"""
Diol
====
"""
from .generic_functional_group import GenericFunctionalGroup
[docs]
class Diol(GenericFunctionalGroup):
"""
Represents a diol functional group.
The structure of the functional group is given by the pseudo-SMILES
``[hydrogen1][oxygen1][atom1][atom2][oxygen2][hydrogen2]``.
"""
def __init__(
self,
atom1,
oxygen1,
hydrogen1,
atom2,
oxygen2,
hydrogen2,
bonders,
deleters,
placers=None,
):
"""
Initialize a :class:`.Diol` instance.
Parameters
----------
atom1 : :class:`.Atom`
The ``[atom1]`` atom.
oxygen1 : :class:`.O`
The ``[oxygen1]`` atom.
hydrogen1 : :class:`.H`
The ``[hydrogen1]`` atom.
atom2 : :class:`.Atom`
The ``[atom2]`` atom.
oxygen2 : :class:`.O`
The ``[oxygen2]`` atom.
hydrogen2 : :class:`.H`
The ``[hydrogen2]`` 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._atom1 = atom1
self._oxygen1 = oxygen1
self._hydrogen1 = hydrogen1
self._atom2 = atom2
self._oxygen2 = oxygen2
self._hydrogen2 = hydrogen2
atoms = (atom1, oxygen1, hydrogen1, atom2, oxygen2, hydrogen2)
super().__init__(
atoms=atoms,
bonders=bonders,
deleters=deleters,
placers=bonders if placers is None else placers,
)
[docs]
def get_atom1(self):
"""
Get the ``[atom1]`` atom.
Returns
-------
:class:`.Atom`
The ``[atom1]`` atom.
"""
return self._atom1
[docs]
def get_oxygen1(self):
"""
Get the ``[oxygen1]`` atom.
Returns
-------
:class:`.O`
The ``[oxygen1]`` atom.
"""
return self._oxygen1
[docs]
def get_hydrogen1(self):
"""
Get the ``[hydrogen1]`` atom.
Returns
-------
:class:`.H`
The ``[hydrogen1]`` atom.
"""
return self._hydrogen1
[docs]
def get_atom2(self):
"""
Get the ``[atom2]`` atom.
Returns
-------
:class:`.Atom`
The ``[atom2]`` atom.
"""
return self._atom2
[docs]
def get_oxygen2(self):
"""
Get the ``[oxygen2]`` atom.
Returns
-------
:class:`.O`
The ``[oxygen2]`` atom.
"""
return self._oxygen2
[docs]
def get_hydrogen2(self):
"""
Get the ``[hydrogen2]`` atom.
Returns
-------
:class:`.H`
The ``[hydrogen2]`` atom.
"""
return self._hydrogen2
[docs]
def clone(self):
clone = super().clone()
clone._atom1 = self._atom1
clone._oxygen1 = self._oxygen1
clone._hydrogen1 = self._hydrogen1
clone._atom2 = self._atom2
clone._oxygen2 = self._oxygen2
clone._hydrogen2 = self._hydrogen2
return clone
[docs]
def with_atoms(self, atom_map):
clone = super().with_atoms(atom_map)
clone._atom1 = atom_map.get(
self._atom1.get_id(),
self._atom1,
)
clone._oxygen1 = atom_map.get(
self._oxygen1.get_id(),
self._oxygen1,
)
clone._hydrogen1 = atom_map.get(
self._hydrogen1.get_id(),
self._hydrogen1,
)
clone._atom2 = atom_map.get(
self._atom2.get_id(),
self._atom2,
)
clone._oxygen2 = atom_map.get(
self._oxygen2.get_id(),
self._oxygen2,
)
clone._hydrogen2 = atom_map.get(
self._hydrogen2.get_id(),
self._hydrogen2,
)
return clone
def __repr__(self):
return (
f"{self.__class__.__name__}("
f"{self._atom1}, {self._oxygen1}, {self._hydrogen1}, "
f"{self._atom2}, {self._oxygen2}, {self._hydrogen2}, "
f"bonders={self._bonders}, deleters={self._deleters})"
)