Graph properties

Methods for analysing the network properties of the kinetic transition network graphs

topsearch.analysis.graph_properties.all_minima_connected(ktn: KineticTransitionNetwork) → bool

Wrapper for checking if the graph is fully connected

topsearch.analysis.graph_properties.are_nodes_connected(ktn: KineticTransitionNetwork, node_i: int, node_j: int) → bool

Check if two minima are connected in a given graph

topsearch.analysis.graph_properties.disconnected_height(ktn: KineticTransitionNetwork, node_i: int, node_j: int, max_ts_energy: float, e_range: float) → float

Return the height at which two nodes become disconnected

topsearch.analysis.graph_properties.get_connections(ktn: KineticTransitionNetwork, min_node: int) → list

Find the transition states directly connected to a given node

topsearch.analysis.graph_properties.remove_edges_threshold(H: MultiGraph, energy1: float) → MultiGraph

Remove any transition states that have an energy above energy1

topsearch.analysis.graph_properties.unconnected_component(ktn: KineticTransitionNetwork) → set

Check which minima are not connected to the global minimum. Return the set of minima that are unconnected