"""
M24L48
======
"""
import numpy as np
from stk._internal.topology_graphs.edge import Edge
from .cage import Cage
from .vertices import LinearVertex, NonLinearVertex
[docs]
class M24L48(Cage):
"""
Represents a cage topology graph.
.. 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.M24L48(
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()
),
)
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 23
| 2-functional groups: 24 to 71
See :class:`.Cage` for more details and examples.
"""
_coord1 = 0.621
_coord2 = -0.621
_coord3 = _coord1 - (_coord1 - _coord2) / 2
_coord4 = -1.5
_coord5 = 1.5
_coord6 = _coord5 - (_coord5 - _coord1) / 2
_vertex_prototypes = (
NonLinearVertex(0, np.array([_coord1, _coord1, _coord4])),
NonLinearVertex(1, np.array([_coord1, _coord1, _coord5])),
NonLinearVertex(2, np.array([_coord1, _coord4, _coord2])),
NonLinearVertex(3, np.array([_coord1, _coord5, _coord2])),
NonLinearVertex(4, np.array([_coord1, _coord2, _coord4])),
NonLinearVertex(5, np.array([_coord1, _coord2, _coord5])),
NonLinearVertex(6, np.array([_coord1, _coord4, _coord1])),
NonLinearVertex(7, np.array([_coord1, _coord5, _coord1])),
NonLinearVertex(8, np.array([_coord2, _coord1, _coord4])),
NonLinearVertex(9, np.array([_coord2, _coord1, _coord5])),
NonLinearVertex(10, np.array([_coord2, _coord2, _coord4])),
NonLinearVertex(11, np.array([_coord2, _coord2, _coord5])),
NonLinearVertex(12, np.array([_coord2, _coord4, _coord1])),
NonLinearVertex(13, np.array([_coord2, _coord5, _coord1])),
NonLinearVertex(14, np.array([_coord2, _coord4, _coord2])),
NonLinearVertex(15, np.array([_coord2, _coord5, _coord2])),
NonLinearVertex(16, np.array([_coord4, _coord1, _coord1])),
NonLinearVertex(17, np.array([_coord4, _coord2, _coord1])),
NonLinearVertex(18, np.array([_coord4, _coord2, _coord2])),
NonLinearVertex(19, np.array([_coord4, _coord1, _coord2])),
NonLinearVertex(20, np.array([_coord5, _coord1, _coord1])),
NonLinearVertex(21, np.array([_coord5, _coord2, _coord1])),
NonLinearVertex(22, np.array([_coord5, _coord2, _coord2])),
NonLinearVertex(23, np.array([_coord5, _coord1, _coord2])),
LinearVertex(24, np.array([_coord1, _coord3, _coord4]), False),
LinearVertex(25, np.array([_coord1, _coord4, _coord3]), False),
LinearVertex(26, np.array([_coord1, _coord3, _coord5]), False),
LinearVertex(27, np.array([_coord1, _coord5, _coord3]), False),
LinearVertex(28, np.array([_coord2, _coord3, _coord4]), False),
LinearVertex(29, np.array([_coord2, _coord4, _coord3]), False),
LinearVertex(30, np.array([_coord2, _coord3, _coord5]), False),
LinearVertex(31, np.array([_coord2, _coord5, _coord3]), False),
LinearVertex(32, np.array([_coord3, _coord1, _coord4]), False),
LinearVertex(33, np.array([_coord4, _coord1, _coord3]), False),
LinearVertex(34, np.array([_coord3, _coord1, _coord5]), False),
LinearVertex(35, np.array([_coord5, _coord1, _coord3]), False),
LinearVertex(36, np.array([_coord3, _coord2, _coord4]), False),
LinearVertex(37, np.array([_coord4, _coord2, _coord3]), False),
LinearVertex(38, np.array([_coord3, _coord2, _coord5]), False),
LinearVertex(39, np.array([_coord5, _coord2, _coord3]), False),
LinearVertex(40, np.array([_coord3, _coord4, _coord1]), False),
LinearVertex(41, np.array([_coord4, _coord3, _coord1]), False),
LinearVertex(42, np.array([_coord3, _coord5, _coord1]), False),
LinearVertex(43, np.array([_coord5, _coord3, _coord1]), False),
LinearVertex(44, np.array([_coord3, _coord4, _coord2]), False),
LinearVertex(45, np.array([_coord4, _coord3, _coord2]), False),
LinearVertex(46, np.array([_coord3, _coord5, _coord2]), False),
