"""
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]``.
"""
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})"
)