Secondary Amino

class SecondaryAmino(nitrogen, hydrogen, atom1, atom2, bonders, deleters, placers=None)[source]

Bases: stk.molecular.functional_groups.functional_groups.generic_functional_group.GenericFunctionalGroup

Represents a secondary amino functional group.

The structure of the functional group is given by the pseudo-SMILES [atom1][nitrogen]([hydrogen])[atom2].

Methods

clone()

Return a clone.

get_atom1()

Get the [atom1] atom.

get_atom2()

Get the [atom2] atom.

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.

get_core_atom_ids()

Yield the ids of core atoms held by the functional group.

get_deleter_ids()

Yield the ids of deleter atoms.

get_deleters()

Yield the deleter atoms in the functional group.

get_hydrogen()

Get the [hydrogen] atom.

get_nitrogen()

Get the [nitrogen] atom.

get_num_bonders()

Get the number of bonder atoms.

get_placer_ids()

Yield the ids of placer atoms.

with_atoms(atom_map)

Return a clone holding different atoms.

with_ids(id_map)

Return a clone holding different atom ids.

__init__(nitrogen, hydrogen, atom1, atom2, bonders, deleters, placers=None)[source]

Initialize a SecondaryAmine instance.

Parameters
  • nitrogen (N) – The [nitrogen] atom

  • hydrogen (H) – The [hydrogen] atom.

  • atom1 (Atom) – The [atom] atom.

  • atom2 (Atom) – The [atom] atom.

  • bonders (tuple of Atom) – The bonder atoms.

  • deleters (tuple of Atom) – The deleter atoms.

  • placers (tuple of Atom, optional) – The placer atoms. If None the bonders will be used.

clone()[source]

Return a clone.

Returns

A clone.

get_atom1()[source]

Get the [atom1] atom.

Returns

The [atom1] atom.

Return type

Atom

get_atom2()[source]

Get the [atom2] atom.

Returns

The [atom2] atom.

Return type

Atom

get_atom_ids()

Yield the ids of all atoms in the functional group.

Yields

The id of an Atom.

Return type

Iterator[int]

get_atoms()

Yield all the atoms in the functional group.

Yields

An atom in the functional group.

Return type

Iterator[Atom]

get_bonder_ids()

Yield the ids of bonder atoms.

Yields

The id of a bonder Atom.

Return type

Iterator[int]

get_bonders()

Yield bonder atoms in the functional group.

These are atoms which have bonds added during ConstructedMolecule construction.

Yields

A bonder atom.

Return type

Iterator[Atom]

get_core_atom_ids()

Yield the ids of core atoms held by the functional group.

Yields

The id of an Atom.

Return type

Iterator[int]

get_deleter_ids()

Yield the ids of deleter atoms.

Yields

The id of a deleter Atom.

Return type

Iterator[int]

get_deleters()

Yield the deleter atoms in the functional group.

These are atoms which are removed during ConstructedMolecule construction.

Yields

A deleter atom.

Return type

Iterator[Atom]

get_hydrogen()[source]

Get the [hydrogen] atom.

Returns

The [hydrogen] atom.

Return type

H

get_nitrogen()[source]

Get the [nitrogen] atom.

Returns

The [nitrogen] atom.

Return type

N

get_num_bonders()

Get the number of bonder atoms.

Return type

int

Returns

The number of bonder atoms.

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.

Yields

The id of an Atom.

Return type

Iterator[int]

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.

Parameters

id_map (dict[int, int]) – Maps the id of an atom in the functional group to the new id the clone should hold. If the id of an atom in the functional group is not found in id_map, the atom will not be replaced in the clone.

Return type

GenericFunctionalGroup

Returns

The clone.