stk.MoleculeState

class stk.MoleculeState

Bases: object

Represents the state of a molecule under construction.

Initialize a _MoleculeState instance.

Methods

clone	Return a clone.
get_atom_infos	Yield the atom infos of the molecule.
get_atoms	Yield the atoms of the molecule.
get_bond_infos	Yield the bond infos of the molecule.
get_bonds	Yield the bonds of the molecule.
get_edge_group_functional_groups	Yield the functional groups associated with edge_group.
get_position_matrix	Get the position matrix of the molecule.
with_placement_results	Return a clone holding the placement results.
with_position_matrix	Return a clone holding the position_matrix.
with_reaction_results	Return a clone holding the reaction results.

clone()

Return a clone.

Returns:

The clone. Has the same type as the original instance.

Return type:

_MoleculeState

get_atom_infos()

Yield the atom infos of the molecule.

Yields:

AtomInfo – An atom info of the molecule.

get_atoms()

Yield the atoms of the molecule.

Yields:

Atom – An atom of the molecule.

get_bond_infos()

Yield the bond infos of the molecule.

Yields:

BondInfo – The bond info of the molecule.

get_bonds()

Yield the bonds of the molecule.

Yields:

Bond – A bond of the molecule.

get_edge_group_functional_groups(edge_group)

Yield the functional groups associated with edge_group.

Parameters:

edge_group (EdgeGroup) – The edge group, whose functional groups are desired.

Yields:

FunctionalGroup – A functional group which belongs to edge_group.

get_position_matrix()

Get the position matrix of the molecule.

Returns:

The position matrix.

Return type:

numpy.ndarray

with_placement_results(vertices, edges, building_blocks, results)

Return a clone holding the placement results.

Parameters:

• vertices (tuple of Vertex) – The vertices used for placement.

• edges (tuple) – For each vertex in vertices, a tuple of Edge instances connected to it.

• building_blocks (tuple of BuildingBlock) – For each vertex in vertices, the building block placed on it.

• results (tuple of _PlacementResult) – For every vertex in vertices, the result of the placement.

Returns:

The clone holding the placement results. Has the same type as the original instance.

Return type:

_MoleculeState

with_position_matrix(position_matrix)

Return a clone holding the position_matrix.

Parameters:

position_matrix (numpy.ndarray) – The position matrix of the clone. The shape of the matrix is (n, 3).

Returns:

The clone holding the new position matrix. Has the same type as the original instance.

Return type:

_MoleculeState

with_reaction_results(reactions, results)

Return a clone holding the reaction results.

Parameters:

• reactions (tuple of Reaction) – The reactions.

• results (ReactionResult) – For each reaction in reactions, its result.

Returns:

The clone holding the reaction results. Has the same type as the original instance.

Return type:

_MoleculeState