stk.cage.AngledVertex

class stk.cage.AngledVertex(id, position, use_neighbor_placement=True, aligner_edge=0)[source]

Bases: _CageVertex

Parameters:

id (int) – The id of the vertex.
position (ndarray) – The position of the vertex.
use_neighbor_placement (bool) – If True, the position of the vertex will be updated based on the neighboring functional groups.
aligner_edge (int) – The edge which is used to align the BuildingBlock placed on the vertex. The first FunctionalGroup is rotated such that it lies exactly on this Edge. Must be between 0 and the number of edges the vertex is connected to.

Methods

`clone`	Return a clone.
`get_aligner_edge`	Return the aligner edge of the vertex.
`get_cell`	Get the cell of the lattice in which the vertex is found.
`get_id`	Get the id.
`get_position`	Get the position.
`init_at_center`	Initialize a `_CageVertex` in the middle of vertices.
`map_functional_groups_to_edges`	Map functional groups to edges.
`place_building_block`	Place building_block on the `Vertex`.
`use_neighbor_placement`	`True` if the position should be updated based on neighbors.
`with_aligner_edge`	Return a clone with a different aligner_edge.
`with_position`	Get a clone at a certain position.
`with_scale`	Get a clone with a scaled position.
`with_use_neighbor_placement`	Return a clone with a different use_neighbor_placement.

classmethod init_at_center(id, vertices)

Initialize a _CageVertex in the middle of vertices.

Parameters:

id (int) – The id of the initialized vertex.
vertices (tuple[Vertex, ...]) – The vertices at whose center this one needs to be.

Returns:

The new vertex.

Return type:

Self

clone()

Return a clone.

Returns:: The clone.

get_aligner_edge()

Return the aligner edge of the vertex.

Returns:: The aligner edge.
Return type:: int

get_cell()

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()

Get the id.

Returns:: The id.
Return type:: int

get_position()

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 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.

use_neighbor_placement()

True if the position should be updated based on neighbors.

Returns:: True if the position of the vertex should be updated based on the positions of functional groups on neighboring vertices.
Return type:: bool

with_aligner_edge(aligner_edge)

Return a clone with a different aligner_edge.

Parameters:: aligner_edge (int) – The aligner edge of the clone.
Returns:: The clone. Has the same type as the original instance.
Return type:: Self

with_position(position)

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)

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

with_use_neighbor_placement(use_neighbor_placement)

Return a clone with a different use_neighbor_placement.

Parameters:: use_neighbor_placement (bool) – True if the position should be updated based on neighbors.
Returns:: The clone. Has the same type as the original instance.
Return type:: Self