How to use the stk.Pd function in stk

To help you get started, we’ve selected a few stk examples, based on popular ways it is used in public projects.

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lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / metal_complex / square_planar / square_planar.py View on Github

import pytest
import stk

from ....case_data import CaseData


_palladium_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], ),
)

_mo_1 = stk.BuildingBlock(
    smiles='c1cc2c(cn1)CCCCC2',
    functional_groups=[
        stk.SmartsFunctionalGroupFactory(
            smarts='[#6]~[#7X2]~[#6]',
            bonders=(1, ),
            deleters=(),
        ),
    ]
)

lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m4l8.py View on Github

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=(),
        ),
    ]

lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m12l24.py View on Github

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=(),
        ),
    ]

lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m2l4_lantern.py View on Github

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=(),
        ),
    ]

lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / metal_complex / paddlewheel / paddlewheel.py View on Github

from ....case_data import CaseData


_copper_atom = stk.BuildingBlock(
    smiles='[Cu+2]',
    functional_groups=(
        stk.SingleAtom(stk.Cu(0, charge=2))
        for i in range(4)
    ),
    position_matrix=([0, 0, 0], ),
)

_palladium_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], ),
)

_bi_1 = stk.BuildingBlock(
    smiles='O=C(O)c1ccc(Br)cc1',
    functional_groups=[
        stk.SmartsFunctionalGroupFactory(
            smarts='[#6]~[#8]~[#1]',
            bonders=(1, ),
            deleters=(2, ),
        ),
        stk.SmartsFunctionalGroupFactory(
            smarts='[#6]~[#8X1]',
            bonders=(1, ),

lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m24l48.py View on Github

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=(),
        ),
    ]

lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m4l4_square.py View on Github

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], ),
)

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(

lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / metal_complex / square_planar / cis_protected_square_planar.py View on Github

import pytest
import stk

from ....case_data import CaseData


_palladium_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], ),
)

_bi_1 = stk.BuildingBlock(
    smiles='NCCN',
    functional_groups=[
        stk.SmartsFunctionalGroupFactory(
            smarts='[#7]~[#6]',
            bonders=(0, ),
            deleters=(),
        ),
    ]
)

How to use the stk.Pd function in stk

To help you get started, we’ve selected a few stk examples, based on popular ways it is used in public projects.

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