"""
Twenty Plus Thirty
==================
"""
import numpy as np
from stk._internal.topology_graphs.edge import Edge
from .cage import Cage
from .vertices import LinearVertex, NonLinearVertex
[docs]
class TwentyPlusThirty(Cage):
"""
Represents a cage topology graph.
.. moldoc::
import moldoc.molecule as molecule
import stk
bb1 = stk.BuildingBlock(
smiles='BrCCBr',
functional_groups=[stk.BromoFactory()],
)
bb2 = stk.BuildingBlock(
smiles='Brc1cc(Br)cc(Br)c1',
functional_groups=[stk.BromoFactory()],
)
cage = stk.ConstructedMolecule(
topology_graph=stk.cage.TwentyPlusThirty((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()
),
)
Nonlinear building blocks with three 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:
| 3-functional groups: 0 to 19
| 2-functional groups: 20 to 49
See :class:`.Cage` for more details and examples.
"""
# Source: http://tinyurl.com/h2dl949
_phi = (1 + np.sqrt(5)) / 2
_x = 1.5
_non_linears = (
NonLinearVertex(0, np.array([_x * _phi, 0.0, _x / _phi])),
NonLinearVertex(1, np.array([_x * -_phi, 0.0, _x / _phi])),
NonLinearVertex(2, np.array([_x * -_phi, 0.0, _x / -_phi])),
NonLinearVertex(3, np.array([_x * _phi, 0.0, _x / -_phi])),
NonLinearVertex(4, np.array([_x / _phi, _x * _phi, 0.0])),
NonLinearVertex(5, np.array([_x / _phi, _x * -_phi, 0.0])),
NonLinearVertex(6, np.array([_x / -_phi, _x * -_phi, 0.0])),
NonLinearVertex(7, np.array([_x / -_phi, _x * _phi, 0.0])),
NonLinearVertex(8, np.array([0.0, _x / _phi, _x * _phi])),
NonLinearVertex(9, np.array([0.0, _x / _phi, _x * -_phi])),
NonLinearVertex(10, np.array([0.0, _x / -_phi, _x * -_phi])),
NonLinearVertex(11, np.array([0.0, _x / -_phi, _x * _phi])),
NonLinearVertex(12, np.array([_x, _x, _x])),
NonLinearVertex(13, np.array([_x, -_x, _x])),
NonLinearVertex(14, np.array([-_x, -_x, _x])),
NonLinearVertex(15, np.array([-_x, _x, _x])),
NonLinearVertex(16, np.array([-_x, _x, -_x])),
NonLinearVertex(17, np.array([_x, _x, -_x])),
NonLinearVertex(18, np.array([_x, -_x, -_x])),
NonLinearVertex(19, np.array([-_x, -_x, -_x])),
)
_vertex_prototypes = (
*_non_linears,
LinearVertex.init_at_center(
id=20,
vertices=(_non_linears[0], _non_linears[13]),
),
LinearVertex.init_at_center(
id=21,
vertices=(_non_linears[0], _non_linears[12]),
),
LinearVertex.init_at_center(
id=22,
vertices=(_non_linears[0], _non_linears[3]),
),
LinearVertex.init_at_center(
id=23,
vertices=(_non_linears[1], _non_linears[14]),
),
LinearVertex.init_at_center(
id=24,
vertices=(_non_linears[1], _non_linears[15]),
),
LinearVertex.init_at_center(
id=25,
vertices=(_non_linears[1], _non_linears[2]),
),
LinearVertex.init_at_center(
id=26,
vertices=(_non_linears[2], _non_linears[19]),
),
LinearVertex.init_at_center(
id=27,
vertices=(_non_linears[2], _non_linears[16]),
),
LinearVertex.init_at_center(
id=28,
vertices=(_non_linears[3], _non_linears[18]),
),
LinearVertex.init_at_center(
id=29,
vertices=(_non_linears[3], _non_linears[17]),
),
LinearVertex.init_at_center(
id=30,
vertices=(_non_linears[4], _non_linears[12]),
),
LinearVertex.init_at_center(
id=31,
vertices=(_non_linears[4], _non_linears[7]),
),
LinearVertex.init_at_center(
id=32,
vertices=(_non_linears[4], _non_linears[17]),
),
LinearVertex.init_at_center(
id=33,
vertices=(_non_linears[5], _non_linears[6]),
),
LinearVertex.init_at_center(
id=34,
vertices=(_non_linears[5], _non_linears[18]),
),
LinearVertex.init_at_center(
id=35,
vertices=(_non_linears[5], _non_linears[13]),
),
LinearVertex.init_at_center(
id=36,
vertices=(_non_linears[6], _non_linears[14]),
),
LinearVertex.init_at_center(
id=37,
vertices=(_non_linears[6], _non_linears[19]),
),
LinearVertex.init_at_center(
id=38,
vertices=(_non_linears[7], _non_linears[15]),
),
LinearVertex.init_at_center(
id=39,
vertices=(_non_linears[7], _non_linears[16]),
),
LinearVertex.init_at_center(
id=40,
vertices=(_non_linears[8], _non_linears[11]),
),
LinearVertex.init_at_center(
id=41,
vertices=(_non_linears[8], _non_linears[12]),
),
LinearVertex.init_at_center(
id=42,
vertices=(_non_linears[8], _non_linears[15]),
),
LinearVertex.init_at_center(
id=43,
