How to use the stk.SingleAtom function in stk

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github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m6l2l3_prism.py View on Github external
import pytest
import stk

from ....case_data import CaseData


metal_atom = stk.BuildingBlock(
    smiles='[Fe+2]',
    functional_groups=(
        stk.SingleAtom(stk.Fe(0, charge=2))
        for i in range(6)
    ),
    position_matrix=([0, 0, 0], ),
)

tritopic_linker = stk.BuildingBlock(
    smiles=(
        '[H]C1=C([H])C(N(C2=C([H])C([H])=C(Br)C([H])=C2[H])C2=C([H])C('
        '[H])=C(Br)C([H])=C2[H])=C([H])C([H])=C1Br'
    ),
    functional_groups=[stk.BromoFactory()]
)
tetratopic_linker = stk.BuildingBlock(
    smiles=(
        '[H]C1=C([H])C(C(C2=C([H])C([H])=C(Br)C([H])=C2[H])C(C2=C([H])'
        'C([H])=C(Br)C([H])=C2[H])C2=C([H])C([H])=C(Br)C([H])=C2[H])=C'
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m12l24.py View on Github external
                                    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]'
                ')C(=C8[H])C8=C([H])C([H])=N(->[Pd+2]9(<-N%10=C([H])'
                'C([H])=C(C([H])=C%10[H])C%10=C([H])C([H])=C([H])C(='
                'C%10[H])C%10=C([H])C([H])=N(->[Pd+2]%11%12<-N%13=C('
                '[H])C([H])=C(C([H])=C%13[H])C%13=C([H])C(=C([H])C(['
                'H])=C%13[H])C%13=C([H])C([H])=N(->[Pd+2]%14(<-N%15='
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m4l6_tetrahedron.py View on Github external
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(
            molecule=stk.ConstructedMolecule(
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m24l48.py View on Github external
                                    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'
                '%14[H])C%14=C([H])C([H])=N(->[Pd+2]%15%16<-N%17=C([H'
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / metal_complex / square_planar / cis_protected_square_planar.py View on Github external
                                    stk.SingleAtom
                                }): 9
                            }
                        )
                    )
                )
            ),
            smiles=(
                '[H]C1([H])C([H])([H])N([H])([H])->[Pd+2]<-N1([H])[H]'
            ),
        ),

        CaseData(
            molecule=stk.ConstructedMolecule(
                stk.metal_complex.CisProtectedSquarePlanar(
                    metals=_palladium_atom,
                    ligands=_bi_1,
github lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m3l6.py View on Github external
import pytest
import stk

from ....case_data import CaseData


metal_atom = stk.BuildingBlock(
    smiles='[Pd+2]',
    functional_groups=(
        stk.SingleAtom(stk.Pd(0, charge=2))
        for i in range(4)
    ),
    position_matrix=([0, 0, 0], ),
)
linker = stk.BuildingBlock(
    smiles=(
        '[H]C1=NC([H])=C([H])C(C2=C([H])C([H])=C([H])C(C3=C([H])C([H]'
        ')=NC([H])=C3[H])=C2[H])=C1[H]'
    ),
    functional_groups=[
        stk.SmartsFunctionalGroupFactory(
            smarts='[#6]~[#7X2]~[#6]',
            bonders=(1, ),
            deleters=(),
        ),
    ]