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How to use the stk.DativeReactionFactory function in stk

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github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / metal_complex / square_planar / bidentate_square_planar.py View on Github external
                    reaction_factory=stk.DativeReactionFactory(
                        stk.GenericReactionFactory(
                            bond_orders={
                                frozenset({
                                    stk.GenericFunctionalGroup,
                                    stk.SingleAtom
                                }): 9
                            }
                        )
                    )
                )
            ),
            smiles=(
                '[H]C1([H])C([H])([H])N([H])([H])->[Pd+2]2(<-N1([H])'
                '[H])<-N([H])([H])C([H])([H])C([H])([H])N->2([H])[H]'
            ),
        ),
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m4l6_tetrahedron.py View on Github external
smarts='[#6]~[#7X2]~[#35]',
            bonders=(1, ),
            deleters=(),
        ),
        stk.SmartsFunctionalGroupFactory(
            smarts='[#6]~[#7X2]~[#6]',
            bonders=(1, ),
            deleters=(),
        ),
    ]
)
iron_complex = stk.ConstructedMolecule(
    stk.metal_complex.OctahedralDelta(
        metals={metal_atom: 0},
        ligands={complex_ligand: (0, 1, 2)},
        reaction_factory=stk.DativeReactionFactory(
            stk.GenericReactionFactory(
                bond_orders={
                    frozenset({
                        stk.GenericFunctionalGroup,
                        stk.SingleAtom
                    }): 9
                }
            )
        )
    )
)
iron_complex = stk.BuildingBlock.init_from_molecule(
    molecule=iron_complex,
    functional_groups=[stk.BromoFactory()]
)
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m3l3_triangle.py View on Github external
                    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'
                '(C([H])=C4[H])C4=C([H])C([H])=N(->[Pd+2]5(<-N6=C([H]'
                ')C([H])=C(C([H])=C6[H])C6=C([H])C([H])=N(->[Pd+2]7(<'
                '-N8=C([H])C([H])=C2C([H])=C8[H])<-N([H])([H])C([H])('
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m4l4_tetrahedron.py View on Github external
smarts='[#6]~[#7X2]~[#35]',
            bonders=(1, ),
            deleters=(),
        ),
        stk.SmartsFunctionalGroupFactory(
            smarts='[#6]~[#7X2]~[#6]',
            bonders=(1, ),
            deleters=(),
        ),
    ]
)
iron_complex = stk.ConstructedMolecule(
    stk.metal_complex.OctahedralDelta(
        metals={metal_atom: 0},
        ligands={complex_ligand: (0, 1, 2)},
        reaction_factory=stk.DativeReactionFactory(
            stk.GenericReactionFactory(
                bond_orders={
                    frozenset({
                        stk.GenericFunctionalGroup,
                        stk.SingleAtom
                    }): 9
                }
            )
        )
    )
)
iron_complex = stk.BuildingBlock.init_from_molecule(
    molecule=iron_complex,
    functional_groups=[stk.BromoFactory()]
)
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m3l3_triangle.py View on Github external
)
palladium_bi_1 = stk.BuildingBlock(
    smiles='[H]N([H])C([H])([H])C([H])([H])N([H])[H]',
    functional_groups=[
        stk.SmartsFunctionalGroupFactory(
            smarts='[#7]~[#6]',
            bonders=(0, ),
            deleters=(),
        ),
    ]
)
palladium_cispbi_sqpl = stk.ConstructedMolecule(
    stk.metal_complex.CisProtectedSquarePlanar(
        metals={metal_atom: 0},
        ligands={palladium_bi_1: 0},
        reaction_factory=stk.DativeReactionFactory(
            stk.GenericReactionFactory(
                bond_orders={
                    frozenset({
                        stk.GenericFunctionalGroup,
                        stk.SingleAtom
                    }): 9
                }
            )
        )
    )
)
palladium_cispbi_sqpl = stk.BuildingBlock.init_from_molecule(
    molecule=palladium_cispbi_sqpl,
    functional_groups=[
        stk.SmartsFunctionalGroupFactory(
            smarts='[Pd]~[#7]',
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m6l12_cube.py View on Github external
                    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('
                '[H])=C([H])C(=C5[H])C5=C([H])C([H])=N(->[Pd+2]67<-N'
                '8=C([H])C([H])=C(C([H])=C8[H])C8=C([H])C([H])=C([H]'
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m8l6_cube.py View on Github external
smarts='[#6]~[#7X2]~[#35]',
            bonders=(1, ),
            deleters=(),
        ),
        stk.SmartsFunctionalGroupFactory(
            smarts='[#6]~[#7X2]~[#6]',
            bonders=(1, ),
            deleters=(),
        ),
    ]
)
iron_complex = stk.ConstructedMolecule(
    stk.metal_complex.OctahedralDelta(
        metals={metal_atom: 0},
        ligands={complex_ligand: (0, 1, 2)},
        reaction_factory=stk.DativeReactionFactory(
            stk.GenericReactionFactory(
                bond_orders={
                    frozenset({
                        stk.GenericFunctionalGroup,
                        stk.SingleAtom
                    }): 9
                }
            )
        )
    )
)
iron_complex = stk.BuildingBlock.init_from_molecule(
    molecule=iron_complex,
    functional_groups=[stk.BromoFactory()]
)
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m12l24.py View on Github external
                    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('
                '[H])=C([H])C(=C5[H])C5=C([H])C([H])=N(->[Pd+2]67<-N'
                '8=C([H])C([H])=C(C([H])=C8[H])C8=C([H])C([H])=C([H]'

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