"""
Fluoro Factory
==============
"""
from stk._internal.functional_group_factories.functional_group_factory import (
FunctionalGroupFactory,
)
from stk._internal.functional_group_factories.utilities import get_atom_ids
from stk._internal.functional_groups.fluoro import Fluoro
[docs]
class FluoroFactory(FunctionalGroupFactory):
"""
Creates :class:`.Fluoro` instances.
Creates functional groups from substructures, which match the
``[*][F]`` functional group string.
Examples
--------
*Creating Functional Groups with the Factory*
You want to create a building block which has :class:`.Fluoro`
functional groups. You want the non-fluorine atom in those
functional groups to be the *bonder* atom, and the fluorine atom
to be the *deleter* atom.
.. testcode:: creating-functional-groups-with-the-factory
import stk
building_block = stk.BuildingBlock(
smiles='FCCCF',
functional_groups=(stk.FluoroFactory(), ),
)
.. testcode:: creating-functional-groups-with-the-factory
:hide:
assert all(
isinstance(functional_group, stk.Fluoro)
for functional_group
in building_block.get_functional_groups()
)
assert building_block.get_num_functional_groups() == 2
See Also
--------
:class:`.GenericFunctionalGroup`
Defines *bonders* and *deleters*.
"""
def __init__(self, bonders=(0,), deleters=(1,), placers=None):
"""
Initialize a :class:`.FluoroFactory` instance.
Parameters
----------
bonders : :class:`tuple` of :class:`int`
The indices of atoms in the functional group string, which
are *bonder* atoms.
deleters : :class:`tuple` of :class:`int`
The indices of atoms in the functional group string, which
are *deleter* atoms.
placers : :class:`tuple` of :class:`int`, optional
The indices of atoms in the functional group string, which
are *placer* atoms. If ``None``, `bonders` will be used.
"""
self._bonders = bonders
self._deleters = deleters
self._placers = bonders if placers is None else placers
[docs]
def get_functional_groups(self, molecule):
for atom_ids in get_atom_ids("[*][F]", molecule):
atoms = tuple(molecule.get_atoms(atom_ids))
yield Fluoro(
fluorine=atoms[1],
atom=atoms[0],
bonders=tuple(atoms[i] for i in self._bonders),
deleters=tuple(atoms[i] for i in self._deleters),
placers=tuple(atoms[i] for i in self._placers),
)