Primary Amino Factory

class PrimaryAminoFactory(bonders=(1), deleters=(2, 3), placers=None)[source]

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

Creates PrimaryAmino instances.

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

Examples

Creating Functional Groups with the Factory

You want to create a building block which has PrimaryAmino functional groups. You want the nitrogen atom to be the bonder atom, and the hydrogen atoms to be the deleter atoms.

import stk

building_block = stk.BuildingBlock(
    smiles='NCCCCN',
    functional_groups=(stk.PrimaryAminoFactory(), ),
)

Changing the Bonder and Deleter Atoms

You want to create a building block which has PrimaryAmino functional groups. You want the non-hydrogen atom bonded to nitrogen to be the bonder atom and the nitrogen and hydrogen atoms to be deleter atoms.

import stk

primary_amino_factory = stk.PrimaryAminoFactory(
    # The index of the atom attached to the nitrogen is 0 in
    # the functional group string (see docstring).
    bonders=(0, ),
    # The indices of the nitrogen and hydrogen atoms in the
    # functional group string (see docstring) are 1, 2 and 3.
    deleters=(1, 2, 3),
)
building_block = stk.BuildingBlock(
    smiles='NCCCCN',
    functional_groups=(primary_amino_factory, ),
)

See also

GenericFunctionalGroup

Defines bonders and deleters.

Methods

get_functional_groups(molecule)

Yield functional groups in molecule.

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

Initialize a PrimaryAminoFactory 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.