LinearVertex(47, np.array([_coord5, _coord3, _coord2]), False),
LinearVertex(48, np.array([_coord1, _coord6, _coord6]), False),
LinearVertex(49, np.array([_coord1, _coord6, -_coord6]), False),
LinearVertex(50, np.array([_coord1, -_coord6, _coord6]), False),
LinearVertex(51, np.array([_coord1, -_coord6, -_coord6]), False),
LinearVertex(52, np.array([_coord2, _coord6, _coord6]), False),
LinearVertex(53, np.array([_coord2, _coord6, -_coord6]), False),
LinearVertex(54, np.array([_coord2, -_coord6, _coord6]), False),
LinearVertex(55, np.array([_coord2, -_coord6, -_coord6]), False),
LinearVertex(56, np.array([_coord6, _coord1, _coord6]), False),
LinearVertex(57, np.array([_coord6, _coord1, -_coord6]), False),
LinearVertex(58, np.array([-_coord6, _coord1, _coord6]), False),
LinearVertex(59, np.array([-_coord6, _coord1, -_coord6]), False),
LinearVertex(60, np.array([_coord6, _coord2, _coord6]), False),
LinearVertex(61, np.array([_coord6, _coord2, -_coord6]), False),
LinearVertex(62, np.array([-_coord6, _coord2, _coord6]), False),
LinearVertex(63, np.array([-_coord6, _coord2, -_coord6]), False),
LinearVertex(64, np.array([_coord6, _coord6, _coord1]), False),
LinearVertex(65, np.array([_coord6, -_coord6, _coord1]), False),
LinearVertex(66, np.array([-_coord6, _coord6, _coord1]), False),
LinearVertex(67, np.array([-_coord6, -_coord6, _coord1]), False),
LinearVertex(68, np.array([_coord6, _coord6, _coord2]), False),
LinearVertex(69, np.array([_coord6, -_coord6, _coord2]), False),
LinearVertex(70, np.array([-_coord6, _coord6, _coord2]), False),
LinearVertex(71, np.array([-_coord6, -_coord6, _coord2]), False),
)
_edge_prototypes = (
Edge(0, _vertex_prototypes[0], _vertex_prototypes[57]),
Edge(1, _vertex_prototypes[0], _vertex_prototypes[32]),
Edge(2, _vertex_prototypes[0], _vertex_prototypes[49]),
Edge(3, _vertex_prototypes[0], _vertex_prototypes[24]),
Edge(4, _vertex_prototypes[1], _vertex_prototypes[26]),
Edge(5, _vertex_prototypes[1], _vertex_prototypes[56]),
Edge(6, _vertex_prototypes[1], _vertex_prototypes[48]),
Edge(7, _vertex_prototypes[1], _vertex_prototypes[34]),
Edge(8, _vertex_prototypes[2], _vertex_prototypes[44]),
Edge(9, _vertex_prototypes[2], _vertex_prototypes[25]),
Edge(10, _vertex_prototypes[2], _vertex_prototypes[69]),
Edge(11, _vertex_prototypes[2], _vertex_prototypes[51]),
Edge(12, _vertex_prototypes[3], _vertex_prototypes[68]),
Edge(13, _vertex_prototypes[3], _vertex_prototypes[49]),
Edge(14, _vertex_prototypes[3], _vertex_prototypes[27]),
Edge(15, _vertex_prototypes[3], _vertex_prototypes[46]),
Edge(16, _vertex_prototypes[4], _vertex_prototypes[51]),
Edge(17, _vertex_prototypes[4], _vertex_prototypes[36]),
Edge(18, _vertex_prototypes[4], _vertex_prototypes[24]),
Edge(19, _vertex_prototypes[4], _vertex_prototypes[61]),
Edge(20, _vertex_prototypes[5], _vertex_prototypes[50]),
Edge(21, _vertex_prototypes[5], _vertex_prototypes[60]),
Edge(22, _vertex_prototypes[5], _vertex_prototypes[26]),
Edge(23, _vertex_prototypes[5], _vertex_prototypes[38]),
Edge(24, _vertex_prototypes[6], _vertex_prototypes[40]),
Edge(25, _vertex_prototypes[6], _vertex_prototypes[25]),
Edge(26, _vertex_prototypes[6], _vertex_prototypes[65]),
Edge(27, _vertex_prototypes[6], _vertex_prototypes[50]),
Edge(28, _vertex_prototypes[7], _vertex_prototypes[64]),
Edge(29, _vertex_prototypes[7], _vertex_prototypes[48]),
Edge(30, _vertex_prototypes[7], _vertex_prototypes[27]),
Edge(31, _vertex_prototypes[7], _vertex_prototypes[42]),
Edge(32, _vertex_prototypes[8], _vertex_prototypes[53]),
Edge(33, _vertex_prototypes[8], _vertex_prototypes[32]),
Edge(34, _vertex_prototypes[8], _vertex_prototypes[28]),
