public class GraphUtil extends Object
ShortestPaths
,
RingSearch
Modifier and Type  Class and Description 

static class 
GraphUtil.EdgeToBondMap
Utility for storing
IBond s indexed by vertex end points. 
Modifier and Type  Method and Description 

static int[] 
cycle(int[][] graph,
int[] vertices)
Arrange the vertices in a simple cyclic path.

static int[][] 
subgraph(int[][] graph,
int[] include)
Create a subgraph by specifying the vertices from the original graph to include in the subgraph.

static int[][] 
toAdjList(IAtomContainer container)
Create an adjacent list representation of the container.

static int[][] 
toAdjList(IAtomContainer container,
GraphUtil.EdgeToBondMap bondMap)
Create an adjacent list representation of the
container and
fill in the bondMap for quick lookup. 
static int[][] 
toAdjListSubgraph(IAtomContainer container,
Set<IBond> include)
Create an adjacent list representation of the container that only
includes bonds that are in the set provided as an argument.

public static int[][] toAdjList(IAtomContainer container)
container
 the moleculeNullPointerException
 the container was nullIllegalArgumentException
 a bond was found which contained atoms
not in the moleculepublic static int[][] toAdjListSubgraph(IAtomContainer container, Set<IBond> include)
container
 the moleculeNullPointerException
 the container was nullIllegalArgumentException
 a bond was found which contained atoms
not in the moleculepublic static int[][] toAdjList(IAtomContainer container, GraphUtil.EdgeToBondMap bondMap)
container
and
fill in the bondMap
for quick lookup.container
 the moleculebondMap
 a map to index the bonds intoNullPointerException
 the container was nullIllegalArgumentException
 a bond was found which contained atoms
not in the moleculepublic static int[][] subgraph(int[][] graph, int[] include)
int[][] g = toAdjList(naphthalene); int[] vs = new int[]{0, 1, 2, 3, 4, 5}; int[][] h = subgraph(g, vs); // for the vertices in h, the provided 'vs' gives the original index for(int v = 0; v < h.length; v++) { // vs[v] is 'v' in 'g' }
graph
 adjacency list graphinclude
 the vertices of he graph to include in the subgraphpublic static int[] cycle(int[][] graph, int[] vertices)
IllegalArgumentException
is thrown.graph
 a graphvertices
 set of verticesIllegalArgumentException
 thrown if the vertices do not form a
cycleRingSearch.isolated()
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