                    m1:range(0,6),
+                    bb1:range(6,18),
+                    bb2:range(18,26)
+                },
+                optimizer=stk.Collapser(),
+            )
+        )
+
+        moldoc_display_molecule = molecule.Molecule(
+            atoms=(
+                molecule.Atom(
+                    atomic_number=atom.get_atomic_number(),
+                    position=position,
+                ) for atom, position in zip(
+                    cage.get_atoms(),
+                    cage.get_position_matrix(),
+                )
+            ),
+            bonds=(
+                molecule.Bond(
+                    atom1_id=bond.get_atom1().get_id(),
+                    atom2_id=bond.get_atom2().get_id(),
+                    order=(
+                        1
+                        if bond.get_order() == 9
+                        else bond.get_order()
+                    ),
+                ) for bond in cage.get_bonds()
+            ),
+        )
+
+    :class:`.Collapser` optimized construction
+
+    .. moldoc::
+
+        import moldoc.molecule as molecule
+        import stk
+
+        m1 = stk.BuildingBlock('[Ti](Br)(Br)(Br)(Br)(Br)(Br)(Br)(Br)', functional_groups=[stk.BromoFactory()])
+
+        bb1 = stk.BuildingBlock('C(OBr)=[O+]Br', functional_groups=[stk.BromoFactory()])
+
+        bb2 = stk.BuildingBlock('[O+](Br)(Br)(Br)', functional_groups=[stk.BromoFactory()])
+
+        cage = stk.ConstructedMolecule(
+            topology_graph = stk.cage.M6L8L12Cuboctahedron(
+                building_blocks = {
+                    m1:range(0,6),
+                    bb1:range(6,18),
+                    bb2:range(18,26)
+                },
+                optimizer=stk.Collapser(),
+            )
+        )
+
+        moldoc_display_molecule = molecule.Molecule(
+            atoms=(
+                molecule.Atom(
+                    atomic_number=atom.get_atomic_number(),
+                    position=position,
+                ) for atom, position in zip(
+                    cage.get_atoms(),
+                    cage.get_position_matrix(),
+                )
+            ),
+            bonds=(
+                molecule.Bond(
+                    atom1_id=bond.get_atom1().get_id(),
+                    atom2_id=bond.get_atom2().get_id(),
+                    order=(
+                        1
+                        if bond.get_order() == 9
+                        else bond.get_order()
+                    ),
+                ) for bond in cage.get_bonds()
+            ),
+        )
+
+    Metal building blocks with eight functional groups are
+    required for this topology.
+
+    One ligand building blocks with two functional groups and another ligand
+    building block with three functional groups are required for
+    this topology.
+
+    When using a :class:`dict` for the `building_blocks` parameter,
+    as in :ref:`cage-topology-graph-examples`:
+    *Multi-Building Block Cage Construction*, a
+    :class:`.BuildingBlock`, with the following number of functional
+    groups, needs to be assigned to each of the following vertex ids:
+
+        | 8-functional groups: 0  to 5
+        | 2-functional groups: 6  to 17
+        | 3-functional groups: 18 to 25
+
+    See :class:`.Cage` for more details and examples.
+
+    """
+
+    _x = np.sqrt(2) / 2
+    _vertex_prototypes = (
+        # M
+        NonLinearVertex(0, np.array([1.5, 0, 0])),
+        NonLinearVertex(1, np.array([0, 1.5, 0])),
+        NonLinearVertex(2, np.array([-1.5, 0, 0])),
+        NonLinearVertex(3, np.array([0, -1.5, 0])),
+        NonLinearVertex(4, np.array([0, 0, 1.5])),
+        NonLinearVertex(5, np.array([0, 0, -1.5])),
+        # L1
+        LinearVertex(6, np.array([2, 2, 0]), False),
+        LinearVertex(7, np.array([2, -2, 0]), False),
+        LinearVertex(8, np.array([2, 0, 2]), False),
+        LinearVertex(9, np.array([2, 0, -2]), False),
+        LinearVertex(10, np.array([-2, 2, 0]), False),
+        LinearVertex(11, np.array([-2, -2, 0]), False),
