Addition of the MOFs core M6L8L12 #529
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| """ | ||
| M6L8L12 Cuboctahedron | ||
| ========== | ||
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| """ | ||
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| import numpy as np | ||
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| from stk._internal.topology_graphs.edge import Edge | ||
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| from .cage import Cage | ||
| from .vertices import LinearVertex, NonLinearVertex | ||
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| class M6L6L12Cuboctahedron(Cage): | ||
| """ | ||
| Represents a cage topology graph. | ||
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| Unoptimized construction | ||
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| .. moldoc:: | ||
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| import moldoc.molecule as molecule | ||
| import stk | ||
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| m1 = stk.BuildingBlock('[Ti](Br)(Br)(Br)(Br)(Br)(Br)(Br)(Br)', functional_groups=[stk.BromoFactory()]) | ||
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There was a problem hiding this comment. Can you change all line lengths to be less than 72, even if in doc string? |
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| bb1 = stk.BuildingBlock('C(OBr)=[O+]Br', functional_groups=[stk.BromoFactory()]) | ||
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| bb2 = stk.BuildingBlock('[O+](Br)(Br)(Br)', functional_groups=[stk.BromoFactory()]) | ||
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| cage = stk.ConstructedMolecule( | ||
| topology_graph = stk.cage.M6L6L12Cuboctahedron( | ||
| building_blocks = { | ||
| m1:range(0,6), | ||
| bb1:range(6,18), | ||
| bb2:range(18,26) | ||
| }, | ||
| optimizer=stk.Nulloptimizer(), | ||
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| ) | ||
| ) | ||
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| 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() | ||
| ), | ||
| ) | ||
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| :class:`.Collapser` optimized construction | ||
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| .. moldoc:: | ||
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| import moldoc.molecule as molecule | ||
| import stk | ||
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| m1 = stk.BuildingBlock('[Ti](Br)(Br)(Br)(Br)(Br)(Br)(Br)(Br)', functional_groups=[stk.BromoFactory()]) | ||
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| bb1 = stk.BuildingBlock('C(OBr)=[O+]Br', functional_groups=[stk.BromoFactory()]) | ||
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| bb2 = stk.BuildingBlock('[O+](Br)(Br)(Br)', functional_groups=[stk.BromoFactory()]) | ||
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| cage = stk.ConstructedMolecule( | ||
| topology_graph = stk.cage.M6L6L12Cuboctahedron( | ||
| building_blocks = { | ||
| m1:range(0,6), | ||
| bb1:range(6,18), | ||
| bb2:range(18,26) | ||
| }, | ||
| optimizer=stk.Collapser(), | ||
| ) | ||
| ) | ||
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| 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() | ||
| ), | ||
| ) | ||
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| Metal building blocks with eight functional groups are | ||
| required for this topology. | ||
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| One ligand building blocks with two functional groups and another ligand | ||
| building block with three functional groups are required for | ||
| this topology. | ||
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| 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: | ||
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| | 8-functional groups: 0 to 5 | ||
| | 2-functional groups: 6 to 17 | ||
| | 3-functional groups: 18 to 25 | ||
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| See :class:`.Cage` for more details and examples. | ||
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| """ | ||
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| _x = np.sqrt(2) | ||
| _vertex_prototypes = ( | ||
| # M | ||
| NonLinearVertex(0, np.array([1, 0, 0])), | ||
| NonLinearVertex(1, np.array([0, 1, 0])), | ||
| NonLinearVertex(2, np.array([-1, 0, 0])), | ||
| NonLinearVertex(3, np.array([0, -1, 0])), | ||
| NonLinearVertex(4, np.array([0, 0, 1])), | ||
| NonLinearVertex(5, np.array([0, 0, -1])), | ||
| # L1 | ||
| LinearVertex(6, np.array([2, 2, 0]), False), | ||
| LinearVertex(7, np.array([2, -2, 0]), False), | ||
| LinearVertex(8, np.array([2, 0, 2]), False), | ||
| LinearVertex(9, np.array([2, 0, -2]), False), | ||
| LinearVertex(10, np.array([-2, 2, 0]), False), | ||
| LinearVertex(11, np.array([-2, -2, 0]), False), | ||
