Source code for stk.molecular.topology_graphs.cage.metal_topologies.m24l48

"""
M24L48
======

"""

from ...topology_graph 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, [_coord1, _coord1, _coord4]), NonLinearVertex(1, [_coord1, _coord1, _coord5]), NonLinearVertex(2, [_coord1, _coord4, _coord2]), NonLinearVertex(3, [_coord1, _coord5, _coord2]), NonLinearVertex(4, [_coord1, _coord2, _coord4]), NonLinearVertex(5, [_coord1, _coord2, _coord5]), NonLinearVertex(6, [_coord1, _coord4, _coord1]), NonLinearVertex(7, [_coord1, _coord5, _coord1]), NonLinearVertex(8, [_coord2, _coord1, _coord4]), NonLinearVertex(9, [_coord2, _coord1, _coord5]), NonLinearVertex(10, [_coord2, _coord2, _coord4]), NonLinearVertex(11, [_coord2, _coord2, _coord5]), NonLinearVertex(12, [_coord2, _coord4, _coord1]), NonLinearVertex(13, [_coord2, _coord5, _coord1]), NonLinearVertex(14, [_coord2, _coord4, _coord2]), NonLinearVertex(15, [_coord2, _coord5, _coord2]), NonLinearVertex(16, [_coord4, _coord1, _coord1]), NonLinearVertex(17, [_coord4, _coord2, _coord1]), NonLinearVertex(18, [_coord4, _coord2, _coord2]), NonLinearVertex(19, [_coord4, _coord1, _coord2]), NonLinearVertex(20, [_coord5, _coord1, _coord1]), NonLinearVertex(21, [_coord5, _coord2, _coord1]), NonLinearVertex(22, [_coord5, _coord2, _coord2]), NonLinearVertex(23, [_coord5, _coord1, _coord2]), LinearVertex(24, [_coord1, _coord3, _coord4], False), LinearVertex(25, [_coord1, _coord4, _coord3], False), LinearVertex(26, [_coord1, _coord3, _coord5], False), LinearVertex(27, [_coord1, _coord5, _coord3], False), LinearVertex(28, [_coord2, _coord3, _coord4], False), LinearVertex(29, [_coord2, _coord4, _coord3], False), LinearVertex(30, [_coord2, _coord3, _coord5], False), LinearVertex(31, [_coord2, _coord5, _coord3], False), LinearVertex(32, [_coord3, _coord1, _coord4], False), LinearVertex(33, [_coord4, _coord1, _coord3], False), LinearVertex(34, [_coord3, _coord1, _coord5], False), LinearVertex(35, [_coord5, _coord1, _coord3], False), LinearVertex(36, [_coord3, _coord2, _coord4], False), LinearVertex(37, [_coord4, _coord2, _coord3], False), LinearVertex(38, [_coord3, _coord2, _coord5], False), LinearVertex(39, [_coord5, _coord2, _coord3], False), LinearVertex(40, [_coord3, _coord4, _coord1], False), LinearVertex(41, [_coord4, _coord3, _coord1], False), LinearVertex(42, [_coord3, _coord5, _coord1], False), LinearVertex(43, [_coord5, _coord3, _coord1], False), LinearVertex(44, [_coord3, _coord4, _coord2], False), LinearVertex(45, [_coord4, _coord3, _coord2], False), LinearVertex(46, [_coord3, _coord5, _coord2], False), LinearVertex(47, [_coord5, _coord3, _coord2], False), LinearVertex(48, [_coord1, _coord6, _coord6], False), LinearVertex(49, [_coord1, _coord6, -_coord6], False), LinearVertex(50, [_coord1, -_coord6, _coord6], False), LinearVertex(51, [_coord1, -_coord6, -_coord6], False), LinearVertex(52, [_coord2, _coord6, _coord6], False), LinearVertex(53, [_coord2, _coord6, -_coord6], False), LinearVertex(54, [_coord2, -_coord6, _coord6], False), LinearVertex(55, [_coord2, -_coord6, -_coord6], False), LinearVertex(56, [_coord6, _coord1, _coord6], False), LinearVertex(57, [_coord6, _coord1, -_coord6], False), LinearVertex(58, [-_coord6, _coord1, _coord6], False), LinearVertex(59, [-_coord6, _coord1, -_coord6], False), LinearVertex(60, [_coord6, _coord2, _coord6], False), LinearVertex(61, [_coord6, _coord2, -_coord6], False), LinearVertex(62, [-_coord6, _coord2, _coord6], False), LinearVertex(63, [-_coord6, _coord2, -_coord6], False), LinearVertex(64, [_coord6, _coord6, _coord1], False), LinearVertex(65, [_coord6, -_coord6, _coord1], False), LinearVertex(66, [-_coord6, _coord6, _coord1], False), LinearVertex(67, [-_coord6, -_coord6, _coord1], False), LinearVertex(68, [_coord6, _coord6, _coord2], False), LinearVertex(69, [_coord6, -_coord6, _coord2], False), LinearVertex(70, [-_coord6, _coord6, _coord2], False), LinearVertex(71, [-_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