"""
Ten Plus Twenty
===============
"""
import numpy as np
from stk._internal.topology_graphs.edge import Edge
from .cage import Cage
from .vertices import LinearVertex, NonLinearVertex
[docs]
class TenPlusTwenty(Cage):
"""
Represents a cage topology graph.
Unoptimized construction
.. moldoc::
import moldoc.molecule as molecule
import stk
bb1 = stk.BuildingBlock(
smiles='BrCCBr',
functional_groups=[stk.BromoFactory()],
)
bb2 = stk.BuildingBlock(
smiles='Brc1c(Br)cc(Br)c(Br)c1',
functional_groups=[stk.BromoFactory()],
)
cage = stk.ConstructedMolecule(
topology_graph=stk.cage.TenPlusTwenty((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=bond.get_order(),
) for bond in cage.get_bonds()
),
)
:class:`.Collapser` optimized construction
.. moldoc::
import moldoc.molecule as molecule
import stk
bb1 = stk.BuildingBlock(
smiles='BrCCBr',
functional_groups=[stk.BromoFactory()],
)
bb2 = stk.BuildingBlock(
smiles='Brc1c(Br)cc(Br)c(Br)c1',
functional_groups=[stk.BromoFactory()],
)
cage = stk.ConstructedMolecule(
topology_graph=stk.cage.TenPlusTwenty(
building_blocks=(bb1, bb2),
optimizer=stk.Collapser(),
),
)
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=bond.get_order(),
) for bond in cage.get_bonds()
),
)
Nonlinear building blocks with four functional groups are
required for this topology.
Linear 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 9
| 2-functional groups: 10 to 29
See :class:`.Cage` for more details and examples.
"""
_x = 1.5
_z = _x / 2
_non_linears = (
NonLinearVertex(0, np.array([-_x, _x, -_z])),
NonLinearVertex(1, np.array([-_x, -_x, -_z])),
NonLinearVertex(2, np.array([_x, _x, -_z])),
NonLinearVertex(3, np.array([_x, -_x, -_z])),
NonLinearVertex(4, np.array([-_x, _x, _z])),
NonLinearVertex(5, np.array([-_x, -_x, _z])),
NonLinearVertex(6, np.array([_x, _x, _z])),
NonLinearVertex(7, np.array([_x, -_x, _z])),
NonLinearVertex(8, np.array([0, 0, _x])),
NonLinearVertex(9, np.array([0, 0, -_x])),
)
_vertex_prototypes = (
*_non_linears,
LinearVertex.init_at_center(
id=10,
vertices=(_non_linears[0], _non_linears[2]),
),
LinearVertex.init_at_center(
id=11,
vertices=(_non_linears[0], _non_linears[1]),
),
LinearVertex.init_at_center(
id=12,
vertices=(_non_linears[1], _non_linears[3]),
),
LinearVertex.init_at_center(
id=13,
vertices=(_non_linears[2], _non_linears[3]),
),
LinearVertex.init_at_center(
id=14,
vertices=(_non_linears[4], _non_linears[6]),
),
LinearVertex.init_at_center(
id=15,
vertices=(_non_linears[4], _non_linears[5]),
),
LinearVertex.init_at_center(
id=16,
vertices=(_non_linears[5], _non_linears[7]),
),
LinearVertex.init_at_center(
id=17,
vertices=(_non_linears[6], _non_linears[7]),
),
LinearVertex.init_at_center(
id=18,
vertices=(_non_linears[0], _non_linears[4]),
),
LinearVertex.init_at_center(
id=19,
vertices=(_non_linears[1], _non_linears[5]),
),
LinearVertex.init_at_center(
id=20,
vertices=(_non_linears[2], _non_linears[6]),
),
LinearVertex.init_at_center(
id=21,
vertices=(_non_linears[3], _non_linears[7]),
),
