[docs]
class FunctionalGroupFactory:
"""
An abstract base class for functional group factories.
The purpose of a functional group factory is to create
:class:`.FunctionalGroup` instances. It allows the user to avoid
creating :class:`.FunctionalGroup` instances manually. The user
will use :meth:`.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.
.. testcode:: using-a-single-functional-group-factory
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, ),
)
.. testcode:: using-a-single-functional-group-factory
:hide:
assert all(
isinstance(functional_group, stk.PrimaryAmino)
for functional_group
in building_block.get_functional_groups()
)
assert building_block.get_num_functional_groups() == 1
*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.
.. testcode:: using-a-subset-of-functional-groups-from-a-factory
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],
),
)
.. testcode:: using-a-subset-of-functional-groups-from-a-factory
:hide:
assert all(
isinstance(functional_group, stk.Bromo)
for functional_group
in building_block.get_functional_groups()
)
assert building_block.get_num_functional_groups() == 3
More usage examples can be found in the docstrings of the
various subclasses.
*Subclass Implementation*
The source of the subclasses, listed in
:mod:`.functional_group_factory`, can serve as good examples.
"""
[docs]
def get_functional_groups(self, molecule):
"""
Yield functional groups in `molecule`.
Parameters
----------
molecule : :class:`.Molecule`
The molecule, whose functional groups are to be found.
Yields
------
:class:`.FunctionalGroup`
A functional group in `molecule`.
Examples
--------
See :class:`.FunctionalGroupFactory`.
"""
raise NotImplementedError()
def __repr__(self) -> str:
return f"{type(self).__name__}()"