"""
Primary Amino
=============
"""
from .generic_functional_group import GenericFunctionalGroup
[docs]
class PrimaryAmino(GenericFunctionalGroup):
"""
Represents a primary amino functional group.
The structure of the functional group is given by the pseudo-SMILES
``[atom][nitrogen]([hydrogen1])[hydrogen2]``.
"""
def __init__(
self,
nitrogen,
hydrogen1,
hydrogen2,
atom,
bonders,
deleters,
placers=None,
):
"""
Initializes a :class:`.PrimaryAmino` instance.
Parameters
----------
nitrogen : :class:`.N`
The ``[nitrogen]`` atom.
hydrogen1 : :class:`.H`
The ``[hydrogen1]`` atom.
hydrogen2 : :class:`.H`
The ``[hydrogen2]`` 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._nitrogen = nitrogen
self._hydrogen1 = hydrogen1
self._hydrogen2 = hydrogen2
self._atom = atom
super().__init__(
atoms=(nitrogen, hydrogen1, hydrogen2, atom),
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_hydrogen1(self):
"""
Get the ``[hydrogen1]`` atom.
Returns
-------
:class:`.H`
The ``[hydrogen1]`` atom.
"""
return self._hydrogen1
[docs]
def get_hydrogen2(self):
"""
Get the ``[hydrogen2]`` atom.
Returns
-------
:class:`.H`
The ``[hydrogen2]`` atom.
"""
return self._hydrogen2
[docs]
def get_atom(self):
"""
Get the ``[atom]`` atom.
Returns
-------
:class:`.Atom`
The ``[atom]`` atom.
"""
return self._atom
def __repr__(self):
return (
f"{self.__class__.__name__}("
f"{self._nitrogen}, {self._hydrogen1}, {self._hydrogen2}, "
f"{self._atom}, bonders={self._bonders}, "
f"deleters={self._deleters}"
")"
)
[docs]
def clone(self):
clone = super().clone()
clone._nitrogen = self._nitrogen
clone._hydrogen1 = self._hydrogen1
clone._hydrogen2 = self._hydrogen2
clone._atom = self._atom
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._hydrogen1 = atom_map.get(
self._hydrogen1.get_id(),
self._hydrogen1,
)
clone._hydrogen2 = atom_map.get(
self._hydrogen2.get_id(),
self._hydrogen2,
)
clone._atom = atom_map.get(
self._atom.get_id(),
self._atom,
)
return clone