Source code for stk.molecular.topology_graphs.cage.metal_topologies.m6l2l3_prism

"""
M6L2L3 Prism
============

"""

import numpy as np

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


[docs]class M6L2L3Prism(Cage): """ Represents a cage topology graph. Unoptimized construction .. moldoc:: import moldoc.molecule as molecule import stk iron_atom = stk.BuildingBlock( smiles='[Fe+2]', functional_groups=( stk.SingleAtom(stk.Fe(0, charge=2)) for i in range(6) ), position_matrix=[[0, 0, 0]], ) bb2 = stk.BuildingBlock( smiles='C1=NC(C=NBr)=CC=C1', functional_groups=[ stk.SmartsFunctionalGroupFactory( smarts='[#6]~[#7X2]~[#35]', bonders=(1, ), deleters=(), ), stk.SmartsFunctionalGroupFactory( smarts='[#6]~[#7X2]~[#6]', bonders=(1, ), deleters=(), ), ], ) complex = stk.ConstructedMolecule( topology_graph=stk.metal_complex.OctahedralDelta( metals=iron_atom, ligands=bb2, optimizer=stk.MCHammer(), ), ) # Assign Bromo functional groups to the metal complex. iron_oct_delta = stk.BuildingBlock.init_from_molecule( molecule=complex, functional_groups=[stk.BromoFactory()], ) # Define building blocks. bb3 = stk.BuildingBlock( smiles=( 'C1=C(C=C(C=C1Br)Br)Br' ), functional_groups=[stk.BromoFactory()], ) bb4 = stk.BuildingBlock( smiles=( 'C1=CC(=CC=C1C2=CC(=C(C=C2C3=CC=C(C=C3)Br)C4=CC=C(C=C' '4)Br)C5=CC=C(C=C5)Br)Br' ), functional_groups=[stk.BromoFactory()], ) cage = stk.ConstructedMolecule( topology_graph=stk.cage.M6L2L3Prism( building_blocks={ iron_oct_delta: range(6), bb3: (6, 7), bb4: range(8, 11), }, ), ) 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 iron_atom = stk.BuildingBlock( smiles='[Fe+2]', functional_groups=( stk.SingleAtom(stk.Fe(0, charge=2)) for i in range(6) ), position_matrix=[[0, 0, 0]], ) bb2 = stk.BuildingBlock( smiles='C1=NC(C=NBr)=CC=C1', functional_groups=[ stk.SmartsFunctionalGroupFactory( smarts='[#6]~[#7X2]~[#35]', bonders=(1, ), deleters=(), ), stk.SmartsFunctionalGroupFactory( smarts='[#6]~[#7X2]~[#6]', bonders=(1, ), deleters=(), ), ], ) complex = stk.ConstructedMolecule( topology_graph=stk.metal_complex.OctahedralDelta( metals=iron_atom, ligands=bb2, optimizer=stk.MCHammer(), ), ) # Assign Bromo functional groups to the metal complex. iron_oct_delta = stk.BuildingBlock.init_from_molecule( molecule=complex, functional_groups=[stk.BromoFactory()], ) # Define building blocks. bb3 = stk.BuildingBlock( smiles=( 'C1=C(C=C(C=C1Br)Br)Br' ), functional_groups=[stk.BromoFactory()], ) bb4 = stk.BuildingBlock( smiles=( 'C1=CC(=CC=C1C2=CC(=C(C=C2C3=CC=C(C=C3)Br)C4=CC=C(C=C' '4)Br)C5=CC=C(C=C5)Br)Br' ), functional_groups=[stk.BromoFactory()], ) cage = stk.ConstructedMolecule( topology_graph=stk.cage.M6L2L3Prism( building_blocks={ iron_oct_delta: range(6), bb3: (6, 7), bb4: range(8, 11), }, 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 three functional groups are required for this topology. Ligand building blocks with three and four functional groups are required for ligand type A and B, respectively, on 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: | 3-functional groups (metal): 0 to 5 | 3-functional groups (ligand A): 6, 7 | 4-functional groups (ligand B): 8 to 10 See :class:`.Cage` for more details and examples. """ _non_linears = ( NonLinearVertex(0, [-1, -1 / np.sqrt(3), 1]), NonLinearVertex(1, [1, -1 / np.sqrt(3), 1]), NonLinearVertex(2, [0, 2 / np.sqrt(3), 1]), NonLinearVertex(3, [-1, -1 / np.sqrt(3), -1]), NonLinearVertex(4, [1, -1 / np.sqrt(3), -1]), NonLinearVertex(5, [0, 2 / np.sqrt(3), -1]), ) _vertex_prototypes = ( *_non_linears, NonLinearVertex.init_at_center( id=6, vertices=( _non_linears[0], _non_linears[1], _non_linears[2], ), ), NonLinearVertex.init_at_center( id=7, vertices=( _non_linears[3], _non_linears[4], _non_linears[5], ), ), NonLinearVertex.init_at_center( id=8, vertices=( _non_linears[0], _non_linears[1], _non_linears[3], _non_linears[4], ), ), NonLinearVertex.init_at_center( id=9, vertices=( _non_linears[1], _non_linears[2], _non_linears[4], _non_linears[5], ), ), NonLinearVertex.init_at_center( id=10, vertices=( _non_linears[2], _non_linears[0], _non_linears[5], _non_linears[3], ), ), ) _edge_prototypes = ( Edge(0, _vertex_prototypes[0], _vertex_prototypes[6]), Edge(1, _vertex_prototypes[0], _vertex_prototypes[8]), Edge(2, _vertex_prototypes[0], _vertex_prototypes[10]), Edge(3, _vertex_prototypes[1], _vertex_prototypes[6]), Edge(4, _vertex_prototypes[1], _vertex_prototypes[8]), Edge(5, _vertex_prototypes[1], _vertex_prototypes[9]), Edge(6, _vertex_prototypes[2], _vertex_prototypes[6]), Edge(7, _vertex_prototypes[2], _vertex_prototypes[9]), Edge(8, _vertex_prototypes[2], _vertex_prototypes[10]), Edge(9, _vertex_prototypes[3], _vertex_prototypes[7]), Edge(10, _vertex_prototypes[3], _vertex_prototypes[8]), Edge(11, _vertex_prototypes[3], _vertex_prototypes[10]), Edge(12, _vertex_prototypes[4], _vertex_prototypes[7]), Edge(13, _vertex_prototypes[4], _vertex_prototypes[8]), Edge(14, _vertex_prototypes[4], _vertex_prototypes[9]), Edge(15, _vertex_prototypes[5], _vertex_prototypes[7]), Edge(16, _vertex_prototypes[5], _vertex_prototypes[9]), Edge(17, _vertex_prototypes[5], _vertex_prototypes[10]), ) _num_windows = 4 _num_window_types = 1