Ring Amine

class RingAmine(nitrogen, hydrogen1, hydrogen2, carbon1, carbon2, hydrogen3, carbon3)[source]

Bases: stk.molecular.functional_groups.functional_groups.functional_group.FunctionalGroup

Represents an amine bonded to a ring.

The structure of the functional group is given by the pseudo-SMILES [hydrogen1][nitrogen]([hydrogen2])[carbon1][carbon2] ([hydrogen3])[carbon3].

Methods

clone()

Return a clone.

get_atom_ids()

Yield the ids of all atoms in the functional group.

get_atoms()

Yield all the atoms in the functional group.

get_carbon1()

Get the [carbon1] atom.

get_carbon2()

Get the [carbon2] atom.

get_carbon3()

Get the [carbon3] atom.

get_core_atom_ids()

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

get_hydrogen1()

Get the [hydrogen1] atom.

get_hydrogen2()

Get the [hydrogen2] atom.

get_hydrogen3()

Get the [hydrogen3] atom.

get_nitrogen()

Get the [nitrogen] atom.

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, hydrogen1, hydrogen2, carbon1, carbon2, hydrogen3, carbon3)[source]

Initializes a RingAmine instance.

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

  • hydrogen1 (H) – The [hydrogen1] atom.

  • hydrogen2 (H) – The [hydrogen2] atom.

  • carbon1 (C) – The [carbon1] atom.

  • carbon2 (C) – The [carbon2] atom.

  • hydrogen3 (H) – The [hydrogen3] atom.

  • carbon3 (C) – The [carbon3] atom.

clone()[source]

Return a clone.

Returns

A clone.

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_carbon1()[source]

Get the [carbon1] atom.

Returns

The [carbon1] atom.

Return type

C

get_carbon2()[source]

Get the [carbon2] atom.

Returns

The [carbon2] atom.

Return type

C

get_carbon3()[source]

Get the [carbon3] atom.

Returns

The [carbon3] atom.

Return type

C

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_hydrogen1()[source]

Get the [hydrogen1] atom.

Returns

The [hydrogen1] atom.

Return type

H

get_hydrogen2()[source]

Get the [hydrogen2] atom.

Returns

The [hydrogen2] atom.

Return type

H

get_hydrogen3()[source]

Get the [hydrogen3] atom.

Returns

The [hydrogen3] atom.

Return type

H

get_nitrogen()[source]

Get the [nitrogen] atom.

Returns

The [nitrogen] atom.

Return type

N

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

FunctionalGroup

Returns

The clone.