Package org.openscience.cdk.graph

Interface Summary

Interface	Description
CycleFinder	Defines a method to find the cycles of a molecule.

Class Summary

Class	Description
AllCycles	Compute all simple cycles (rings) in a graph.
AllPairsShortestPaths	Utility to determine the shortest paths between all pairs of atoms in a molecule.
AtomContainerAtomPermutor	An atom container atom permutor that uses ranking and unranking to calculate the next permutation in the series.
AtomContainerBondPermutor	This class allows the user to iterate through the set of all possible permutations of the bond order in a given atom container.
AtomContainerPermutor	The base class for permutors of atom containers, with a single abstract method containerFromPermutation that should be implemented in concrete derived classes.
BFSShortestPath	Deprecated Use ShortestPaths
BiconnectivityInspector	Deprecated Use RingSearch or Cycles.markRingAtomsAndBonds(IAtomContainer)
ConnectedComponents	Compute the connected components of an adjacency list.
ConnectivityChecker	Tool class for checking whether the (sub)structure in an AtomContainer is connected.
Cycles	A utility class for storing and computing the cycles of a chemical graph.
EssentialCycles	Determine the uniquely defined essential cycles of a graph.
GraphUtil	Collection of static utilities for manipulating adjacency list representations stored as a int[][].
GraphUtil.EdgeToBondMap	Utility for storing IBonds indexed by vertex end points.
Matching	A matching is an independent edge set of a graph.
MinimalPathIterator	Deprecated use ShortestPaths
MinimumCycleBasis	Compute the minimum cycle basis (MCB) of a graph.
MoleculeGraphs	Deprecated
PathTools	Tools class with methods for handling molecular graphs.
Permutor	General permutation generator, that uses orderly generation by ranking and unranking.
RelevantCycles	Compute the relevant cycles (CR) of a graph.
ShortestPaths	Find and reconstruct the shortest paths from a given start atom to any other connected atom.
SpanningTree	Spanning tree of a molecule.
TripletShortCycles	Compute the shortest cycles through each vertex triple.