stk.FunctionalGroupFactory

class stk.FunctionalGroupFactory

Bases: object

An abstract base class for functional group factories.

The purpose of a functional group factory is to create FunctionalGroup instances. It allows the user to avoid creating FunctionalGroup instances manually. The user will use get_functional_groups() to achieve this. Subclasses of this class are made to customize the automatic creation process.

Examples

Using a Single Functional Group From a Factory

You have a building block with two functional groups, but you want to use just one.

import stk

amino_factory = stk.PrimaryAminoFactory()
building_block = stk.BuildingBlock('NCCN')
amino_group1, *rest = amino_factory.get_functional_groups(
    molecule=building_block,
)
building_block = building_block.with_functional_groups(
    functional_groups=(amino_group1, ),
)

Using a Subset of Functional Groups From a Factory

You have multiple functional groups, but you want the building block to use a specific subset.

import stk

bromo_factory = stk.BromoFactory()
building_block = stk.BuildingBlock('BrCC(Br)CC(Br)CC(Br)CCBr')
bromo_groups = tuple(bromo_factory.get_functional_groups(
    molecule=building_block,
))
building_block = building_block.with_functional_groups(
    functional_groups=(
        bromo_groups[0],
        bromo_groups[3],
        bromo_groups[4],
    ),
)

More usage examples can be found in the docstrings of the various subclasses.

Subclass Implementation

The source of the subclasses, listed in functional_group_factory, can serve as good examples.

Methods

get_functional_groups

Yield functional groups in molecule.

get_functional_groups(molecule)

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.