Edge(35, _vertex_prototypes[8], _vertex_prototypes[59]),
Edge(36, _vertex_prototypes[9], _vertex_prototypes[34]),
Edge(37, _vertex_prototypes[9], _vertex_prototypes[52]),
Edge(38, _vertex_prototypes[9], _vertex_prototypes[30]),
Edge(39, _vertex_prototypes[9], _vertex_prototypes[58]),
Edge(40, _vertex_prototypes[10], _vertex_prototypes[63]),
Edge(41, _vertex_prototypes[10], _vertex_prototypes[28]),
Edge(42, _vertex_prototypes[10], _vertex_prototypes[36]),
Edge(43, _vertex_prototypes[10], _vertex_prototypes[55]),
Edge(44, _vertex_prototypes[11], _vertex_prototypes[38]),
Edge(45, _vertex_prototypes[11], _vertex_prototypes[54]),
Edge(46, _vertex_prototypes[11], _vertex_prototypes[62]),
Edge(47, _vertex_prototypes[11], _vertex_prototypes[30]),
Edge(48, _vertex_prototypes[12], _vertex_prototypes[67]),
Edge(49, _vertex_prototypes[12], _vertex_prototypes[54]),
Edge(50, _vertex_prototypes[12], _vertex_prototypes[29]),
Edge(51, _vertex_prototypes[12], _vertex_prototypes[40]),
Edge(52, _vertex_prototypes[13], _vertex_prototypes[42]),
Edge(53, _vertex_prototypes[13], _vertex_prototypes[31]),
Edge(54, _vertex_prototypes[13], _vertex_prototypes[66]),
Edge(55, _vertex_prototypes[13], _vertex_prototypes[52]),
Edge(56, _vertex_prototypes[14], _vertex_prototypes[71]),
Edge(57, _vertex_prototypes[14], _vertex_prototypes[55]),
Edge(58, _vertex_prototypes[14], _vertex_prototypes[44]),
Edge(59, _vertex_prototypes[14], _vertex_prototypes[29]),
Edge(60, _vertex_prototypes[15], _vertex_prototypes[46]),
Edge(61, _vertex_prototypes[15], _vertex_prototypes[31]),
Edge(62, _vertex_prototypes[15], _vertex_prototypes[70]),
Edge(63, _vertex_prototypes[15], _vertex_prototypes[53]),
Edge(64, _vertex_prototypes[16], _vertex_prototypes[66]),
Edge(65, _vertex_prototypes[16], _vertex_prototypes[58]),
Edge(66, _vertex_prototypes[16], _vertex_prototypes[41]),
Edge(67, _vertex_prototypes[16], _vertex_prototypes[33]),
Edge(68, _vertex_prototypes[17], _vertex_prototypes[41]),
Edge(69, _vertex_prototypes[17], _vertex_prototypes[37]),
Edge(70, _vertex_prototypes[17], _vertex_prototypes[67]),
Edge(71, _vertex_prototypes[17], _vertex_prototypes[62]),
Edge(72, _vertex_prototypes[18], _vertex_prototypes[45]),
Edge(73, _vertex_prototypes[18], _vertex_prototypes[37]),
Edge(74, _vertex_prototypes[18], _vertex_prototypes[71]),
Edge(75, _vertex_prototypes[18], _vertex_prototypes[63]),
Edge(76, _vertex_prototypes[19], _vertex_prototypes[70]),
Edge(77, _vertex_prototypes[19], _vertex_prototypes[59]),
Edge(78, _vertex_prototypes[19], _vertex_prototypes[45]),
Edge(79, _vertex_prototypes[19], _vertex_prototypes[33]),
Edge(80, _vertex_prototypes[20], _vertex_prototypes[43]),
Edge(81, _vertex_prototypes[20], _vertex_prototypes[35]),
Edge(82, _vertex_prototypes[20], _vertex_prototypes[56]),
Edge(83, _vertex_prototypes[20], _vertex_prototypes[64]),
Edge(84, _vertex_prototypes[21], _vertex_prototypes[43]),
Edge(85, _vertex_prototypes[21], _vertex_prototypes[39]),
Edge(86, _vertex_prototypes[21], _vertex_prototypes[65]),
Edge(87, _vertex_prototypes[21], _vertex_prototypes[60]),
Edge(88, _vertex_prototypes[22], _vertex_prototypes[69]),
Edge(89, _vertex_prototypes[22], _vertex_prototypes[61]),
Edge(90, _vertex_prototypes[22], _vertex_prototypes[47]),
Edge(91, _vertex_prototypes[22], _vertex_prototypes[39]),
Edge(92, _vertex_prototypes[23], _vertex_prototypes[47]),
Edge(93, _vertex_prototypes[23], _vertex_prototypes[57]),
Edge(94, _vertex_prototypes[23], _vertex_prototypes[68]),
Edge(95, _vertex_prototypes[23], _vertex_prototypes[35]),
)
_num_windows = 26
_num_window_types = 2