Package 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:
    main
    Belongs to CDK module:
    core

    • 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.