Source code for stk.molecular.functional_groups.functional_groups.alcohol



from __future__ import annotations

import typing

from ...atoms import Atom, H, O
from .generic_functional_group import GenericFunctionalGroup

[docs]class Alcohol(GenericFunctionalGroup): """ Represents an alcohol functional group. The structure of the functional group is given by the pseudo-SMILES ``[atom][oxygen][hydrogen]``. """
[docs] def __init__( self, oxygen: O, # noqa: Not an ambiguous name. hydrogen: H, atom: Atom, bonders: tuple[Atom, ...], deleters: tuple[Atom, ...], placers: typing.Optional[tuple[Atom, ...]] = None, ) -> None: """ Initialize a :class:`.Alcohol` instance. Parameters: oxygen: The oxygen atom. hydrogen: The hydrogen atom. atom: The atom to which the alcohol is attached. bonders: The bonder atoms. deleters: The deleter atoms. placers: The placer atoms. If ``None`` the `bonders` will be used. """ self._oxygen = oxygen self._hydrogen = hydrogen self._atom = atom atoms = (oxygen, hydrogen, atom) super().__init__( atoms=atoms, bonders=bonders, deleters=deleters, placers=bonders if placers is None else placers, )
[docs] def get_oxygen(self) -> O: # noqa: Not an ambiguous name. """ Get the oxygen atom. Returns: The oxygen atom. """ return self._oxygen
[docs] def get_hydrogen(self) -> H: """ Get the hydrogen atom. Returns: The hydrogen atom. """ return self._hydrogen
[docs] def get_atom(self) -> Atom: """ Get the atom to which the functional group is attached. Returns: The atom to which the functional group is attached. """ return self._atom
[docs] def clone(self) -> Alcohol: clone = self._clone() clone._oxygen = self._oxygen clone._hydrogen = self._hydrogen clone._atom = self._atom return clone
def _with_ids( self, id_map: dict[int, int], ) -> Alcohol: super()._with_ids(id_map) if (oxygen_id := self._oxygen.get_id()) in id_map: self._oxygen = self._oxygen.with_id(id_map[oxygen_id]) if (hydrogen_id := self._hydrogen.get_id()) in id_map: self._hydrogen = self._hydrogen.with_id( id=id_map[hydrogen_id], ) if (atom_id := self._atom.get_id()) in id_map: self._atom = self._atom.with_id(id_map[atom_id]) return self
[docs] def with_ids( self, id_map: dict[int, int], ) -> Alcohol: return self.clone()._with_ids(id_map)
def __repr__(self) -> str: return ( f"{self.__class__.__name__}(" f"{self._oxygen}, {self._hydrogen}, {self._atom}, " f"bonders={self._bonders}, deleters={self._deleters})" )