"""
Diol 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.diol import Diol
[docs]
class DiolFactory(FunctionalGroupFactory):
"""
Creates :class:`.Diol` instances.
Creates functional groups from substructures, which match the
``[H][O][#6]~[#6][O][H]`` functional group string.
Examples
--------
*Creating Functional Groups with the Factory*
You want to create a building block which has :class:`.Diol`
functional groups. You want the carbon atoms in those functional
groups to be the *bonder* atoms, and the OH groups to be a leaving
groups.
.. testcode:: creating-functional-groups-with-the-factory
import stk
building_block = stk.BuildingBlock(
smiles='CCCC(O)C(O)CCCC',
functional_groups=(stk.DiolFactory(), ),
)
.. testcode:: creating-functional-groups-with-the-factory
:hide:
assert all(
isinstance(functional_group, stk.Diol)
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:`.Diol`
functional groups. You want the oxygen atoms to be the *bonder*
atoms and the hydrogen atoms to be the *deleter* atoms.
.. testcode:: changing-the-bonder-and-deleter-atoms
import stk
diol_factory = stk.DiolFactory(
# The indices of the oxygen atoms in the functional
# group string (see docstring) are 1 and 4.
bonders=(1, 4),
# The indices of the hydrogen atoms in the functional
# group string (see docstring) are 0 and 5.
deleters=(0, 5),
)
building_block = stk.BuildingBlock(
smiles='CCCC(O)C(O)CCCC',
functional_groups=(diol_factory, ),
)
.. testcode:: changing-the-bonder-and-deleter-atoms
:hide:
fg, = building_block.get_functional_groups()
assert fg.get_num_bonders() == 2
assert sum(1 for _ in fg.get_deleters()) == 2
assert all(
isinstance(atom, stk.O)
for functional_group
in building_block.get_functional_groups()
for atom
in functional_group.get_bonders()
)
assert all(
isinstance(atom, 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=(2, 3),
deleters=(0, 1, 4, 5),
placers=None,
):
"""
Initialize a :class:`.DiolFactory` 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):
ids = get_atom_ids("[H][O][#6]~[#6][O][H]", molecule)
for atom_ids in ids:
atoms = tuple(molecule.get_atoms(atom_ids))
yield Diol(
hydrogen1=atoms[0],
oxygen1=atoms[1],
atom1=atoms[2],
atom2=atoms[3],
oxygen2=atoms[4],
hydrogen2=atoms[5],
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),
)