Source code for stk.molecular.topology_graphs.cof.square

"""
Square
======

"""

import numpy as np

from ..topology_graph import Edge
from .cof import Cof
from .vertices import LinearVertex, NonLinearVertex


[docs]class Square(Cof): """ Represents a sqaure COF topology graph. Unoptimized construction .. moldoc:: import moldoc.molecule as molecule import stk cof = stk.ConstructedMolecule( topology_graph=stk.cof.PeriodicSquare( building_blocks=( stk.BuildingBlock( smiles='BrCC(Br)', functional_groups=[stk.BromoFactory()], ), stk.BuildingBlock( smiles='BrC1=C(Br)C(Br)=C1Br', functional_groups=[stk.BromoFactory()], ), ), lattice_size=(3, 3, 1), ), ) moldoc_display_molecule = molecule.Molecule( atoms=( molecule.Atom( atomic_number=atom.get_atomic_number(), position=position, ) for atom, position in zip( cof.get_atoms(), cof.get_position_matrix(), ) ), bonds=( molecule.Bond( atom1_id=bond.get_atom1().get_id(), atom2_id=bond.get_atom2().get_id(), order=bond.get_order(), ) for bond in cof.get_bonds() if all(p == 0 for p in bond.get_periodicity()) ), ) ``Collapser(scale_steps=False)`` optimized construction .. moldoc:: import moldoc.molecule as molecule import stk cof = stk.ConstructedMolecule( topology_graph=stk.cof.PeriodicSquare( building_blocks=( stk.BuildingBlock( smiles='BrCC(Br)', functional_groups=[stk.BromoFactory()], ), stk.BuildingBlock( smiles='BrC1=C(Br)C(Br)=C1Br', functional_groups=[stk.BromoFactory()], ), ), lattice_size=(3, 3, 1), optimizer=stk.Collapser(scale_steps=False), ), ) moldoc_display_molecule = molecule.Molecule( atoms=( molecule.Atom( atomic_number=atom.get_atomic_number(), position=position, ) for atom, position in zip( cof.get_atoms(), cof.get_position_matrix(), ) ), bonds=( molecule.Bond( atom1_id=bond.get_atom1().get_id(), atom2_id=bond.get_atom2().get_id(), order=bond.get_order(), ) for bond in cof.get_bonds() if all(p == 0 for p in bond.get_periodicity()) ), ) Building blocks with four and two functional groups are required for this topology graph. When using a :class:`dict` for the `building_blocks` parameter, as in :ref:`cof-topology-graph-examples`: *Multi-Building Block COF 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 | 2-functional groups: 1 to 2 See :class:`.Cof` for more details and examples. """ _lattice_constants = _a, _b, _c = ( np.array([1., 0., 0.]), np.array([0., 1., 0.]), np.array([0., 0., 1.]) ) _non_linears = ( NonLinearVertex(0, (0.5)*_a + (0.5)*_b + (0.5)*_c), ) _vertex_prototypes = ( *_non_linears, LinearVertex.init_at_shifted_center( id=1, vertices=(_non_linears[0], _non_linears[0]), cell_shifts=((0, 0, 0), (1, 0, 0)), lattice_constants=_lattice_constants, ), LinearVertex.init_at_shifted_center( id=2, vertices=(_non_linears[0], _non_linears[0]), cell_shifts=((0, 0, 0), (0, 1, 0)), lattice_constants=_lattice_constants, ), ) _edge_prototypes = ( Edge(0, _vertex_prototypes[1], _vertex_prototypes[0]), Edge( id=1, vertex1=_vertex_prototypes[1], vertex2=_vertex_prototypes[0], periodicity=(1, 0, 0), ), Edge(2, _vertex_prototypes[2], _vertex_prototypes[0]), Edge( id=3, vertex1=_vertex_prototypes[2], vertex2=_vertex_prototypes[0], periodicity=(0, 1, 0), ), )