Pair selection

Routines that act on a KineticTransitionNetwork object to select pairs of minima for sampling by different criteria

topsearch.analysis.pair_selection.closest_enumeration(ktn: KineticTransitionNetwork, similarity: StandardSimilarity, coords: StandardCoordinates, neighbours: int) → list

Selector that attempts to connect all minima in the fewest number of attempts by connecting each minimum to its N nearest neighbours. Returns a list of pairs

topsearch.analysis.pair_selection.connect_to_set(ktn: KineticTransitionNetwork, similarity: StandardSimilarity, coords: StandardCoordinates, node1: int, cycles: int) → list

Finds all minima connected to node1 and finds the pairs closest in distance where one is connected and one is not. Returns the set of minima pairs in a list for use in connect_unconnected

topsearch.analysis.pair_selection.connect_unconnected(ktn: KineticTransitionNetwork, similarity: StandardSimilarity, coords: StandardCoordinates, neighbours: int) → list

Find all minima not connected to global minimum set and their nearest neighbours. Return the list of minima pairs

topsearch.analysis.pair_selection.read_pairs(text_path: str = '')

Read the set of pairs from the file pairs.txt

topsearch.analysis.pair_selection.unique_pairs(initial_pairs: list) → list

Remove any repeated pairs from a given list