+        LinearVertex(12, np.array([-2, 0, 2]), False),
+        LinearVertex(13, np.array([-2, 0, -2]), False),
+        LinearVertex(14, np.array([0, 2, 2]), False),
+        LinearVertex(15, np.array([0, 2, -2]), False),
+        LinearVertex(16, np.array([0, -2, 2]), False),
+        LinearVertex(17, np.array([0, -2, -2]), False),
+        # L2
+        LinearVertex(18, np.array([_x, _x, _x]), False),
+        LinearVertex(19, np.array([-_x, _x, _x]), False),
+        LinearVertex(20, np.array([-_x, -_x, _x]), False),
+        LinearVertex(21, np.array([_x, -_x, _x]), False),
+        LinearVertex(22, np.array([_x, _x, -_x]), False),
+        LinearVertex(23, np.array([-_x, _x, -_x]), False),
+        LinearVertex(24, np.array([-_x, -_x, -_x]), False),
+        LinearVertex(25, np.array([_x, -_x, -_x]), False),
+    )
+
+    _edge_prototypes = (
+        # Outer shell
+        Edge(0, _vertex_prototypes[0], _vertex_prototypes[6]),
+        Edge(1, _vertex_prototypes[0], _vertex_prototypes[7]),
+        Edge(2, _vertex_prototypes[0], _vertex_prototypes[8]),
+        Edge(3, _vertex_prototypes[0], _vertex_prototypes[9]),
+        Edge(4, _vertex_prototypes[1], _vertex_prototypes[6]),
+        Edge(5, _vertex_prototypes[1], _vertex_prototypes[10]),
+        Edge(6, _vertex_prototypes[1], _vertex_prototypes[14]),
+        Edge(7, _vertex_prototypes[1], _vertex_prototypes[15]),
+        Edge(8, _vertex_prototypes[2], _vertex_prototypes[10]),
+        Edge(9, _vertex_prototypes[2], _vertex_prototypes[11]),
+        Edge(10, _vertex_prototypes[2], _vertex_prototypes[12]),
+        Edge(11, _vertex_prototypes[2], _vertex_prototypes[13]),
+        Edge(12, _vertex_prototypes[3], _vertex_prototypes[7]),
+        Edge(13, _vertex_prototypes[3], _vertex_prototypes[11]),
+        Edge(14, _vertex_prototypes[3], _vertex_prototypes[16]),
+        Edge(15, _vertex_prototypes[3], _vertex_prototypes[17]),
+        Edge(16, _vertex_prototypes[4], _vertex_prototypes[8]),
+        Edge(17, _vertex_prototypes[4], _vertex_prototypes[12]),
+        Edge(18, _vertex_prototypes[4], _vertex_prototypes[14]),
+        Edge(19, _vertex_prototypes[4], _vertex_prototypes[16]),
+        Edge(20, _vertex_prototypes[5], _vertex_prototypes[9]),
+        Edge(21, _vertex_prototypes[5], _vertex_prototypes[13]),
+        Edge(22, _vertex_prototypes[5], _vertex_prototypes[15]),
+        Edge(23, _vertex_prototypes[5], _vertex_prototypes[17]),
+        # Inner shell
+        Edge(24, _vertex_prototypes[0], _vertex_prototypes[18]),
+        Edge(25, _vertex_prototypes[0], _vertex_prototypes[21]),
+        Edge(26, _vertex_prototypes[0], _vertex_prototypes[22]),
+        Edge(27, _vertex_prototypes[0], _vertex_prototypes[25]),
+        Edge(28, _vertex_prototypes[1], _vertex_prototypes[18]),
+        Edge(29, _vertex_prototypes[1], _vertex_prototypes[19]),
+        Edge(30, _vertex_prototypes[1], _vertex_prototypes[22]),
+        Edge(31, _vertex_prototypes[1], _vertex_prototypes[23]),
+        Edge(32, _vertex_prototypes[2], _vertex_prototypes[19]),
+        Edge(33, _vertex_prototypes[2], _vertex_prototypes[20]),
+        Edge(34, _vertex_prototypes[2], _vertex_prototypes[23]),
+        Edge(35, _vertex_prototypes[2], _vertex_prototypes[24]),
+        Edge(36, _vertex_prototypes[3], _vertex_prototypes[20]),
+        Edge(37, _vertex_prototypes[3], _vertex_prototypes[21]),
+        Edge(38, _vertex_prototypes[3], _vertex_prototypes[24]),
+        Edge(39, _vertex_prototypes[3], _vertex_prototypes[25]),
+        Edge(40, _vertex_prototypes[4], _vertex_prototypes[18]),
+        Edge(41, _vertex_prototypes[4], _vertex_prototypes[19]),
+        Edge(42, _vertex_prototypes[4], _vertex_prototypes[20]),
+        Edge(43, _vertex_prototypes[4], _vertex_prototypes[21]),
+        Edge(44, _vertex_prototypes[5], _vertex_prototypes[22]),
+        Edge(45, _vertex_prototypes[5], _vertex_prototypes[23]),
+        Edge(46, _vertex_prototypes[5], _vertex_prototypes[24]),
+        Edge(47, _vertex_prototypes[5], _vertex_prototypes[25]),
+    )
+
+    _num_windows = 8
+    _num_window_types = 1

