org.openscience.cdk.ringsearch

Interface CyclicVertexSearch

public interface CyclicVertexSearch

Describes a search to identify vertices which belong to elementary cycles and if those cycles are isolated or are part of a fused system. We define a cycle as isolated if it edge disjoint with all other cycles. This corresponds to the isolated and spiro rings of a chemical structures.

Author:

John May

Source code:

master

Belongs to CDK module:

core

Method Summary

Modifier and Type	Method and Description
int[]	cyclic() The set of cyclic vertices.
boolean	cyclic(int v) Returns true if the vertex v is in a cycle.
boolean	cyclic(int u, int v) Is the edge between the two vertices u and v in a cycle?
int[][]	fused() Construct the sets of vertices which belong to fused cycle systems (share at least one edge).
int[][]	isolated() Construct the sets of vertices which belong to isolated cycles.
int	numCycles() Returns the number of cycles (circuit rank, frère jacques number, num SSSR).
int[]	vertexColor() Build an indexed lookup of vertex color.

Method Detail

numCycles

int numCycles()

Returns the number of cycles (circuit rank, frère jacques number, num SSSR).

Returns:

number of cycles

cyclic

boolean cyclic(int v)

Returns true if the vertex v is in a cycle.

Parameters:

v - a vertex identifier by index

Returns:

whether the vertex is in a cycle

cyclic

boolean cyclic(int u,
               int v)

Is the edge between the two vertices u and v in a cycle?

Parameters:

u - a vertex

v - another vertex

Returns:

whether the edge is cycle

cyclic

int[] cyclic()

The set of cyclic vertices.

Returns:

the cyclic vertices of the molecule.

isolated

int[][] isolated()

Construct the sets of vertices which belong to isolated cycles. Each row in the array describes a set of cyclic vertices which is edge disjoint with all other elementary cycles.

Returns:

vertices belonging to the isolated rings

fused

int[][] fused()

Construct the sets of vertices which belong to fused cycle systems (share at least one edge). Each row in the array describes a set of vertices in a separate fused system. Each fused system is edge disjoint with every other fused system.

Returns:

vertices belonging to the fused cycles

vertexColor

int[] vertexColor()

Build an indexed lookup of vertex color. The vertex color indicates which cycle a given vertex belongs. If a vertex belongs to more then one cycle it is colored '0'. If a vertex belongs to no cycle it is colored '-1'.

Returns:

vertex colors