vertices=(_non_linears[9], _non_linears[10]),
),
LinearVertex.init_at_center(
id=44,
vertices=(_non_linears[9], _non_linears[17]),
),
LinearVertex.init_at_center(
id=45,
vertices=(_non_linears[9], _non_linears[16]),
),
LinearVertex.init_at_center(
id=46,
vertices=(_non_linears[10], _non_linears[18]),
),
LinearVertex.init_at_center(
id=47,
vertices=(_non_linears[10], _non_linears[19]),
),
LinearVertex.init_at_center(
id=48,
vertices=(_non_linears[11], _non_linears[14]),
),
LinearVertex.init_at_center(
id=49, vertices=(_non_linears[11], _non_linears[13])
),
)
_edge_prototypes = (
Edge(0, _vertex_prototypes[20], _vertex_prototypes[0]),
Edge(1, _vertex_prototypes[20], _vertex_prototypes[13]),
Edge(2, _vertex_prototypes[21], _vertex_prototypes[0]),
Edge(3, _vertex_prototypes[21], _vertex_prototypes[12]),
Edge(4, _vertex_prototypes[22], _vertex_prototypes[0]),
Edge(5, _vertex_prototypes[22], _vertex_prototypes[3]),
Edge(6, _vertex_prototypes[23], _vertex_prototypes[1]),
Edge(7, _vertex_prototypes[23], _vertex_prototypes[14]),
Edge(8, _vertex_prototypes[24], _vertex_prototypes[1]),
Edge(9, _vertex_prototypes[24], _vertex_prototypes[15]),
Edge(10, _vertex_prototypes[25], _vertex_prototypes[1]),
Edge(11, _vertex_prototypes[25], _vertex_prototypes[2]),
Edge(12, _vertex_prototypes[26], _vertex_prototypes[2]),
Edge(13, _vertex_prototypes[26], _vertex_prototypes[19]),
Edge(14, _vertex_prototypes[27], _vertex_prototypes[2]),
Edge(15, _vertex_prototypes[27], _vertex_prototypes[16]),
Edge(16, _vertex_prototypes[28], _vertex_prototypes[3]),
Edge(17, _vertex_prototypes[28], _vertex_prototypes[18]),
Edge(18, _vertex_prototypes[29], _vertex_prototypes[3]),
Edge(19, _vertex_prototypes[29], _vertex_prototypes[17]),
Edge(20, _vertex_prototypes[30], _vertex_prototypes[4]),
Edge(21, _vertex_prototypes[30], _vertex_prototypes[12]),
Edge(22, _vertex_prototypes[31], _vertex_prototypes[4]),
Edge(23, _vertex_prototypes[31], _vertex_prototypes[7]),
Edge(24, _vertex_prototypes[32], _vertex_prototypes[4]),
Edge(25, _vertex_prototypes[32], _vertex_prototypes[17]),
Edge(26, _vertex_prototypes[33], _vertex_prototypes[5]),
Edge(27, _vertex_prototypes[33], _vertex_prototypes[6]),
Edge(28, _vertex_prototypes[34], _vertex_prototypes[5]),
Edge(29, _vertex_prototypes[34], _vertex_prototypes[18]),
Edge(30, _vertex_prototypes[35], _vertex_prototypes[5]),
Edge(31, _vertex_prototypes[35], _vertex_prototypes[13]),
Edge(32, _vertex_prototypes[36], _vertex_prototypes[6]),
Edge(33, _vertex_prototypes[36], _vertex_prototypes[14]),
Edge(34, _vertex_prototypes[37], _vertex_prototypes[6]),
Edge(35, _vertex_prototypes[37], _vertex_prototypes[19]),
Edge(36, _vertex_prototypes[38], _vertex_prototypes[7]),
Edge(37, _vertex_prototypes[38], _vertex_prototypes[15]),
Edge(38, _vertex_prototypes[39], _vertex_prototypes[7]),
Edge(39, _vertex_prototypes[39], _vertex_prototypes[16]),
Edge(40, _vertex_prototypes[40], _vertex_prototypes[8]),
Edge(41, _vertex_prototypes[40], _vertex_prototypes[11]),
Edge(42, _vertex_prototypes[41], _vertex_prototypes[8]),
Edge(43, _vertex_prototypes[41], _vertex_prototypes[12]),
Edge(44, _vertex_prototypes[42], _vertex_prototypes[8]),
Edge(45, _vertex_prototypes[42], _vertex_prototypes[15]),
Edge(46, _vertex_prototypes[43], _vertex_prototypes[9]),
Edge(47, _vertex_prototypes[43], _vertex_prototypes[10]),
Edge(48, _vertex_prototypes[44], _vertex_prototypes[9]),
Edge(49, _vertex_prototypes[44], _vertex_prototypes[17]),
Edge(50, _vertex_prototypes[45], _vertex_prototypes[9]),
Edge(51, _vertex_prototypes[45], _vertex_prototypes[16]),
Edge(52, _vertex_prototypes[46], _vertex_prototypes[10]),
Edge(53, _vertex_prototypes[46], _vertex_prototypes[18]),
Edge(54, _vertex_prototypes[47], _vertex_prototypes[10]),
Edge(55, _vertex_prototypes[47], _vertex_prototypes[19]),
Edge(56, _vertex_prototypes[48], _vertex_prototypes[11]),
Edge(57, _vertex_prototypes[48], _vertex_prototypes[14]),
Edge(58, _vertex_prototypes[49], _vertex_prototypes[11]),
Edge(59, _vertex_prototypes[49], _vertex_prototypes[13]),
)
_num_windows = 12
_num_window_types = 1