Esempi in Python per Br

Esempio n. 1

File: conftest.py Progetto: supramolecular-toolkit/stk

def get_case_data_1() -> CaseData:
    return CaseData(
        molecule=stk.BuildingBlock(
            smiles='Br[C+2][N+]Cl',
            functional_groups=[stk.BromoFactory()],
            placer_ids=(0, ),
        ),
        result=stk.BuildingBlock.init(
            atoms=(
                stk.Cl(0),
                stk.Br(1),
                stk.C(2, 2),
                stk.N(3, 1),
            ),
            bonds=(
                stk.Bond(stk.Cl(0), stk.N(3, 1), 1),
                stk.Bond(stk.Br(1), stk.C(2, 2), 1),
                stk.Bond(stk.C(2, 2), stk.N(3, 1), 1),
            ),
            position_matrix=np.array([
            ]),
            functional_groups=(
                stk.Bromo(
                    bromine=stk.Br(1),
                    atom=stk.C(2, 2),
                    bonders=(stk.C(2, 2), ),
                    deleters=(stk.Br(1), ),
                ),
            ),
            placer_ids=(1, ),
        )
    )

Esempio n. 2

     atom=stk.C(5),
     bonders=(stk.C(0), ),
     deleters=(stk.N(2), stk.H(3), stk.H(4)),
 ),
 stk.BoronicAcid(
     boron=stk.B(0),
     oxygen1=stk.O(1),
     hydrogen1=stk.H(2),
     oxygen2=stk.O(3),
     hydrogen2=stk.H(4),
     atom=stk.C(5),
     bonders=(stk.B(0), ),
     deleters=(stk.O(1), stk.H(2), stk.O(3), stk.H(4)),
 ),
 stk.Bromo(
     bromine=stk.Br(0),
     atom=stk.C(1),
     bonders=(stk.C(1), ),
     deleters=(stk.Br(0), ),
 ),
 stk.CarboxylicAcid(
     carbon=stk.C(0),
     oxygen1=stk.O(1),
     oxygen2=stk.O(5),
     hydrogen=stk.H(6),
     atom=stk.C(8),
     bonders=(stk.C(0), ),
     deleters=(stk.O(5), stk.H(6)),
 ),
 stk.Fluoro(
     fluorine=stk.F(12),

Esempio n. 3

File: dibromo.py Progetto: lukasturcani/stk

def dibromo(get_atom_ids):
    a, b, c, d = get_atom_ids(4)
    return _dibromo(stk.Br(a), stk.C(b), stk.Br(c), stk.C(d))

Esempio n. 4

             deleters=(stk.F(3), ),
         ),
         stk.Fluoro(
             fluorine=stk.F(6),
             atom=stk.C(5),
             bonders=(stk.C(5), ),
             deleters=(stk.F(6), ),
         ),
     ),
 ),
 lambda: CaseData(
     factory=stk.BromoFactory(),
     molecule=stk.BuildingBlock('BrCC(Br)CCBr'),
     functional_groups=(
         stk.Bromo(
             bromine=stk.Br(0),
             atom=stk.C(1),
             bonders=(stk.C(1), ),
             deleters=(stk.Br(0), ),
         ),
         stk.Bromo(
             bromine=stk.Br(3),
             atom=stk.C(2),
             bonders=(stk.C(2), ),
             deleters=(stk.Br(3), ),
         ),
         stk.Bromo(
             bromine=stk.Br(6),
             atom=stk.C(5),
             bonders=(stk.C(5), ),
             deleters=(stk.Br(6), ),

Esempio n. 5

File: conftest.py Progetto: lukasturcani/stk

bb2 = stk.BuildingBlock('IS[O+]', [stk.IodoFactory()])
canonical_bb2 = bb2.with_canonical_atom_ordering()


@pytest.fixture(
    params=(
        lambda: CaseData(
            molecule=stk.BuildingBlock(
                smiles='Br[C+2][N+]Cl',
                functional_groups=[stk.BromoFactory()],
                placer_ids=(0, ),
            ),
            result=stk.BuildingBlock.init(
                atoms=(
                    stk.Cl(0),
                    stk.Br(1),
                    stk.C(2, 2),
                    stk.N(3, 1),
                ),
                bonds=(
                    stk.Bond(stk.Cl(0), stk.N(3, 1), 1),
                    stk.Bond(stk.Br(1), stk.C(2, 2), 1),
                    stk.Bond(stk.C(2, 2), stk.N(3, 1), 1),
                ),
                position_matrix=np.array([
                ]),
                functional_groups=(
                    stk.Bromo(
                        bromine=stk.Br(1),
                        atom=stk.C(2, 2),
                        bonders=(stk.C(2, 2), ),

Esempio n. 6

 params=(
     lambda: CaseData(
         building_block=stk.BuildingBlock.init_from_molecule(
             molecule=stk.BuildingBlock('Br[C+2][C+2]Br'), ),
         functional_groups=(),
         core_atom_ids=(0, 1, 2, 3),
         placer_ids=(0, 1, 2, 3),
     ),
     lambda: CaseData(
         building_block=stk.BuildingBlock.init_from_molecule(
             molecule=stk.BuildingBlock('Br[C+2][C+2]Br'),
             functional_groups=[stk.BromoFactory()],
         ),
         functional_groups=(
             stk.Bromo(
                 bromine=stk.Br(0),
                 atom=stk.C(1, 2),
                 bonders=(stk.C(1, 2), ),
                 deleters=(stk.Br(0), ),
             ),
             stk.Bromo(
                 bromine=stk.Br(3),
                 atom=stk.C(2, 2),
                 bonders=(stk.C(2, 2), ),
                 deleters=(stk.Br(3), ),
             ),
         ),
         core_atom_ids=(1, 2),
         placer_ids=(1, 2),
     ),
     lambda: CaseData(

Esempio n. 7

File: bromo.py Progetto: zaeemnajeeb/stk

def bromo(get_atom_ids):
    a, b = get_atom_ids(2)
    return _bromo(stk.Br(a), stk.C(b))

Esempio n. 8

File: init.py Progetto: supramolecular-toolkit/stk

import pytest
import numpy as np
import stk

from ..case_data import CaseData


@pytest.fixture(
    scope='session',
    params=(
        lambda: CaseData(
            building_block=stk.BuildingBlock.init(
                atoms=(stk.Br(0), stk.C(1, 2), stk.C(2, 2), stk.Br(3)),
                bonds=(
                    stk.Bond(stk.Br(0), stk.C(1, 2), 1),
                    stk.Bond(stk.C(1, 2), stk.C(2, 2), 1),
                    stk.Bond(stk.C(2, 2), stk.Br(3), 1),
                ),
                position_matrix=np.array([
                    [0., 0., 0.],
                    [1., 1., 1.],
                    [2., 2., 2.],
                    [3., 3., 3.],
                ]),
            ),
            functional_groups=(),
            core_atom_ids=(0, 1, 2, 3),
            placer_ids=(0, 1, 2, 3),
        ),
        lambda: CaseData(
            building_block=stk.BuildingBlock.init(