stk.GenericFunctionalGroup

class stk.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.

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.

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

clone()

Return a clone.

Returns:

A clone.

Return type:

GenericFunctionalGroup

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.

Returns:

The number of bonder atoms.

Return type:

int

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.

Returns:

The clone.

Return type:

GenericFunctionalGroup

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:

GenericFunctionalGroup