class pele.landscape.TSGraph(database, minima=None, no_edges=False)[source]

Wrapper to represent a database object as a graph

This class is primarily used by DoubleEndedConnect and has a number of utility functions for that purpose. If you want access to the networkx Graph object, it is stored as self.graph

Parameters :

database :

the database object to represent

minima : list of minima, optional

if none, include all minima and transition states from the database, else include only the minima in the list

no_edges : bool, optional

If true include no transition states in the graph. This is used, for example, to try to find a new connection between two minima.


a graph can be easily constructed from a database:

>>> graph = TSGraph(database)

the networkx graph is accessed directly by

>>> networkx_graph = graph.graph


addMinimum(minimum) add a minimum to the database and graph
areConnected(min1, min2)
getPath(min1, min2)
mergeMinima(min1, min2) delete minima2. all transition states pointing to min2 should

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