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How to use the stk.GenericFunctionalGroup function in stk

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github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m3l6.py View on Github external
                                    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]6(<-N'
                '7=C([H])C([H])=C(C([H])=C7[H])C7=C([H])C([H])=C([H]'
                ')C(=C7[H])C7=C([H])C([H])=N(->[Pd+2](<-N8=C([H])C(['
                'H])=C(C([H])=C8[H])C8=C([H])C(=C([H])C([H])=C8[H])C'
                '8=C([H])C([H])=N->3C([H])=C8[H])(<-N3=C([H])C([H])='
                'C(C([H])=C3[H])C3=C([H])C(=C([H])C([H])=C3[H])C3=C('
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m4l4_square.py View on Github external
                                    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])=C(C([H])=C8[H])C8=C([H])C([H])=N(->'
                '[Pd+2]9(<-N%10=C([H])C([H])=C2C([H])=C%10[H])<-N([H]'
                ')([H])C([H])([H])C([H])([H])N->9([H])[H])C([H])=C8[H'
                '])<-N([H])([H])C([H])([H])C([H])([H])N->7([H])[H])C('
                '[H])=C6[H])<-N([H])([H])C([H])([H])C([H])([H])N->5(['
                'H])[H])C([H])=C4[H])<-N([H])([H])C([H])([H])C([H])(['
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / metal_complex / octahedral / octahedral_lambda.py View on Github external
                                    stk.GenericFunctionalGroup,
                                    stk.SingleAtom
                                }): 9
                            }
                        )
                    )
                )
            ),
            smiles=(
                '[H]C1=C([H])C([H])=N2->[Fe+2]34(<-N(Br)=C([H])C2=C1[H'
                '])(<-N(Br)=C([H])C1=C([H])C([H])=C([H])C([H])=N->31)'
                '<-N(Br)=C([H])C1=C([H])C([H])=C([H])C([H])=N->41'
            ),
        ),
    ),
)
def metal_complex_octahedral_lambda(request):
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / metal_complex / octahedral / octahedral_delta.py View on Github external
                                    stk.GenericFunctionalGroup,
                                    stk.SingleAtom
                                }): 9
                            }
                        )
                    )
                )
            ),
            smiles=(
                '[H]C1=C([H])C([H])=N2->[Fe+2]34(<-N(Br)=C([H])C2=C1[H'
                '])(<-N(Br)=C([H])C1=C([H])C([H])=C([H])C([H])=N->31)'
                '<-N(Br)=C([H])C1=C([H])C([H])=C([H])C([H])=N->41'
            ),
        ),
    ),
)
def metal_complex_octahedral_delta(request):
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / metal_complex / square_planar / bidentate_square_planar.py View on Github external
                                    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]'
            ),
        ),
    ),
)
def metal_complex_bidentate_square_planar(request):
    return request.param
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m24l48.py View on Github external
                                    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<-N8='
                'C([H])C([H])=C(C([H])=C8[H])C8=C([H])C([H])=C([H])C('
                '=C8[H])C8=C([H])C([H])=N(->[Pd+2]9%10<-N%11=C([H])C('
                '[H])=C(C([H])=C%11[H])C%11=C([H])C([H])=C([H])C(=C%1'
                '1[H])C%11=C([H])C([H])=N(->[Pd+2]%12%13<-N%14=C([H])'
                'C([H])=C(C([H])=C%14[H])C%14=C([H])C([H])=C([H])C(=C'
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m4l6_tetrahedron.py View on Github external
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()]
)


@pytest.fixture(
    params=(
        CaseData(
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m3l3_triangle.py View on Github external
                                    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])('
                '[H])C([H])([H])N->7([H])[H])C([H])=C6[H])<-N([H])([H'
                '])C([H])([H])C([H])([H])N->5([H])[H])C([H])=C4[H])<-'
                'N([H])([H])C([H])([H])C([H])([H])N->3([H])[H])=C1[H]'
            ),
        ),
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m4l4_tetrahedron.py View on Github external
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()]
)


@pytest.fixture(
    params=(
        CaseData(
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m4l6_tetrahedron_spacer.py View on Github external
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()]
)


@pytest.fixture(
    params=(
        CaseData(

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