pele.landscape.TSGraph

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

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

minimalist of minima, optional

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

no_edgesbool, 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.

See also

DoubleEndedConnect

Examples

a graph can be easily constructed from a database:

>>> graph = TSGraph(database)

the networkx graph is accessed directly by

>>> networkx_graph = graph.graph

Methods

addMinimum(minimum)	add a minimum to the database and graph
addTransitionState(ts)
areConnected(min1, min2)
getPath(min1, min2)
mergeMinima(min1, min2)	delete minima2.
refresh()

Attributes