Source code for stk.molecular.functional_groups.functional_groups.thiol



from .generic_functional_group import GenericFunctionalGroup

[docs]class Thiol(GenericFunctionalGroup): """ Represents a thiol functional group. The structure of the functional group is given by the pseudo-SMILES ``[atom][sulfur][hydrogen]``. """
[docs] def __init__( self, sulfur, hydrogen, atom, bonders, deleters, placers=None, ): """ Initialize a :class:`.Thiol` instance. Parameters ---------- sulfur : :class:`.S` The ``[sulfur]`` 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._sulfur = sulfur self._hydrogen = hydrogen self._atom = atom super().__init__( atoms=(sulfur, hydrogen, atom), bonders=bonders, deleters=deleters, placers=bonders if placers is None else placers, )
[docs] def get_sulfur(self): """ Get the ``[sulfur]`` atom. Returns ------- :class:`.S` The ``[sulfur]`` atom. """ return self._sulfur
[docs] def get_hydrogen(self): """ Get the ``[hydrogen]`` atom. Returns ------- :class:`.H` The ``[hydrogen]`` atom. """ return self._hydrogen
[docs] def get_atom(self): """ Get the ``[atom]`` atom. Returns ------- :class:`.Atom` The ``[atom]`` atom. """ return self._atom
[docs] def clone(self): clone = super().clone() clone._sulfur = self._sulfur clone._hydrogen = self._hydrogen clone._atom = self._atom return clone
[docs] def with_atoms(self, atom_map): clone = super().with_atoms(atom_map) clone._sulfur = atom_map.get( self._sulfur.get_id(), self._sulfur, ) 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._sulfur}, {self._hydrogen}, {self._atom}, " f"bonders={self._bonders}, deleters={self._deleters})" )