"""
Alcohol 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.alcohol import Alcohol
[docs]
class AlcoholFactory(FunctionalGroupFactory):
"""
Creates :class:`.Alcohol` instances.
Creates functional groups from substructures, which match the
``[*][O][H]`` functional group string.
Examples
--------
*Creating Functional Groups with the Factory*
You want to create a building block which has :class:`.Alcohol`
functional groups. You want the oxygen atom in those functional
groups to be the bonder atom, and the hydrogen atom to be the
deleter atom.
.. testcode:: creating-functional-groups-with-the-factory
import stk
building_block = stk.BuildingBlock(
smiles='OCCCO',
functional_groups=(stk.AlcoholFactory(), ),
)
.. testcode:: creating-functional-groups-with-the-factory
:hide:
assert all(
isinstance(functional_group, stk.Alcohol)
for functional_group
in building_block.get_functional_groups()
)
assert building_block.get_num_functional_groups() == 2
*Changing the Bonder and Deleter Atoms*
You want to create a building block which has :class:`.Alcohol`
functional groups. You want the OH group to be
treated as a leaving group. This means the non-hydrogen atom bonded
to oxygen is the *bonder* atom and both the oxygen and hydrogen
atoms are *deleter* atoms.
.. testcode:: changing-the-bonder-and-deleter-atoms
import stk
alcohol_factory = stk.AlcoholFactory(
# The index of the non-hydrogen atom connected to oxygen
# is 0 in the functional group string (see docstring).
bonders=(0, ),
# The indices of the oxygen and hydrogen atoms in the
# functional group string (see docstring) are
# 1 and 2, respectively.
deleters=(1, 2),
)
building_block = stk.BuildingBlock(
smiles='OCCCO',
functional_groups=(alcohol_factory, ),
)
.. testcode:: changing-the-bonder-and-deleter-atoms
:hide:
fg1, fg2 = building_block.get_functional_groups()
assert fg1.get_num_bonders() == 1
assert sum(1 for _ in fg1.get_deleters()) == 2
assert fg2.get_num_bonders() == 1
assert sum(1 for _ in fg2.get_deleters()) == 2
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.O, stk.H))
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,), deleters=(2,), placers=None):
"""
Initialize an :class:`.AlcoholFactory` 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("[*][O][H]", molecule):
atoms = tuple(molecule.get_atoms(atom_ids))
yield Alcohol(
oxygen=atoms[1],
hydrogen=atoms[2],
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),
)