stk.PrimaryAmino
- class stk.PrimaryAmino(nitrogen, hydrogen1, hydrogen2, atom, bonders, deleters, placers=None)[source]
Bases:
GenericFunctionalGroup
Represents a primary amino functional group.
The structure of the functional group is given by the pseudo-SMILES
[atom][nitrogen]([hydrogen1])[hydrogen2]
.Initializes a
PrimaryAmino
instance.- Parameters:
Methods
Return a clone.
Get the
[atom]
atom.Yield the ids of all atoms in the functional group.
Yield all the atoms in the functional group.
Yield the ids of bonder atoms.
Yield bonder atoms in the functional group.
Yield the ids of core atoms held by the functional group.
Yield the ids of deleter atoms.
Yield the deleter atoms in the functional group.
Get the
[hydrogen1]
atom.Get the
[hydrogen2]
atom.Get the
[nitrogen]
atom.Get the number of bonder atoms.
Yield the ids of placer atoms.
Return a clone holding different atoms.
Return a clone holding different atom ids.
- get_atom_ids()
Yield the ids of all atoms in the functional group.
- get_atoms()
Yield all the atoms in the functional group.
- get_bonder_ids()
Yield the ids of bonder atoms.
- get_bonders()
Yield bonder atoms in the functional group.
These are atoms which have bonds added during
ConstructedMolecule
construction.
- get_core_atom_ids()
Yield the ids of core atoms held by the functional group.
See also
- get_deleter_ids()
Yield the ids of deleter atoms.
- get_deleters()
Yield the deleter atoms in the functional group.
These are atoms which are removed during
ConstructedMolecule
construction.
- get_num_bonders()
Get the number of bonder atoms.
- Returns:
The number of bonder atoms.
- Return type:
- get_placer_ids()
Yield the ids of placer atoms.
Placer atoms are those, which should be used to calculate the position of the functional group.
- with_atoms(atom_map)[source]
Return a clone holding different atoms.
- Parameters:
atom_map – Maps the id of an atom in the functional group to the new atom the clone should hold. If the id of an atom in the functional group is not found in atom_map, the atom will not be replaced in the clone.
- Returns:
The clone.
- with_ids(id_map)
Return a clone holding different atom ids.