| LinearVertex(12, np.array([-2, 0, 2]), False), | ||
| LinearVertex(13, np.array([-2, 0, -2]), False), | ||
| LinearVertex(14, np.array([0, 2, 2]), False), | ||
| LinearVertex(15, np.array([0, 2, -2]), False), | ||
| LinearVertex(16, np.array([0, -2, 2]), False), | ||
| LinearVertex(17, np.array([0, -2, -2]), False), | ||
| # L2 | ||
| LinearVertex(18, np.array([ _x, _x, _x]), False), | ||
| LinearVertex(19, np.array([-_x, _x, _x]), False), | ||
| LinearVertex(20, np.array([-_x,-_x, _x]), False), | ||
| LinearVertex(21, np.array([ _x,-_x, _x]), False), | ||
| LinearVertex(22, np.array([ _x, _x,-_x]), False), | ||
| LinearVertex(23, np.array([-_x, _x,-_x]), False), | ||
| LinearVertex(24, np.array([-_x,-_x,-_x]), False), | ||
| LinearVertex(25, np.array([ _x,-_x,-_x]), False), | ||
| ) | ||
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| _edge_prototypes = ( | ||
| # Outer shell | ||
| Edge(0, _vertex_prototypes[0], _vertex_prototypes[6]), | ||
| Edge(1, _vertex_prototypes[0], _vertex_prototypes[7]), | ||
| Edge(2, _vertex_prototypes[0], _vertex_prototypes[8]), | ||
| Edge(3, _vertex_prototypes[0], _vertex_prototypes[9]), | ||
| Edge(4, _vertex_prototypes[1], _vertex_prototypes[6]), | ||
| Edge(5, _vertex_prototypes[1], _vertex_prototypes[10]), | ||
| Edge(6, _vertex_prototypes[1], _vertex_prototypes[14]), | ||
| Edge(7, _vertex_prototypes[1], _vertex_prototypes[15]), | ||
| Edge(8, _vertex_prototypes[2], _vertex_prototypes[10]), | ||
| Edge(9, _vertex_prototypes[2], _vertex_prototypes[11]), | ||
| Edge(10, _vertex_prototypes[2], _vertex_prototypes[12]), | ||
| Edge(11, _vertex_prototypes[2], _vertex_prototypes[13]), | ||
| Edge(12, _vertex_prototypes[3], _vertex_prototypes[7]), | ||
| Edge(13, _vertex_prototypes[3], _vertex_prototypes[11]), | ||
| Edge(14, _vertex_prototypes[3], _vertex_prototypes[16]), | ||
| Edge(15, _vertex_prototypes[3], _vertex_prototypes[17]), | ||
| Edge(16, _vertex_prototypes[4], _vertex_prototypes[8]), | ||
| Edge(17, _vertex_prototypes[4], _vertex_prototypes[12]), | ||
| Edge(18, _vertex_prototypes[4], _vertex_prototypes[14]), | ||
| Edge(19, _vertex_prototypes[4], _vertex_prototypes[16]), | ||
| Edge(20, _vertex_prototypes[5], _vertex_prototypes[9]), | ||
| Edge(21, _vertex_prototypes[5], _vertex_prototypes[13]), | ||
| Edge(22, _vertex_prototypes[5], _vertex_prototypes[15]), | ||
| Edge(23, _vertex_prototypes[5], _vertex_prototypes[17]), | ||
| # Inner shell | ||
| Edge(24, _vertex_prototypes[0], _vertex_prototypes[18]), | ||
| Edge(25, _vertex_prototypes[0], _vertex_prototypes[21]), | ||
| Edge(26, _vertex_prototypes[0], _vertex_prototypes[22]), | ||
| Edge(27, _vertex_prototypes[0], _vertex_prototypes[25]), | ||
| Edge(28, _vertex_prototypes[1], _vertex_prototypes[18]), | ||
| Edge(29, _vertex_prototypes[1], _vertex_prototypes[19]), | ||
| Edge(30, _vertex_prototypes[1], _vertex_prototypes[22]), | ||
| Edge(31, _vertex_prototypes[1], _vertex_prototypes[23]), | ||
| Edge(32, _vertex_prototypes[2], _vertex_prototypes[19]), | ||
| Edge(33, _vertex_prototypes[2], _vertex_prototypes[20]), | ||
| Edge(34, _vertex_prototypes[2], _vertex_prototypes[23]), | ||
| Edge(35, _vertex_prototypes[2], _vertex_prototypes[24]), | ||
| Edge(36, _vertex_prototypes[3], _vertex_prototypes[20]), | ||
| Edge(37, _vertex_prototypes[3], _vertex_prototypes[21]), | ||
| Edge(38, _vertex_prototypes[3], _vertex_prototypes[24]), | ||
| Edge(39, _vertex_prototypes[3], _vertex_prototypes[25]), | ||
| Edge(40, _vertex_prototypes[4], _vertex_prototypes[18]), | ||
| Edge(41, _vertex_prototypes[4], _vertex_prototypes[19]), | ||
| Edge(42, _vertex_prototypes[4], _vertex_prototypes[20]), | ||
| Edge(43, _vertex_prototypes[4], _vertex_prototypes[21]), | ||
| Edge(44, _vertex_prototypes[5], _vertex_prototypes[22]), | ||
| Edge(45, _vertex_prototypes[5], _vertex_prototypes[23]), | ||
| Edge(46, _vertex_prototypes[5], _vertex_prototypes[24]), | ||
| Edge(47, _vertex_prototypes[5], _vertex_prototypes[25]), | ||
| ) | ||
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| _num_windows = 8 | ||
| _num_window_types = 1 | ||
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no need to add docstrings to internal modules
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I added the tests to both files above, however when I run the tests locally I get an
'CallSpec2' object has no attribute 'funcargs'message... I guess it might be a problem of the pytest version I have installed?I am not sure, it is the first time I have to run a real test 🤣
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Ahh yes, this issue should be solved in the latest version of
stkby limiting the pytest version to < 8 (see thepyproject.tomlfile). You may need to reinstall your development version withjust devto get the tests working.