Class RGraph
 java.lang.Object

 org.openscience.cdk.isomorphism.mcss.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 : CC=O and G2 : CCC=0 1 2 3 1 2 3 4
The resulting RGraph(G1,G2) will contain 3 nodes:
 Node A : association between bond CC : 12 in G1 and 12 in G2
 Node B : association between bond CC : 12 in G1 and 23 in G2
 Node C : association between bond C=0 : 23 in G1 and 34 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:
 20020717
 Requires:
 java1.4+


Constructor Summary
Constructors Constructor Description RGraph()
Constructor for the RGraph object and creates an empty RGraph.

Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addNode(RNode newNode)
Adds a new node to the RGraph.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).void
clear()
Reinitialisation of the TGraph.int
getFirstGraphSize()
Returns the size of the first of the two compared graphs.List<RNode>
getGraph()
Returns the graph object of this RGraph.int
getSecondGraphSize()
Returns the size of the second of the two compared graphs.List<BitSet>
getSolutions()
Returns the list of solutions.void
parse(BitSet c1, BitSet c2, boolean findAllStructure, boolean findAllMap)
Parsing of the RGraph.BitSet
projectG1(BitSet set)
Projects a RGraph bitset on the source graph G1.BitSet
projectG2(BitSet set)
Projects a RGraph bitset on the source graph G2.void
setAllMap(boolean findAllMap)
Sets the 'finAllMap' option.void
setAllStructure(boolean findAllStructure)
Sets the 'AllStructres' option.void
setFirstGraphSize(int n1)
Sets the size of the first of the two compared graphs.void
setMaxIteration(int it)
Sets the maxIteration for the RGraph parsing.void
setSecondGraphSize(int n2)
Returns the size of the second of the two compared graphs.void
setStart(long start)
void
setTimeout(long timeout)
Sets the time in milliseconds until the substructure search will be breaked.String
toString()
Returns a string representation of the 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 G1c2
 constrain on the graph G2findAllStructure
 true if we want all results to be generatedfindAllMap
 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.

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.

