stk.rotaxane.AxleVertex

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

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()

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(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 The building block which is needs to have functional groups assigned to edges.
edges – 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.

place_building_block(building_block, edges)[source]

Place building_block on the Vertex.

Parameters:

building_block – The building block molecule which is to be placed on the vertex.
edges – The edges to which the vertex is attached.

Returns:

The position matrix of building_block after being placed.

with_position(position)

Get a clone at a certain position.

with_scale(scale)

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