org.openscience.cdk.graph

Interface CycleFinder

public interface CycleFinder

Defines a method to find the cycles of a molecule. The distinction between a cycle and a ring is that cycles are stored as indices (int[]) while rings are stored as atoms (IAtom[]) in a IRing.

Author:

John May

Source code:

master

Belongs to CDK module:

core

Method Summary

Modifier and Type	Method and Description
Cycles	find(IAtomContainer molecule) Find the cycles of the provided molecule.
Cycles	find(IAtomContainer molecule, int length) Find the cycles of the provided molecule.
Cycles	find(IAtomContainer molecule, int[][] graph, int length) Find the cycles of the provided molecule when an adjacent relation (graph) is already available.

Method Detail

find

Cycles find(IAtomContainer molecule)
     throws Intractable

Find the cycles of the provided molecule.

Parameters:

molecule - a molecule, can be disconnected.

Returns:

an instance for querying the cycles (rings) in the molecule

Throws:

Intractable - thrown if problem could not be solved within some predefined bounds.

find

Cycles find(IAtomContainer molecule,
            int length)
     throws Intractable

Find the cycles of the provided molecule.

Parameters:

molecule - a molecule, can be disconnected.

length - maximum length cycle to find (set to molecule.getAtomCount() for all)

Returns:

an instance for querying the cycles (rings) in the molecule

Throws:

Intractable - thrown if problem could not be solved within some predefined bounds.

find

Cycles find(IAtomContainer molecule,
            int[][] graph,
            int length)
     throws Intractable

Find the cycles of the provided molecule when an adjacent relation (graph) is already available. The graph can be obtained through GraphUtil.toAdjList(IAtomContainer), for convenience find(IAtomContainer, int) will automatically create the graph.

Parameters:

molecule - input structure

graph - adjacency list representation for fast traversal

length - maximum length cycle to find (set to molecule.getAtomCount() for all)

Returns:

an instance for querying the cycles (rings) in the molecule

Throws:

Intractable - thrown if problem could not be solved within some predefined bounds.