stko.functional_groups.ThreeSiteFG

class stko.functional_groups.ThreeSiteFG(neigh1, binder, neigh2, bonders, deleters)[source]

Bases: object

Represents FG sites like N atom in pyridine functional group.

Warning

This code is only present in the latest versions of stko that require Python 3.11!

The structure of the functional group is given by the pseudo-SMILES [neighbour][binder][neighbour].

Contains stk.GenericFunctionalGroup.

Parameters:

  • neigh1 (Atom) – The first neighbour atom.

  • binder (Atom) – The central atom that forms the bond.

  • neigh2 (Atom) – The second neighbour atom.

  • bonders (tuple[Atom, ...]) – The bonder atoms, this should be the same ID as binder.

  • deleters (tuple[Atom, ...]) – The deleter atoms, there should be none.

Methods

clone

get_atom_ids

get_atoms

get_binder

get_bonder_ids

get_bonders

get_core_atom_ids

get_deleter_ids

get_deleters

get_neigh1

get_neigh2

get_num_bonders

get_placer_ids

with_atoms

with_ids

clone()[source]
Return type:

Self

get_atom_ids()[source]
Return type:

Iterator[int]

get_atoms()[source]
Return type:

Iterator[Atom]

get_binder()[source]
Return type:

Atom

get_bonder_ids()[source]
Return type:

Iterator[int]

get_bonders()[source]
Return type:

Iterator[Atom]

get_core_atom_ids()[source]
Return type:

Iterator[int]

get_deleter_ids()[source]
Return type:

Iterator[int]

get_deleters()[source]
Return type:

Iterator[Atom]

get_neigh1()[source]
Return type:

Atom

get_neigh2()[source]
Return type:

Atom

get_num_bonders()[source]
Return type:

int

get_placer_ids()[source]
Return type:

Iterator[int]

with_atoms(atom_map)[source]
Parameters:

atom_map (dict[int, Atom])

Return type:

Self

with_ids(id_map)[source]
Parameters:

id_map (dict[int, int])

Return type:

Self