LinearVertex.init_at_center(
id=22,
vertices=(_non_linears[8], _non_linears[4]),
),
LinearVertex.init_at_center(
id=23,
vertices=(_non_linears[8], _non_linears[5]),
),
LinearVertex.init_at_center(
id=24,
vertices=(_non_linears[8], _non_linears[6]),
),
LinearVertex.init_at_center(
id=25,
vertices=(_non_linears[8], _non_linears[7]),
),
LinearVertex.init_at_center(
id=26,
vertices=(_non_linears[9], _non_linears[0]),
),
LinearVertex.init_at_center(
id=27,
vertices=(_non_linears[9], _non_linears[1]),
),
LinearVertex.init_at_center(
id=28,
vertices=(_non_linears[9], _non_linears[2]),
),
LinearVertex.init_at_center(
id=29,
vertices=(_non_linears[9], _non_linears[3]),
),
)
_edge_prototypes = (
Edge(0, _vertex_prototypes[10], _vertex_prototypes[0]),
Edge(1, _vertex_prototypes[10], _vertex_prototypes[2]),
Edge(2, _vertex_prototypes[11], _vertex_prototypes[0]),
Edge(3, _vertex_prototypes[11], _vertex_prototypes[1]),
Edge(4, _vertex_prototypes[12], _vertex_prototypes[1]),
Edge(5, _vertex_prototypes[12], _vertex_prototypes[3]),
Edge(6, _vertex_prototypes[13], _vertex_prototypes[2]),
Edge(7, _vertex_prototypes[13], _vertex_prototypes[3]),
Edge(8, _vertex_prototypes[14], _vertex_prototypes[4]),
Edge(9, _vertex_prototypes[14], _vertex_prototypes[6]),
Edge(10, _vertex_prototypes[15], _vertex_prototypes[4]),
Edge(11, _vertex_prototypes[15], _vertex_prototypes[5]),
Edge(12, _vertex_prototypes[16], _vertex_prototypes[5]),
Edge(13, _vertex_prototypes[16], _vertex_prototypes[7]),
Edge(14, _vertex_prototypes[17], _vertex_prototypes[6]),
Edge(15, _vertex_prototypes[17], _vertex_prototypes[7]),
Edge(16, _vertex_prototypes[18], _vertex_prototypes[0]),
Edge(17, _vertex_prototypes[18], _vertex_prototypes[4]),
Edge(18, _vertex_prototypes[19], _vertex_prototypes[1]),
Edge(19, _vertex_prototypes[19], _vertex_prototypes[5]),
Edge(20, _vertex_prototypes[20], _vertex_prototypes[2]),
Edge(21, _vertex_prototypes[20], _vertex_prototypes[6]),
Edge(22, _vertex_prototypes[21], _vertex_prototypes[3]),
Edge(23, _vertex_prototypes[21], _vertex_prototypes[7]),
Edge(24, _vertex_prototypes[22], _vertex_prototypes[8]),
Edge(25, _vertex_prototypes[22], _vertex_prototypes[4]),
Edge(26, _vertex_prototypes[23], _vertex_prototypes[8]),
Edge(27, _vertex_prototypes[23], _vertex_prototypes[5]),
Edge(28, _vertex_prototypes[24], _vertex_prototypes[8]),
Edge(29, _vertex_prototypes[24], _vertex_prototypes[6]),
Edge(30, _vertex_prototypes[25], _vertex_prototypes[8]),
Edge(31, _vertex_prototypes[25], _vertex_prototypes[7]),
Edge(32, _vertex_prototypes[26], _vertex_prototypes[9]),
Edge(33, _vertex_prototypes[26], _vertex_prototypes[0]),
Edge(34, _vertex_prototypes[27], _vertex_prototypes[9]),
Edge(35, _vertex_prototypes[27], _vertex_prototypes[1]),
Edge(36, _vertex_prototypes[28], _vertex_prototypes[9]),
Edge(37, _vertex_prototypes[28], _vertex_prototypes[2]),
Edge(38, _vertex_prototypes[29], _vertex_prototypes[9]),
Edge(39, _vertex_prototypes[29], _vertex_prototypes[3]),
)
_num_windows = 12
_num_window_types = 2