stk.Aldehyde

class stk.Aldehyde(carbon, oxygen, hydrogen, atom, bonders, deleters, placers=None)

Bases: GenericFunctionalGroup

Represents an aldehyde functional group.

The structure of the functional group is given by the pseudo-SMILES [atom][carbon](=[oxygen])[hydrogen].

Initialize a Aldehyde instance.

Parameters:

• carbon (C) – The carbon atom.

• oxygen (O) – The oxygen atom.

• hydrogen (H) – The hydrogen atom.

• atom (Atom) – The atom to which the functional group is attached.

• bonders (tuple[Atom, ...]) – The bonder atoms.

• deleters (tuple[Atom, ...]) – The deleter atoms.

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

Methods

clone	Return a clone.
get_atom	Get the atom to which the functional group is attached.
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_carbon	Get the carbon atom.
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_hydrogen	Get the hydrogen atom.
get_num_bonders	Get the number of bonder atoms.
get_oxygen	Get the oxygen 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.

Return type:

Aldehyde

get_atom()

Get the atom to which the functional group is attached.

Returns:

The atom to which the functional group is attached.

Return type:

Atom

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_carbon()

Get the carbon atom.

Returns:

The carbon 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_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_hydrogen()

Get the hydrogen atom.

Returns:

The hydrogen atom.

Return type:

H

get_num_bonders()

Get the number of bonder atoms.

Returns:

The number of bonder atoms.

Return type:

int

get_oxygen()

Get the oxygen atom.

Returns:

The oxygen atom.

Return type:

O

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:

Aldehyde