Source code for stk.molecular.topology_graphs.cage.metal_topologies.m4l4_tetrahedron

"""
M4L4 Tetrahedron
================

"""

import numpy as np

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


[docs]class M4L4Tetrahedron(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()], ) cage = stk.ConstructedMolecule( topology_graph=stk.cage.M4L4Tetrahedron( building_blocks={ iron_oct_delta: (0, 1, 2, 3), bb3: (4, 5, 6, 7), }, ), ) 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:`.MCHammer` 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()], ) cage = stk.ConstructedMolecule( topology_graph=stk.cage.M4L4Tetrahedron( building_blocks={ iron_oct_delta: (0, 1, 2, 3), bb3: (4, 5, 6, 7), }, optimizer=stk.MCHammer(), ), ) 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() ), ) Building blocks 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: | 3-functional groups (metal): 0 to 3 | 3-functional groups (linker): 4 to 7 See :class:`.Cage` for more details and examples. """ _non_linears = ( NonLinearVertex(0, [0, 0, np.sqrt(6)/2]), NonLinearVertex(1, [-1, -np.sqrt(3)/3, -np.sqrt(6)/6]), NonLinearVertex(2, [1, -np.sqrt(3)/3, -np.sqrt(6)/6]), NonLinearVertex(3, [0, 2*np.sqrt(3)/3, -np.sqrt(6)/6]), ) _vertex_prototypes = ( *_non_linears, NonLinearVertex.init_at_center( id=4, vertices=( _non_linears[0], _non_linears[1], _non_linears[2], ), ), NonLinearVertex.init_at_center( id=5, vertices=( _non_linears[0], _non_linears[1], _non_linears[3], ), ), NonLinearVertex.init_at_center( id=6, vertices=( _non_linears[0], _non_linears[2], _non_linears[3], ), ), NonLinearVertex.init_at_center( id=7, vertices=( _non_linears[1], _non_linears[2], _non_linears[3], ), ), ) _edge_prototypes = ( Edge(0, _vertex_prototypes[0], _vertex_prototypes[4]), Edge(1, _vertex_prototypes[0], _vertex_prototypes[5]), Edge(2, _vertex_prototypes[0], _vertex_prototypes[6]), Edge(3, _vertex_prototypes[1], _vertex_prototypes[4]), Edge(4, _vertex_prototypes[1], _vertex_prototypes[5]), Edge(5, _vertex_prototypes[1], _vertex_prototypes[7]), Edge(6, _vertex_prototypes[2], _vertex_prototypes[4]), Edge(7, _vertex_prototypes[2], _vertex_prototypes[6]), Edge(8, _vertex_prototypes[2], _vertex_prototypes[7]), Edge(9, _vertex_prototypes[3], _vertex_prototypes[5]), Edge(10, _vertex_prototypes[3], _vertex_prototypes[6]), Edge(11, _vertex_prototypes[3], _vertex_prototypes[7]), ) _num_windows = 4 _num_window_types = 1