"""
Carboxylic Acid
===============
"""
from .generic_functional_group import GenericFunctionalGroup
[docs]
class CarboxylicAcid(GenericFunctionalGroup):
"""
Represents a carboxylic acid functional group.
The structure of the functional group is given by the pseudo-SMILES
``[atom][carbon](=[oxygen1])[oxygen2][hydrogen]``.
"""
def __init__(
self,
carbon,
oxygen1,
oxygen2,
hydrogen,
atom,
bonders,
deleters,
placers=None,
):
"""
Initialize a :class:`.CarboxylicAcid` instance.
Parameters
----------
carbon : :class:`.C`
The ``[carbon]`` atom.
oxygen1 : :class:`.O`
The ``[oxygen1]`` atom.
oxygen2 : :class:`.O`
The ``[oxygen2]`` atom.
hydrogen : :class:`.H`
The ``[hydrogen]`` atom.
atom : :class:`.Atom`
The ``[atom]`` atom.
bonders : :class:`tuple` of :class:`.Atom`
The bonder atoms.
deleters : :class:`tuple` of :class:`.Atom`
The deleter atoms.
placers : :class:`tuple` of :class:`.Atom`, optional
The placer atoms. If ``None`` the `bonders` will be used.
"""
self._carbon = carbon
self._oxygen1 = oxygen1
self._oxygen2 = oxygen2
self._hydrogen = hydrogen
self._atom = atom
super().__init__(
atoms=(carbon, oxygen1, oxygen2, hydrogen, atom),
bonders=bonders,
deleters=deleters,
placers=bonders if placers is None else placers,
)
[docs]
def get_carbon(self):
"""
Get the ``[carbon]`` atom.
Returns
-------
:class:`.C`
The ``[carbon]`` atom.
"""
return self._carbon
[docs]
def get_oxygen1(self):
"""
Get the ``[oxygen1]`` atom.
Returns
-------
:class:`.O`
The ``[oxygen]`` atom.
"""
return self._oxygen1
[docs]
def get_oxygen2(self):
"""
Get the ``[oxygen2]`` atom.
Returns
-------
:class:`.O`
The ``[oxygen2]`` atom.
"""
return self._oxygen2
[docs]
def get_hydrogen(self):
"""
Get the ``[hydrogen]`` atom.
Returns
-------
:class:``
The ``[hydrogen]`` atom.
"""
return self._hydrogen
[docs]
def get_atom(self):
"""
Get the ``[atom]`` atom.
Returns
-------
:class:``
The ``[atom]`` atom.
"""
return self._atom
[docs]
def clone(self):
clone = super().clone()
clone._carbon = self._carbon
clone._oxygen1 = self._oxygen1
clone._oxygen2 = self._oxygen2
clone._hydrogen = self._hydrogen
clone._atom = self._atom
return clone
[docs]
def with_atoms(self, atom_map):
clone = super().with_atoms(atom_map)
clone._carbon = atom_map.get(
self._carbon.get_id(),
self._carbon,
)
clone._oxygen1 = atom_map.get(
self._oxygen1.get_id(),
self._oxygen1,
)
clone._oxygen2 = atom_map.get(
self._oxygen2.get_id(),
self._oxygen2,
)
clone._hydrogen = atom_map.get(
self._hydrogen.get_id(),
self._hydrogen,
)
clone._atom = atom_map.get(
self._atom.get_id(),
self._atom,
)
return clone
def __repr__(self):
return (
f"{self.__class__.__name__}("
f"{self._carbon}, {self._oxygen1}, {self._oxygen2}, "
f"{self._hydrogen}, {self._atom}, "
f"bonders={self._bonders}, deleters={self._deleters})"
)