Source code for stk.molecular.topology_graphs.cage.metal_topologies.m3l6

"""
M3L6
====

"""

import numpy as np

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


[docs]class M3L6(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(4) ), position_matrix=[[0, 0, 0]], ) bb2 = stk.BuildingBlock( smiles=( 'C1=NC=CC(C2=CC=CC(C3=C' 'C=NC=C3)=C2)=C1' ), functional_groups=[ stk.SmartsFunctionalGroupFactory( smarts='[#6]~[#7X2]~[#6]', bonders=(1, ), deleters=(), ), ], ) cage = stk.ConstructedMolecule( topology_graph=stk.cage.M3L6( building_blocks=(bb1, 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(4) ), position_matrix=[[0, 0, 0]], ) bb2 = stk.BuildingBlock( smiles=( 'C1=NC=CC(C2=CC=CC(C3=C' 'C=NC=C3)=C2)=C1' ), functional_groups=[ stk.SmartsFunctionalGroupFactory( smarts='[#6]~[#7X2]~[#6]', bonders=(1, ), deleters=(), ), ], ) cage = stk.ConstructedMolecule( topology_graph=stk.cage.M3L6( building_blocks=(bb1, 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() ), ) Metal building blocks with four functional groups are required for this topology. Ligand building blocks with two 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: | 4-functional groups: 0 to 2 | 2-functional groups: 3 to 8 See :class:`.Cage` for more details and examples. """ _R, _theta = 1, 0 _vertex_prototypes = ( NonLinearVertex( id=0, position=[_R*np.cos(_theta), _R*np.sin(_theta), 0] ), NonLinearVertex( id=1, position=[ _R*np.cos(_theta+(4*np.pi/3)), _R*np.sin(_theta+(4*np.pi/3)), 0 ] ), NonLinearVertex( id=2, position=[ _R*np.cos(_theta+(2*np.pi/3)), _R*np.sin(_theta+(2*np.pi/3)), 0 ] ), LinearVertex( id=3, position=[ _R*np.cos((_theta+np.pi/4)), _R*np.sin((_theta+np.pi/4)), 0.5 ], use_neighbor_placement=False ), LinearVertex( id=4, position=[ _R*np.cos((_theta+1*np.pi/3)), _R*np.sin((_theta+1*np.pi/3)), -0.5 ], use_neighbor_placement=False ), LinearVertex( id=5, position=[ _R*np.cos((_theta+1*np.pi/3)+(4*np.pi/3)), _R*np.sin((_theta+1*np.pi/3)+(4*np.pi/3)), 0.5 ], use_neighbor_placement=False ), LinearVertex( id=6, position=[ _R*np.cos((_theta+1*np.pi/3)+(4*np.pi/3)), _R*np.sin((_theta+1*np.pi/3)+(4*np.pi/3)), -0.5 ], use_neighbor_placement=False ), LinearVertex( id=7, position=[ _R*np.cos((_theta+1*np.pi/3)+(2*np.pi/3)), _R*np.sin((_theta+1*np.pi/3)+(2*np.pi/3)), 0.5 ], use_neighbor_placement=False ), LinearVertex( id=8, position=[ _R*np.cos((_theta+1*np.pi/3)+(2*np.pi/3)), _R*np.sin((_theta+1*np.pi/3)+(2*np.pi/3)), -0.5 ], use_neighbor_placement=False ), ) _edge_prototypes = ( Edge(0, _vertex_prototypes[0], _vertex_prototypes[3]), Edge(1, _vertex_prototypes[0], _vertex_prototypes[4]), Edge(2, _vertex_prototypes[0], _vertex_prototypes[5]), Edge(3, _vertex_prototypes[0], _vertex_prototypes[6]), Edge(4, _vertex_prototypes[1], _vertex_prototypes[5]), Edge(5, _vertex_prototypes[1], _vertex_prototypes[6]), Edge(6, _vertex_prototypes[1], _vertex_prototypes[7]), Edge(7, _vertex_prototypes[1], _vertex_prototypes[8]), Edge(8, _vertex_prototypes[2], _vertex_prototypes[3]), Edge(9, _vertex_prototypes[2], _vertex_prototypes[4]), Edge(10, _vertex_prototypes[2], _vertex_prototypes[7]), Edge(11, _vertex_prototypes[2], _vertex_prototypes[8]), ) _num_windows = 2 _num_window_types = 1