"""
Dibromo 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.dibromo import Dibromo
[docs]
class DibromoFactory(FunctionalGroupFactory):
"""
Creates :class:`.Dibromo` instances.
Creates functional groups from substructures, which match the
``[Br][#6]~[#6][Br]`` functional group string.
Examples
--------
*Creating Functional Groups with the Factory*
You want to create a building block which has :class:`.Dibromo`
functional groups. You want the non-bromine atoms of the functional
group to be the *bonder* atoms and the bromine atoms to be the
*deleter* atoms.
.. testcode:: creating-functional-groups-with-the-factory
import stk
building_block = stk.BuildingBlock(
smiles='BrCC(Br)CCCC',
functional_groups=(stk.DibromoFactory(), ),
)
.. testcode:: creating-functional-groups-with-the-factory
:hide:
assert all(
isinstance(functional_group, stk.Dibromo)
for functional_group
in building_block.get_functional_groups()
)
assert building_block.get_num_functional_groups() == 1
*Changing the Bonder and Deleter Atoms*
You want to create a building block which has :class:`.Dibromo`
functional groups, You want only one of non-bromine atoms to be
a *bonder* atom and its neighboring bromine atom to be a
*deleter* atom.
.. testcode:: changing-the-bonder-and-deleter-atoms
import stk
dibromo_factory = stk.DibromoFactory(
# The index of one of the non-bromine atoms in the
# functional group string (see docstring) is 1.
bonders=(1, ),
# The neighboring bromine atom has an index of 0.
deleters=(0, ),
)
building_block = stk.BuildingBlock(
smiles='BrCC(Br)CCC',
functional_groups=(dibromo_factory, ),
)
.. testcode:: changing-the-bonder-and-deleter-atoms
:hide:
fg, = building_block.get_functional_groups()
assert fg.get_num_bonders() == 1
assert sum(1 for _ in fg.get_deleters()) == 1
assert all(
isinstance(atom, stk.C)
for functional_group
in building_block.get_functional_groups()
for atom
in functional_group.get_bonders()
)
assert all(
isinstance(atom, stk.Br)
for functional_group
in building_block.get_functional_groups()
for atom
in functional_group.get_deleters()
)
See Also
--------
:class:`.GenericFunctionalGroup`
Defines *bonders* and *deleters*.
"""
def __init__(self, bonders=(1, 2), deleters=(0, 3), placers=None):
"""
Initialize a :class:`.DibromoFactory` 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("[Br][#6]~[#6][Br]", molecule):
atoms = tuple(molecule.get_atoms(atom_ids))
yield Dibromo(
atom1=atoms[1],
bromine1=atoms[0],
atom2=atoms[2],
bromine2=atoms[3],
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),
)