Interface  Description 

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

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 
Utility class that finds the shortest bond path between two atoms using
a breadth first search.

BiconnectivityInspector 
Finds the biconnected components of a graph.

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
IBond s indexed by vertex end points. 
Matching 
A matching is an independent edge set of a graph.

MinimalPathIterator 
Iterates over all shortest paths between two vertices in an undirected, unweighted graph.

MinimumCycleBasis 
Compute the minimum cycle basis (MCB) of a graph.

MoleculeGraphs 
Utility class to create a molecule graph for use with JGraphT.

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 (C_{R}) 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.

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