Generic Functional Group

class GenericFunctionalGroup(atoms, bonders, deleters, placers=None)

Bases: FunctionalGroup

A functional group which defines general atomic classes.

Bonders are atoms which should have bonds added by a Reaction. Deleters are atoms which should be removed by a Reaction.

This interface allows the same reactions to be carried out across different functional groups, without knowing which specific elements it holds.

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_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_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__(atoms, bonders, deleters, placers=None)

Initialize a GenericFunctionalGroup.

Parameters:

• atoms (tuple[Atom, ...]) – The atoms in the functional group.

• bonders (tuple[Atom, ...]) – The bonder atoms in the functional group.

• deleters (tuple[Atom, ...]) – The deleter atoms in the functional group.

• placers (Optional[tuple[Atom, ...]]) – The placer atoms of the functional group. If None, the bonders will be used.

clone()

Return a clone.

Return type:

GenericFunctionalGroup

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_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]

See also

BuildingBlock.get_core_atom_ids()

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_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)

Return a clone holding different atoms.

Parameters:

atom_map (dict[int, Atom]) – 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.

Return type:

GenericFunctionalGroup

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.