"""
Secondary Amino
===============
"""
from .generic_functional_group import GenericFunctionalGroup
[docs]
class SecondaryAmino(GenericFunctionalGroup):
"""
Represents a secondary amino functional group.
The structure of the functional group is given by the pseudo-SMILES
``[atom1][nitrogen]([hydrogen])[atom2]``.
"""
def __init__(
self,
nitrogen,
hydrogen,
atom1,
atom2,
bonders,
deleters,
placers=None,
):
"""
Initialize a :class:`.SecondaryAmine` instance.
Parameters
----------
nitrogen : :class:`.N`
The ``[nitrogen]`` atom
hydrogen : :class:`.H`
The ``[hydrogen]`` atom.
atom1 : :class:`.Atom`
The ``[atom]`` atom.
atom2 : :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._nitrogen = nitrogen
self._hydrogen = hydrogen
self._atom1 = atom1
self._atom2 = atom2
super().__init__(
atoms=(nitrogen, hydrogen, atom1, atom2),
bonders=bonders,
deleters=deleters,
placers=bonders if placers is None else placers,
)
[docs]
def get_nitrogen(self):
"""
Get the ``[nitrogen]`` atom.
Returns
-------
:class:`.N`
The ``[nitrogen]`` atom.
"""
return self._nitrogen
[docs]
def get_hydrogen(self):
"""
Get the ``[hydrogen]`` atom.
Returns
-------
:class:`.H`
The ``[hydrogen]`` atom.
"""
return self._hydrogen
[docs]
def get_atom1(self):
"""
Get the ``[atom1]`` atom.
Returns
-------
:class:`.Atom`
The ``[atom1]`` atom.
"""
return self._atom1
[docs]
def get_atom2(self):
"""
Get the ``[atom2]`` atom.
Returns
-------
:class:`.Atom`
The ``[atom2]`` atom.
"""
return self._atom2
[docs]
def clone(self):
clone = super().clone()
clone._nitrogen = self._nitrogen
clone._hydrogen = self._hydrogen
clone._atom1 = self._atom1
clone._atom2 = self._atom2
return clone
[docs]
def with_atoms(self, atom_map):
clone = super().with_atoms(atom_map)
clone._nitrogen = atom_map.get(
self._nitrogen.get_id(),
self._nitrogen,
)
clone._hydrogen = atom_map.get(
self._hydrogen.get_id(),
self._hydrogen,
)
clone._atom1 = atom_map.get(
self._atom1.get_id(),
self._atom1,
)
clone._atom2 = atom_map.get(
self._atom2.get_id(),
self._atom2,
)
return clone
def __repr__(self):
return (
f"{self.__class__.__name__}("
f"{self._nitrogen}, {self._hydrogen}, {self._atom1}, "
f"{self._atom2}, "
f"bonders={self._bonders}, deleters={self._deleters})"
)