How to use the stk.cage function in stk

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github lukasturcani / stk / tests / fixtures / populations.py View on Github external
bb1 = stk.BuildingBlock('NC(CCO)CN', ['amine'])
    bb2 = stk.BuildingBlock('[Br]CCCC[Br]', ['bromine'])
    bb3 = stk.BuildingBlock('[I]COCC[I]', ['iodine'])
    bb4 = stk.BuildingBlock('O=CC(C=O)CC=O', ['aldehyde'])

    c1 = stk.ConstructedMolecule(
        building_blocks=[bb2],
        topology_graph=stk.polymer.Linear('A', 3)
    )
    c2 = stk.ConstructedMolecule(
        building_blocks=[bb1, bb4],
        topology_graph=stk.cage.FourPlusSix()
    )
    c3 = stk.ConstructedMolecule(
        building_blocks=[bb1, bb4],
        topology_graph=stk.cage.EightPlusTwelve()
    )
    c4 = stk.ConstructedMolecule(
        building_blocks=[bb2, bb3],
        topology_graph=stk.polymer.Linear('AB', 3)
    )

    return bb1, bb2, bb3, bb4, c1, c2, c3, c4
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m12l24.py View on Github external
                stk.cage.M12L24(
                    building_blocks=(metal_atom, linker),
                    reaction_factory=stk.DativeReactionFactory(
                        stk.GenericReactionFactory(
                            bond_orders={
                                frozenset({
                                    stk.GenericFunctionalGroup,
                                    stk.SingleAtom
                                }): 9
                            }
                        )
                    )
                )
            ),
            smiles=(
                '[H]C1=C([H])C2=C([H])C(=C1[H])C1=C([H])C([H])=N(->['
                'Pd+2]34<-N5=C([H])C([H])=C(C([H])=C5[H])C5=C([H])C('
github lukasturcani / stk / tests / molecular / topology_graphs / test_cage_topologies.py View on Github external
def test_vertex(
    tmp_amine2,
    tmp_aldehyde3,
    tmp_aldehyde4,
    tmp_aldehyde5
):
    topology_graphs = (
        stk.cage.SixPlusEight(),
        stk.cage.OnePlusOne(),
        stk.cage.TwoPlusTwo(),
        stk.cage.FourPlusFour(),
        stk.cage.TwelvePlusThirty(),
        stk.cage.TwoPlusFour(),
        stk.cage.ThreePlusSix(),
        stk.cage.FourPlusEight(),
        stk.cage.FivePlusTen(),
        stk.cage.SixPlusTwelve(),
        stk.cage.EightPlusSixteen(),
        stk.cage.TenPlusTwenty(),
        stk.cage.TwoPlusThree(),
        stk.cage.FourPlusSix(),
        stk.cage.FourPlusSix2(),
        stk.cage.SixPlusNine(),
        stk.cage.EightPlusTwelve(),
        stk.cage.TwentyPlusThirty()
    )
github lukasturcani / stk / tests / fixtures / constructed_molecules / cages.py View on Github external
def tmp_twelve_plus_thirty(tmp_amine2, tmp_aldehyde5):
    return stk.ConstructedMolecule(
        building_blocks=[tmp_amine2, tmp_aldehyde5],
        topology_graph=stk.cage.TwelvePlusThirty()
    )
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m4l8.py View on Github external
                stk.cage.M4L8(
                    building_blocks={
                        metal_atom: range(4),
                        linker: range(4, 12)
                    },
                    reaction_factory=stk.DativeReactionFactory(
                        stk.GenericReactionFactory(
                            bond_orders={
                                frozenset({
                                    stk.GenericFunctionalGroup,
                                    stk.SingleAtom
                                }): 9
                            }
                        )
                    )
                )
            ),
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m4l4_square.py View on Github external
                stk.cage.M4L4Square(
                    corners=palladium_cispbi_sqpl,
                    linkers=linker,
                    reaction_factory=stk.DativeReactionFactory(
                        stk.GenericReactionFactory(
                            bond_orders={
                                frozenset({
                                    stk.GenericFunctionalGroup,
                                    stk.GenericFunctionalGroup
                                }): 9
                            }
                        )
                    )
                )
            ),
            smiles=(
                '[H]C1=C2C([H])=C([H])N(->[Pd+2]3(<-N4=C([H])C([H])=C'
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m6l12_cube.py View on Github external
                stk.cage.M6L12Cube(
                    building_blocks={
                        metal_atom: range(6),
                        linker: range(6, 18)
                    },
                    reaction_factory=stk.DativeReactionFactory(
                        stk.GenericReactionFactory(
                            bond_orders={
                                frozenset({
                                    stk.GenericFunctionalGroup,
                                    stk.SingleAtom
                                }): 9
                            }
                        )
                    )
                )
            ),
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m4l4_tetrahedron.py View on Github external
                stk.cage.M4L4Tetrahedron(
                    building_blocks={
                        iron_complex: range(4),
                        tritopic_linker: range(4, 8)
                    },
                )
            ),
            smiles=(
                '[H]C1=C([H])C([H])=N2->[Fe+2]3456<-N7=C([H])C([H])=C'
                '([H])C([H])=C7C([H])=N->3C3=C([H])C([H])=C(C([H])=C3'
                '[H])N3C7=C([H])C([H])=C(C([H])=C7[H])N7->[Fe+2]89%10'
                '(<-N%11=C([H])C([H])=C([H])C([H])=C%11C([H])=N->8C8='
                'C([H])C([H])=C(C([H])=C8[H])N(C8=C([H])C([H])=C(C([H'
                '])=C8[H])N->4=C([H])C2=C1[H])C1=C([H])C([H])=C(C([H]'
                ')=C1[H])N1->[Fe+2]248(<-N%11=C([H])C([H])=C([H])C([H'
                '])=C%11C=1[H])<-N1=C([H])C([H])=C([H])C([H])=C1C([H]'
                ')=N->2C1=C([H])C([H])=C(C([H])=C1[H])N(C1=C([H])C([H'
github lukasturcani / stk / tests / molecular / topology_graphs / test_cage_topologies.py View on Github external
def test_vertex(
    tmp_amine2,
    tmp_aldehyde3,
    tmp_aldehyde4,
    tmp_aldehyde5
):
    topology_graphs = (
        stk.cage.SixPlusEight(),
        stk.cage.OnePlusOne(),
        stk.cage.TwoPlusTwo(),
        stk.cage.FourPlusFour(),
        stk.cage.TwelvePlusThirty(),
        stk.cage.TwoPlusFour(),
        stk.cage.ThreePlusSix(),
        stk.cage.FourPlusEight(),
        stk.cage.FivePlusTen(),
        stk.cage.SixPlusTwelve(),
        stk.cage.EightPlusSixteen(),
        stk.cage.TenPlusTwenty(),
        stk.cage.TwoPlusThree(),
        stk.cage.FourPlusSix(),
        stk.cage.FourPlusSix2(),
        stk.cage.SixPlusNine(),
        stk.cage.EightPlusTwelve(),