stk.Vertex

class stk.Vertex(id, position)[source]

Bases: object

An abstract base class for TopologyGraph vertices.

Notes

You might notice that some of the public methods of this abstract base class are implemented. This is purely for convenience when implementing subclasses. The implemented public methods are simply default implementations, which can be safely ignored or overridden, when implementing subclasses. Any private methods are implementation details of these default implementations.

Initialize a Vertex.

Parameters:

id (int) – The id of the vertex.
position (tuple[float, float, float] | ndarray) – The position of the vertex.

Methods

`clone`	Return a clone.
`get_cell`	Get the cell of the lattice in which the vertex is found.
`get_id`	Get the id.
`get_position`	Get the position.
`map_functional_groups_to_edges`	Map functional groups to edges.
`place_building_block`	Place building_block on the `Vertex`.
`with_position`	Get a clone at a certain position.
`with_scale`	Get a clone with a scaled position.

clone()[source]

Return a clone.

Returns:: The clone.
Return type:: Self

get_cell()[source]

Get the cell of the lattice in which the vertex is found.

Returns:: The cell of the lattice in which the vertex is found.
Return type:: ndarray

get_id()[source]

Get the id.

Returns:: The id.
Return type:: int

get_position()[source]

Get the position.

Returns:: The position of the Vertex.
Return type:: ndarray

map_functional_groups_to_edges(building_block, edges)[source]

Map functional groups to edges.

Each functional group in building_block needs to be assigned to an edge in edges.

Parameters:

building_block (BuildingBlock) – BuildingBlock The building block which is needs to have functional groups assigned to edges.
edges (tuple[Edge, ...]) – The edges to which the vertex is attached.

Returns:

A mapping from the id of a functional group in building_block to the id of the edge in edges it is assigned to.

Return type:

dict[int, int]

place_building_block(building_block, edges)[source]

Place building_block on the Vertex.

Parameters:

building_block (BuildingBlock) – The building block molecule which is to be placed on the vertex.
edges (tuple[Edge, ...]) – The edges to which the vertex is attached.

Returns:

The position matrix of building_block after being placed.

Return type:

ndarray

with_position(position)[source]

Get a clone at a certain position.

Parameters:: position (ndarray) – The desired position of the clone.
Returns:: The clone.
Return type:: Self

with_scale(scale)[source]

Get a clone with a scaled position.

Parameters:: scale (float | tuple[float, float, float]) – The value by which the position of the Vertex is scaled. Can be a single number if all axes are scaled by the same amount or a tuple of three numbers if each axis is scaled by a different value.
Returns:: The clone.
Return type:: Self