Source code for stk.molecular.topology_graphs.cage.metal_topologies.m12l24

"""
M12L24
======

"""

from ...topology_graph import Edge
from ..cage import Cage
from ..vertices import LinearVertex, NonLinearVertex


[docs]class M12L24(Cage): """ Represents a cage topology graph. .. moldoc:: import moldoc.molecule as molecule import stk bb1 = stk.BuildingBlock( smiles='[Pd+2]', functional_groups=( stk.SingleAtom(stk.Pd(0, charge=2)) for i in range(4) ), position_matrix=[[0, 0, 0]], ) bb2 = stk.BuildingBlock( smiles=( 'C1=NC=CC(C2=CC=CC(C3=C' 'C=NC=C3)=C2)=C1' ), functional_groups=[ stk.SmartsFunctionalGroupFactory( smarts='[#6]~[#7X2]~[#6]', bonders=(1, ), deleters=(), ), ], ) cage = stk.ConstructedMolecule( topology_graph=stk.cage.M12L24( building_blocks=(bb1, bb2), ), ) 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 four functional groups are required for this topology. Ligand building blocks with two 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: | 4-functional groups: 0 to 11 | 2-functional groups: 12 to 35 See :class:`.Cage` for more details and examples. """ _vertex_prototypes = ( NonLinearVertex(0, [1, 0, 0]), NonLinearVertex(1, [-1, 0, 0]), NonLinearVertex(2, [0, 1, 0]), NonLinearVertex(3, [0, -1, 0]), NonLinearVertex(4, [0.5, 0.5, 0.707]), NonLinearVertex(5, [0.5, -0.5, 0.707]), NonLinearVertex(6, [-0.5, 0.5, 0.707]), NonLinearVertex(7, [-0.5, -0.5, 0.707]), NonLinearVertex(8, [0.5, 0.5, -0.707]), NonLinearVertex(9, [0.5, -0.5, -0.707]), NonLinearVertex(10, [-0.5, 0.5, -0.707]), NonLinearVertex(11, [-0.5, -0.5, -0.707]), LinearVertex(12, [0.9, 0.31, 0.31], False), LinearVertex(13, [0.9, 0.31, -0.31], False), LinearVertex(14, [0.9, -0.31, 0.31], False), LinearVertex(15, [0.9, -0.31, -0.31], False), LinearVertex(16, [-0.9, 0.31, 0.31], False), LinearVertex(17, [-0.9, 0.31, -0.31], False), LinearVertex(18, [-0.9, -0.31, 0.31], False), LinearVertex(19, [-0.9, -0.31, -0.31], False), LinearVertex(20, [0.31, 0.9, 0.31], False), LinearVertex(21, [0.31, 0.9, -0.31], False), LinearVertex(22, [-0.31, 0.9, 0.31], False), LinearVertex(23, [-0.31, 0.9, -0.31], False), LinearVertex(24, [0.31, -0.9, 0.31], False), LinearVertex(25, [0.31, -0.9, -0.31], False), LinearVertex(26, [-0.31, -0.9, 0.31], False), LinearVertex(27, [-0.31, -0.9, -0.31], False), LinearVertex(28, [0.58, 0, 0.82], False), LinearVertex(29, [-0.58, 0, 0.82], False), LinearVertex(30, [0, 0.58, 0.82], False), LinearVertex(31, [0, -0.58, 0.82], False), LinearVertex(32, [0.58, 0, -0.82], False), LinearVertex(33, [-0.58, 0, -0.82], False), LinearVertex(34, [0, 0.58, -0.82], False), LinearVertex(35, [0, -0.58, -0.82], False), ) _edge_prototypes = ( Edge(0, _vertex_prototypes[0], _vertex_prototypes[12]), Edge(1, _vertex_prototypes[0], _vertex_prototypes[13]), Edge(2, _vertex_prototypes[0], _vertex_prototypes[14]), Edge(3, _vertex_prototypes[0], _vertex_prototypes[15]), Edge(4, _vertex_prototypes[1], _vertex_prototypes[16]), Edge(5, _vertex_prototypes[1], _vertex_prototypes[17]), Edge(6, _vertex_prototypes[1], _vertex_prototypes[18]), Edge(7, _vertex_prototypes[1], _vertex_prototypes[19]), Edge(8, _vertex_prototypes[2], _vertex_prototypes[20]), Edge(9, _vertex_prototypes[2], _vertex_prototypes[21]), Edge(10, _vertex_prototypes[2], _vertex_prototypes[22]), Edge(11, _vertex_prototypes[2], _vertex_prototypes[23]), Edge(12, _vertex_prototypes[3], _vertex_prototypes[24]), Edge(13, _vertex_prototypes[3], _vertex_prototypes[25]), Edge(14, _vertex_prototypes[3], _vertex_prototypes[26]), Edge(15, _vertex_prototypes[3], _vertex_prototypes[27]), Edge(16, _vertex_prototypes[4], _vertex_prototypes[28]), Edge(17, _vertex_prototypes[4], _vertex_prototypes[30]), Edge(18, _vertex_prototypes[4], _vertex_prototypes[12]), Edge(19, _vertex_prototypes[4], _vertex_prototypes[20]), Edge(20, _vertex_prototypes[5], _vertex_prototypes[14]), Edge(21, _vertex_prototypes[5], _vertex_prototypes[24]), Edge(22, _vertex_prototypes[5], _vertex_prototypes[28]), Edge(23, _vertex_prototypes[5], _vertex_prototypes[31]), Edge(24, _vertex_prototypes[6], _vertex_prototypes[16]), Edge(25, _vertex_prototypes[6], _vertex_prototypes[29]), Edge(26, _vertex_prototypes[6], _vertex_prototypes[30]), Edge(27, _vertex_prototypes[6], _vertex_prototypes[22]), Edge(28, _vertex_prototypes[7], _vertex_prototypes[18]), Edge(29, _vertex_prototypes[7], _vertex_prototypes[26]), Edge(30, _vertex_prototypes[7], _vertex_prototypes[31]), Edge(31, _vertex_prototypes[7], _vertex_prototypes[29]), Edge(32, _vertex_prototypes[8], _vertex_prototypes[13]), Edge(33, _vertex_prototypes[8], _vertex_prototypes[32]), Edge(34, _vertex_prototypes[8], _vertex_prototypes[34]), Edge(35, _vertex_prototypes[8], _vertex_prototypes[21]), Edge(36, _vertex_prototypes[9], _vertex_prototypes[15]), Edge(37, _vertex_prototypes[9], _vertex_prototypes[32]), Edge(38, _vertex_prototypes[9], _vertex_prototypes[35]), Edge(39, _vertex_prototypes[9], _vertex_prototypes[25]), Edge(40, _vertex_prototypes[10], _vertex_prototypes[17]), Edge(41, _vertex_prototypes[10], _vertex_prototypes[23]), Edge(42, _vertex_prototypes[10], _vertex_prototypes[34]), Edge(43, _vertex_prototypes[10], _vertex_prototypes[33]), Edge(44, _vertex_prototypes[11], _vertex_prototypes[19]), Edge(45, _vertex_prototypes[11], _vertex_prototypes[33]), Edge(46, _vertex_prototypes[11], _vertex_prototypes[27]), Edge(47, _vertex_prototypes[11], _vertex_prototypes[35]), ) _num_windows = 14 _num_window_types = 2