Source code for stk.molecular.topology_graphs.cage.metal_topologies.m6l12_cube

"""
M6L12 Cube
==========

"""

import numpy as np

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


[docs]class M6L12Cube(Cage): """ Represents a cage topology graph. Unoptimized construction .. 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.M6L12Cube( 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() ), ) :class:`.Collapser` optimized construction .. 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.M6L12Cube( building_blocks=(bb1, bb2), 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 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 5 | 2-functional groups: 6 to 17 See :class:`.Cage` for more details and examples. """ _x = np.sqrt(2) _vertex_prototypes = ( NonLinearVertex(0, [_x, 0, 0]), NonLinearVertex(1, [0, _x, 0]), NonLinearVertex(2, [-_x, 0, 0]), NonLinearVertex(3, [0, -_x, 0]), NonLinearVertex(4, [0, 0, _x]), NonLinearVertex(5, [0, 0, -_x]), LinearVertex(6, [1, 1, 0], False), LinearVertex(7, [1, -1, 0], False), LinearVertex(8, [1, 0, 1], False), LinearVertex(9, [1, 0, -1], False), LinearVertex(10, [-1, 1, 0], False), LinearVertex(11, [-1, -1, 0], False), LinearVertex(12, [-1, 0, 1], False), LinearVertex(13, [-1, 0, -1], False), LinearVertex(14, [0, 1, 1], False), LinearVertex(15, [0, 1, -1], False), LinearVertex(16, [0, -1, 1], False), LinearVertex(17, [0, -1, -1], False), ) _edge_prototypes = ( 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]), ) _num_windows = 8 _num_window_types = 1