Source code for stk.molecular.functional_groups.functional_groups.primary_amino

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]``. """
[docs] 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