Package org.openscience.cdk.isomorphism.mcss

Class RGraph

  • public class RGraph
extends Object
    This class implements the Resolution Graph (RGraph). The RGraph is a graph based representation of the search problem. An RGraph is constructed from the two compared graphs (G1 and G2). Each vertex (node) in the RGraph represents a possible association from an edge in G1 with an edge in G2. Thus two compatible bonds in two molecular graphs are represented by a vertex in the RGraph. Each edge in the RGraph corresponds to a common adjacency relationship between the 2 couple of compatible edges associated to the 2 RGraph nodes forming this edge.

    Example: 

        G1 : C-C=O  and G2 : C-C-C=0
         1 2 3           1 2 3 4

    The resulting RGraph(G1,G2) will contain 3 nodes:

    • Node A : association between bond C-C : 1-2 in G1 and 1-2 in G2
    • Node B : association between bond C-C : 1-2 in G1 and 2-3 in G2
    • Node C : association between bond C=0 : 2-3 in G1 and 3-4 in G2
    The RGraph will also contain one edge representing the adjacency between node B and C that is : bonds 1-2 and 2-3 in G1 and bonds 2-3 and 3-4 in G2.

    Once the RGraph has been built from the two compared graphs it becomes a very interesting tool to perform all kinds of structural search (isomorphism, substructure search, maximal common substructure,....).

    The search may be constrained by mandatory elements (e.g. bonds that have to be present in the mapped common substructures).

    Performing a query on an RGraph requires simply to set the constrains (if any) and to invoke the parsing method (parse())

    The RGraph has been designed to be a generic tool. It may be constructed from any kind of source graphs, thus it is not restricted to a chemical context.

    The RGraph model is independent from the CDK model and the link between both model is performed by the RTools class. In this way the RGraph class may be reused in other graph context (conceptual graphs,....)

    Important note: This implementation of the algorithm has not been optimized for speed at this stage. It has been written with the goal to clearly retrace the principle of the underlined search method. There is room for optimization in many ways including the the algorithm itself.

    This algorithm derives from the algorithm described in [Tonnelier, C. et. al.. Tetrahedron Comput. Methodol.. 1990. 3] and modified in the thesis of T. Hanser [Hanser, Th., Apprentissage automatique de méthodes de synthèse à partir d'exemples, 1993, ?Institute?].

    Author:
    Stephane Werner from IXELIS mail@ixelis.net
    Source code:
    main
    Belongs to CDK module:
    standard
    Created on:
    2002-07-17
    Requires:
    java1.4+

    • Constructor Detail

      • RGraph

        public RGraph()
        Constructor for the RGraph object and creates an empty RGraph.

    • Method Detail

      • getFirstGraphSize

        public int getFirstGraphSize()
        Returns the size of the first of the two compared graphs.
        Returns:
        The size of the first of the two compared graphs

      • getSecondGraphSize

        public int getSecondGraphSize()
        Returns the size of the second of the two compared graphs.
        Returns:
        The size of the second of the two compared graphs

      • setFirstGraphSize

        public void setFirstGraphSize​(int n1)
        Sets the size of the first of the two compared graphs.
        Parameters:
        n1 - The size of the second of the two compared graphs

      • setSecondGraphSize

        public void setSecondGraphSize​(int n2)
        Returns the size of the second of the two compared graphs.
        Parameters:
        n2 - The size of the second of the two compared graphs

      • clear

        public void clear()
        Reinitialisation of the TGraph.

      • getGraph

        public List<RNode> getGraph()
        Returns the graph object of this RGraph.
        Returns:
        The graph object, a list

      • addNode

        public void addNode​(RNode newNode)
        Adds a new node to the RGraph.
        Parameters:
        newNode - The node to add to the graph

      • parse

        public void parse​(BitSet c1,
                  BitSet c2,
                  boolean findAllStructure,
                  boolean findAllMap)
        Parsing of the RGraph. This is the main method to perform a query. Given the constrains c1 and c2 defining mandatory elements in G1 and G2 and given the search options, this method builds an initial set of starting nodes (B) and parses recursively the RGraph to find a list of solution according to these parameters.
        Parameters:
        c1 - constrain on the graph G1
        c2 - constrain on the graph G2
        findAllStructure - true if we want all results to be generated
        findAllMap - true is we want all possible 'mappings'

      • getSolutions

        public List<BitSet> getSolutions()
        Returns the list of solutions.
        Returns:
        The solution list

      • bitSetToRMap

        public List<RMap> bitSetToRMap​(BitSet set)
        Converts a RGraph bitset (set of RNode) to a list of RMap that represents the mapping between to substructures in G1 and G2 (the projection of the RGraph bitset on G1 and G2).
        Parameters:
        set - the BitSet
        Returns:
        the RMap list

      • setAllStructure

        public void setAllStructure​(boolean findAllStructure)
        Sets the 'AllStructres' option. If true all possible solutions will be generated. If false the search will stop as soon as a solution is found. (e.g. when we just want to know if a G2 is a substructure of G1 or not).
        Parameters:
        findAllStructure -

      • setAllMap

        public void setAllMap​(boolean findAllMap)
        Sets the 'finAllMap' option. If true all possible 'mappings' will be generated. If false the search will keep only one 'mapping' per structure association.
        Parameters:
        findAllMap -

      • setMaxIteration

        public void setMaxIteration​(int it)
        Sets the maxIteration for the RGraph parsing. If set to -1, then no iteration maximum is taken into account.
        Parameters:
        it - The new maxIteration value

      • toString

        public String toString()
        Returns a string representation of the RGraph.
        Overrides:
        toString in class Object
        Returns:
        the string representation of the RGraph

      • projectG1

        public BitSet projectG1​(BitSet set)
        Projects a RGraph bitset on the source graph G1.
        Parameters:
        set - RGraph BitSet to project
        Returns:
        The associate BitSet in G1

      • projectG2

        public BitSet projectG2​(BitSet set)
        Projects a RGraph bitset on the source graph G2.
        Parameters:
        set - RGraph BitSet to project
        Returns:
        The associate BitSet in G2

      • setTimeout

        public void setTimeout​(long timeout)
        Sets the time in milliseconds until the substructure search will be breaked.
        Parameters:
        timeout - Time in milliseconds. -1 to ignore the timeout.

      • setStart

        public void setStart​(long start)
        Parameters:
        start - The start time in milliseconds.