Source code for stk.molecular.topology_graphs.cage.metal_topologies.m3l3_triangle

"""
M3L3 Triangle
=============

"""

import numpy as np

from ....reactions import GenericReactionFactory
from ...topology_graph import Edge, NullOptimizer
from ..cage import Cage
from ..vertices import AngledVertex, LinearVertex


[docs]class M3L3Triangle(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(2) ), position_matrix=[[0, 0, 0]], ) bb2 = stk.BuildingBlock( smiles=( 'C1=CC(=CC=C1C2=CC=NC=C2)C3=CC=NC=C3' ), functional_groups=[ stk.SmartsFunctionalGroupFactory( smarts='[#6]~[#7X2]~[#6]', bonders=(1, ), deleters=(), ), ], ) cage = stk.ConstructedMolecule( topology_graph=stk.cage.M3L3Triangle( corners=bb1, linkers=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:`.MCHammer` 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(2) ), position_matrix=[[0, 0, 0]], ) bb2 = stk.BuildingBlock( smiles=( 'C1=CC(=CC=C1C2=CC=NC=C2)C3=CC=NC=C3' ), functional_groups=[ stk.SmartsFunctionalGroupFactory( smarts='[#6]~[#7X2]~[#6]', bonders=(1, ), deleters=(), ), ], ) cage = stk.ConstructedMolecule( topology_graph=stk.cage.M3L3Triangle( corners=bb1, linkers=bb2, 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() ), ) Both `corner` and `linker` vertices require building blocks with two functional groups for this topology. This class replaces the `building_blocks` parameter with the `corner` and `linker` parameters. See :class:`.Cage` for more details and examples. """
[docs] def __init__( self, corners, linkers, vertex_alignments=None, reaction_factory=GenericReactionFactory(), num_processes=1, optimizer=NullOptimizer(), ): """ Initialize a :class:`.M3L3Triangle`. Parameters ---------- corners : :class:`dict` or :class:`.BuildingBlock` Can be a :class:`dict` which maps the :class:`.BuildingBlock` instances to the ids of the vertices it should be placed on. Can also be a :class:`.BuildingBlock` instance, which should be placed on all corner vertices on the topology graph. linkers : :class:`dict` or :class:`.BuildingBlock` Can be a :class:`dict` which maps the :class:`.BuildingBlock` instances to the ids of the vertices it should be placed on. Can also be a :class:`.BuildingBlock` instance, which should be placed on all linker vertices on the topology graph. vertex_alignments : :class:`dict`, optional A mapping from the id of a :class:`.Vertex` to an :class:`.Edge` connected to it. The :class:`.Edge` is used to align the first :class:`.FunctionalGroup` of a :class:`.BuildingBlock` placed on that vertex. Only vertices which need to have their default edge changed need to be present in the :class:`dict`. If ``None`` then the default edge is used for each vertex. Changing which :class:`.Edge` is used will mean that the topology graph represents different structural isomers. The edge is referred to by a number between ``0`` (inclusive) and the number of edges the vertex is connected to (exclusive). reaction_factory : :class:`.ReactionFactory`, optional The reaction factory to use for creating bonds between building blocks. num_processes : :class:`int`, optional The number of parallel processes to create during :meth:`construct`. optimizer : :class:`.Optimizer`, optional Used to optimize the structure of the constructed molecule. """ if isinstance(corners, dict): building_blocks = corners else: building_blocks = {corners: (0, 1, 2)} if isinstance(linkers, dict): linkers_dict = linkers else: linkers_dict = {linkers: (3, 4, 5)} building_blocks.update( (building_block, vertices) for building_block, vertices in linkers_dict.items() ) super().__init__( building_blocks, vertex_alignments=vertex_alignments, reaction_factory=reaction_factory, num_processes=num_processes, optimizer=optimizer, )
_x = 2*np.sqrt(3)/4 _y = 2 _angled_vertices = ( AngledVertex(0, [0, _x, 0]), AngledVertex(1, [_y/2, -_x, 0]), AngledVertex(2, [-_y/2, -_x, 0]), ) _vertex_prototypes = ( *_angled_vertices, LinearVertex.init_at_center( id=3, vertices=(_angled_vertices[0], _angled_vertices[1]), ), LinearVertex.init_at_center( id=4, vertices=(_angled_vertices[1], _angled_vertices[2]), ), LinearVertex.init_at_center( id=5, vertices=(_angled_vertices[2], _angled_vertices[0]), ), ) _edge_prototypes = ( Edge(0, _vertex_prototypes[0], _vertex_prototypes[3]), Edge(1, _vertex_prototypes[1], _vertex_prototypes[3]), Edge(2, _vertex_prototypes[1], _vertex_prototypes[4]), Edge(3, _vertex_prototypes[2], _vertex_prototypes[4]), Edge(4, _vertex_prototypes[2], _vertex_prototypes[5]), Edge(5, _vertex_prototypes[0], _vertex_prototypes[5]), ) _num_windows = 1 _num_window_types = 1