Boronic Acid Factory

class BoronicAcidFactory(bonders=(1), deleters=(2, 3, 4, 5), placers=None)[source]

Bases: stk.molecular.functional_groups.factories.functional_group_factory.FunctionalGroupFactory

Creates BoronicAcid instances.

Creates functional groups from substructures, which match the [*][B]([O][H])[O][H] functional group string.

Examples

Creating Functional Groups with the Factory

You want to create a building block which has BoronicAcid functional groups. You want the boron atom in those functional groups to be the bonder atom and the OH groups to be deleter atoms.

import stk

building_block = stk.BuildingBlock(
    smiles='OB(O)CCCB(O)O',
    functional_groups=(stk.BoronicAcidFactory(), ),
)

Changing the Bonder and Deleter Atoms

You want to create a building block which has BoronicAcid functional groups. You want the oxygen atoms to be treated as bonder atoms, and the hydrogen atoms to be treated as deleter atoms.

import stk

boronic_acid_factory = stk.BoronicAcidFactory(
    # The indices of the oxygen atoms in the functional
    # group string (see docstring) are 2 and 4.
    bonders=(2, 4),
    # The indices of the hydrogen atoms in the
    # functional group string (see docstring) are 3 and 5.
    deleters=(3, 5),
)
building_block = stk.BuildingBlock(
    smiles='OB(O)CCCB(O)O',
    functional_groups=(boronic_acid_factory, ),
)

See also

GenericFunctionalGroup

Defines bonders and deleters.

Methods

get_functional_groups(molecule)

Yield functional groups in molecule.

__init__(bonders=(1), deleters=(2, 3, 4, 5), placers=None)[source]

Initialize a BoronicAcidFactory instance.

Parameters
  • bonders (tuple of int) – The indices of atoms in the functional group string, which are bonder atoms.

  • deleters (tuple of int) – The indices of atoms in the functional group string, which are deleter atoms.

  • placers (tuple of int, optional) – The indices of atoms in the functional group string, which are placer atoms. If None, bonders will be used.

get_functional_groups(molecule)[source]

Yield functional groups in molecule.

Parameters

molecule (Molecule) – The molecule, whose functional groups are to be found.

Yields

FunctionalGroup – A functional group in molecule.

Examples

See FunctionalGroupFactory.