Package org.openscience.cdk.graph
package org.openscience.cdk.graph

ClassDescriptionCompute all simple cycles (rings) in a graph.Utility to determine the shortest paths between all pairs of atoms in a molecule.An atom container atom permutor that uses ranking and unranking to calculate the next permutation in the series.This class allows the user to iterate through the set of all possible permutations of the bond order in a given atom container.The base class for permutors of atom containers, with a single abstract method
containerFromPermutation
that should be implemented in concrete derived classes.Deprecated.Deprecated.Compute the connected components of an adjacency list.Tool class for checking whether the (sub)structure in an AtomContainer is connected.Defines a method to find the cycles of a molecule.A utility class for storing and computing the cycles of a chemical graph.Determine the uniquely defined essential cycles of a graph.Collection of static utilities for manipulating adjacency list representations stored as a int[][].Utility for storingIBond
s indexed by vertex end points.A matching is an independent edge set of a graph.Deprecated.useShortestPaths
Compute the minimum cycle basis (MCB) of a graph.Deprecated.Tools class with methods for handling molecular graphs.General permutation generator, that uses orderly generation by ranking and unranking.Compute the relevant cycles (C_{R}) of a graph.Find and reconstruct the shortest paths from a given start atom to any other connected atom.Spanning tree of a molecule.Compute the shortest cycles through each vertex triple.
ShortestPaths