cgexplore.scram.TopologyCode¶

class cgexplore.scram.TopologyCode(idx, vertex_map)[source]¶

Naming convention for topology graphs.

Methods

`contains_doubles`	True if the graph contains "double-walls".
`contains_parallels`	True if the graph contains "1-loops".
`contains_xs`	True if the graph contains cycles of size x.
`get_as_string`	Convert TopologyCode to string of the vertex map.
`get_graph`	Convert TopologyCode to a graph.
`get_layout`	Take a graph and generate a layout from graph vertex positions.
`get_number_connected_components`	Get the number of connected components.
`get_nx_graph`	Convert TopologyCode to a networkx graph.
`get_weighted_graph`	Convert TopologyCode to a graph.

Attributes

`idx`
`vertex_map`

Parameters:

contains_doubles()[source]¶

True if the graph contains “double-walls”.

contains_parallels()[source]¶

True if the graph contains “1-loops”.

contains_xs(x)[source]¶

True if the graph contains cycles of size x.

Important

Warning: This does not currently handle repeated cycles, inverse cycles and shifted cycles.

get_as_string()[source]¶

Convert TopologyCode to string of the vertex map.

get_graph()[source]¶

Convert TopologyCode to a graph.

get_layout(layout_type, scale)[source]¶

Take a graph and generate a layout from graph vertex positions.

Important

Warning: There is no guarantee the graph layout will give identical coordinates in multiple runs.

Parameters:

layout_type (str) – Which networkx layout to use (of spring, kamada, spectral).
scale (float) – Scale factor to apply to eventual constructed molecule.

Returns:

Vertex positions.

Return type:

dict[int, ndarray[tuple[Any, …], dtype[float64]]]

get_number_connected_components()[source]¶

Get the number of connected components.

get_nx_graph()[source]¶

Convert TopologyCode to a networkx graph.

get_weighted_graph()[source]¶

Convert TopologyCode to a graph.