Source code for stk.molecular.topology_graphs.cage.metal_topologies.m4l4_square

"""
M4L4 Square
===========

"""

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


[docs]class M4L4Square(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.M4L4Square( 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.M4L4Square( 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:`.M4L4Square`. 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, 3)} if isinstance(linkers, dict): linkers_dict = linkers else: linkers_dict = {linkers: (4, 5, 6, 7)} 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, )
_vertex_prototypes = ( AngledVertex(0, [1, 1, 0]), AngledVertex(1, [1, -1, 0]), AngledVertex(2, [-1, -1, 0]), AngledVertex(3, [-1, 1, 0]), LinearVertex(4, [1, 0, 0], False), LinearVertex(5, [0, -1, 0], False), LinearVertex(6, [-1, 0, 0], False), LinearVertex(7, [0, 1, 0], False), ) _edge_prototypes = ( Edge(0, _vertex_prototypes[0], _vertex_prototypes[4]), Edge(1, _vertex_prototypes[1], _vertex_prototypes[4]), Edge(2, _vertex_prototypes[1], _vertex_prototypes[5]), Edge(3, _vertex_prototypes[2], _vertex_prototypes[5]), Edge(4, _vertex_prototypes[2], _vertex_prototypes[6]), Edge(5, _vertex_prototypes[3], _vertex_prototypes[6]), Edge(6, _vertex_prototypes[3], _vertex_prototypes[7]), Edge(7, _vertex_prototypes[0], _vertex_prototypes[7]), ) _num_windows = 1 _num_window_types = 1