"""
Carboxylic Acid 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.carboxylic_acid import CarboxylicAcid
[docs]
class CarboxylicAcidFactory(FunctionalGroupFactory):
"""
Creates :class:`.CarboxylicAcid` instances.
Creates functional groups from substructures, which match the
``[*][C](=[O])[O][H]`` functional group string.
Examples
--------
*Creating Functional Groups with the Factory*
You want to create a building block which has
:class:`.CarboxylicAcid` functional groups. You want the carbon
atom in those functional
groups to be the *bonder* atom, and the OH group to be a leaving
group.
.. testcode:: creating-functional-groups-with-the-factory
import stk
building_block = stk.BuildingBlock(
smiles='OC(=O)CC(=O)O',
functional_groups=(stk.CarboxylicAcidFactory(), ),
)
.. testcode:: creating-functional-groups-with-the-factory
:hide:
assert all(
isinstance(functional_group, stk.CarboxylicAcid)
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:`.CarboxylicAcid` functional groups. You want the carbon
atom to be the *bonder* atom and the oxygen atom to be the
*deleter* atom.
.. testcode:: changing-the-bonder-and-deleter-atoms
import stk
carboxylic_acid_factory = stk.CarboxylicAcidFactory(
# The index of the carbon atom in the functional
# group string (see docstring) is 1.
bonders=(1, ),
# The index of the oxygen atom in the functional
# group string (see docstring) is 2.
deleters=(2, ),
)
building_block = stk.BuildingBlock(
smiles='OC(=O)CC(=O)O',
functional_groups=(carboxylic_acid_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()) == 1
assert fg2.get_num_bonders() == 1
assert sum(1 for _ in fg2.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.O)
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=(3, 4), placers=None):
"""
Initialize a :class:`.CarboxylicAcidFactory` 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("[*][C](=[O])[O][H]", molecule):
atoms = tuple(molecule.get_atoms(atom_ids))
yield CarboxylicAcid(
carbon=atoms[1],
oxygen1=atoms[2],
oxygen2=atoms[3],
hydrogen=atoms[4],
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),
)