topo_metrics.symbols#

Classes#

`VertexSymbol`	Vertex Symbol (VS) representation.
`CARVS`	Cummulative All-Rings Vertex Symbol (CARVS) vector.

Functions#

`pad_carvs`(→ Sequence[CARVS])	Pad the vectors of a list of CARVS objects to the same length.
`pad_carvs_per_atom`(...)	Pad the CARVs per atom to the same length.
`get_all_topological_distances`(→ numpy.ndarray)	Compute the topological distances between all pairs of CARVS objects.

Module Contents#

class topo_metrics.symbols.VertexSymbol[source]#

Bases: NamedTuple

Vertex Symbol (VS) representation.

vector[source]#: The Vertex Symbol vector.

vector_all_rings[source]#: The Vertex Symbol vector considering all rings.

vector: list[list[int]][source]#

vector_all_rings: list[list[int]][source]#

to_str(all_rings: bool = False) → str[source]#

Returns the string representation of the VertexSymbol.

If all_rings is True, ring counts are grouped and formatted with multiplicity. Otherwise, only the smallest ring sizes are shown, with multiplicity for repeated values.

Parameters:: all_rings – If True, ring counts are grouped and formatted with multiplicity. Otherwise, only the smallest ring sizes are shown, with multiplicity for repeated values.
Return type:: A string representation of the VertexSymbol.

class topo_metrics.symbols.CARVS[source]#

Bases: NamedTuple

Cummulative All-Rings Vertex Symbol (CARVS) vector.

vector[source]#: The CARVS vector.

spread[source]#: The standard deviation of the CARVS vectors in the network.

is_single_node[source]#: True if the CARVS vector is for a single-node network, False otherwise.

vector: numpy.typing.NDArray[numpy.floating][source]#

spread: float[source]#

is_single_node: bool[source]#

classmethod from_list(carvs_list: Sequence[CARVS]) → CARVS[source]#

Construct a CARVS object from a list of CARVS objects, averaging the vectors and spreads.

Parameters:

carvs_list – One or more CARVS objects to be averaged.

Returns:

A new CARVS object whose vector is the average of all input vectors,
whose spread is the average of all input spreads, and whose
’is_single_node’ is True only if it is True for every entry in
carvs_list.

Raises:

ValueError – If carvs_list is empty or if the vectors in carvs_list do not all have the same length.

topo_metrics.symbols.pad_carvs(carvs_list: Sequence[CARVS]) → Sequence[CARVS][source]#

Pad the vectors of a list of CARVS objects to the same length.

Parameters:: carvs_list – A list of CARVS objects.
Return type:: A list of CARVS objects with the vectors padded to the same length.

topo_metrics.symbols.pad_carvs_per_atom(all_carvs: list[numpy.typing.NDArray[numpy.int_]]) → list[numpy.typing.NDArray[numpy.int_]][source]#

Pad the CARVs per atom to the same length.

Parameters:: all_carvs – List of CARVs per atom.
Return type:: List of padded CARVs per atom.

topo_metrics.symbols.get_all_topological_distances(carvs: list[CARVS]) → numpy.ndarray[source]#

Compute the topological distances between all pairs of CARVS objects.