src/stk/cage.py

@@ -22,6 +22,9 @@
 from stk._internal.topology_graphs.cage.m4l8 import M4L8
 from stk._internal.topology_graphs.cage.m6l2l3_prism import M6L2L3Prism
 from stk._internal.topology_graphs.cage.m6l12_cube import M6L12Cube
+from stk._internal.topology_graphs.cage.m6l8l12_cuboctahedron import (
+    M6L8L12Cuboctahedron,
+)
 from stk._internal.topology_graphs.cage.m8l6_cube import M8L6Cube
 from stk._internal.topology_graphs.cage.m12l24 import M12L24
 from stk._internal.topology_graphs.cage.m24l48 import M24L48
@@ -57,6 +60,7 @@
     "M4L6TetrahedronSpacer",
     "M6L2L3Prism",
     "M6L12Cube",
+    "M6L8L12Cuboctahedron",
     "M8L6Cube",
     "M12L24",
     "M24L48",

tests/molecular/molecules/molecule/fixtures/cage/cage.py

@@ -41,6 +41,7 @@
         lazy_fixture("metal_cage_m4l8"),
         lazy_fixture("metal_cage_m6l2l3_prism"),
         lazy_fixture("metal_cage_m6l12_cube"),
+        lazy_fixture("metal_cage_m6l8l12_cuboctahedron"),
         lazy_fixture("metal_cage_m8l6_cube"),
         lazy_fixture("metal_cage_m12l24"),
         lazy_fixture("metal_cage_m24l48"),

tests/molecular/molecules/molecule/fixtures/cage/metal_topologies/__init__.py

@@ -8,6 +8,7 @@
 from .m4l8 import *  # noqa
 from .m6l2l3_prism import *  # noqa
 from .m6l12_cube import *  # noqa
+from .m6l8l12_cuboctahedron import *  # noqa
 from .m8l6_cube import *  # noqa
 from .m12l24 import *  # noqa
 from .m24l48 import *  # noqa

tests/molecular/molecules/molecule/fixtures/cage/metal_topologies/m6l8l12_cuboctahedron.py

@@ -0,0 +1,83 @@
+import pytest
+import stk
+
+from ....case_data import CaseData
+from ...building_blocks import get_linker, get_pd_atom
+
+
+@pytest.fixture(
+    scope="session",
+    params=(
+        lambda name: CaseData(
+            molecule=stk.ConstructedMolecule(
+                topology_graph=stk.cage.M6L8L12Cuboctahedron(
+                    building_blocks={
+                        get_pd_atom(): range(6),
+                        get_linker(): range(6, 18),
+                        get_linker(): range(18, 26),
+                    },
+                    reaction_factory=stk.DativeReactionFactory(
+                        reaction_factory=stk.GenericReactionFactory(
+                            bond_orders={
+                                frozenset(
+                                    {
+                                        stk.GenericFunctionalGroup,
+                                        stk.SingleAtom,
+                                    }
+                                ): 9,
+                            },
+                        ),
+                    ),
+                ),
+            ),
+            smiles=(
+                "[H]C1=[O+][Zr]234567OC([H])=[O+][Zr]89%10%11%12%13O"
+                "C([H])=[O+][Zr]%14%15%16%17%18%19OC([H])=[O+][Hf]%2"
+                "0%21([O+]=C([H])O[Zr]%22%23(O1)(OC([H])=[O+]%14)(OC"
+                "([H])=[O+][Hf]([O+]=C([H])O2)([O+]=C([H])O8)([O+]=C"
+                "([H])O%15)([O+]%223)([O+]49)([O+]%23%16)[O+]%10%17)"
+                "([O+]5%20)[O+]%18%21)([O+]=C([H])O6)([O+]=C([H])O%1"
+                "1)([O+]7%12)[O+]%13%19"
+            ),
+            name=name,
+        ),
+        lambda name: CaseData(
+            molecule=stk.ConstructedMolecule(
+                topology_graph=stk.cage.M6L12Cube(
+                    building_blocks={
+                        get_pd_atom(): range(6),
+                        get_linker(): range(6, 18),
+                        get_linker(): range(18, 26),
+                    },
+                    reaction_factory=stk.DativeReactionFactory(
+                        reaction_factory=stk.GenericReactionFactory(
+                            bond_orders={
+                                frozenset(
+                                    {
+                                        stk.GenericFunctionalGroup,
+                                        stk.SingleAtom,
+                                    }
+                                ): 9,
+                            },
+                        ),
+                    ),
+                    scale_multiplier=1.2,
+                ),
+            ),
+            smiles=(
+                "[H]C1=[O+][Zr]234567OC([H])=[O+][Zr]89%10%11%12%13O"
+                "C([H])=[O+][Zr]%14%15%16%17%18%19OC([H])=[O+][Hf]%2"
+                "0%21([O+]=C([H])O[Zr]%22%23(O1)(OC([H])=[O+]%14)(OC"
+                "([H])=[O+][Hf]([O+]=C([H])O2)([O+]=C([H])O8)([O+]=C"
+                "([H])O%15)([O+]%223)([O+]49)([O+]%23%16)[O+]%10%17)"
+                "([O+]5%20)[O+]%18%21)([O+]=C([H])O6)([O+]=C([H])O%1"
+                "1)([O+]7%12)[O+]%13%19"
+            ),
+            name=name,
+        ),
+    ),
+)
+def metal_cage_m6l8l12_cuboctahedron(request) -> CaseData:
+    return request.param(
+        f"{request.fixturename}{request.param_index}",
+    )