Ring Amine

class 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].

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)

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()

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.

Return type:

FunctionalGroup

Returns:

The clone.