Source code for stk.molecular.functional_groups.functional_groups.carboxylic_acid

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]``. """
[docs] 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})" )