stk.RingAmine

class stk.RingAmine(nitrogen, hydrogen1, hydrogen2, carbon1, carbon2, hydrogen3, carbon3)

Bases: 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].

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.

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	Return a clone holding different atoms.
with_ids	Return a clone holding different atom ids.

clone()

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()

Get the [carbon1] atom.

Returns:

The [carbon1] atom.

Return type:

C

get_carbon2()

Get the [carbon2] atom.

Returns:

The [carbon2] atom.

Return type:

C

get_carbon3()

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]

See also

BuildingBlock.get_core_atom_ids()

get_hydrogen1()

Get the [hydrogen1] atom.

Returns:

The [hydrogen1] atom.

Return type:

H

get_hydrogen2()

Get the [hydrogen2] atom.

Returns:

The [hydrogen2] atom.

Return type:

H

get_hydrogen3()

Get the [hydrogen3] atom.

Returns:

The [hydrogen3] atom.

Return type:

H

get_nitrogen()

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)

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.

Returns:

The clone.

Return type:

FunctionalGroup