@Deprecated public class CDKRGraph extends Object
Example:
G1 : C-C=O and G2 : C-C-C=0 1 2 3 1 2 3 4
The resulting CDKRGraph(G1,G2) will contain 3 nodes:
Once the CDKRGraph has been built from the two compared graphs maxIterator 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 CDKRGraph requires simply to set the constrains (if any) and to invoke the parsing method (parse())
The CDKRGraph has been designed to be a generic tool. It may be constructed from any kind of source graphs, thus maxIterator is not restricted to a chemical context.
The CDKRGraph model is indendant from the CDK model and the link between both model is performed by the RTools class. In this way the CDKRGraph 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?).
Constructor and Description |
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CDKRGraph()
Deprecated.
Constructor for the CDKRGraph object and creates an empty CDKRGraph.
|
Modifier and Type | Method and Description |
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void |
addNode(CDKRNode newNode)
Deprecated.
Adds a new node to the CDKRGraph.
|
List<CDKRMap> |
bitSetToRMap(BitSet set)
Deprecated.
Converts a CDKRGraph bitset (set of CDKRNode)
to a list of CDKRMap that represents the
mapping between to substructures in G1 and G2
(the projection of the CDKRGraph bitset on G1
and G2).
|
void |
clear()
Deprecated.
Reinitialisation of the TGraph.
|
int |
getFirstGraphSize()
Deprecated.
Returns the size of the first of the two
compared graphs.
|
List<CDKRNode> |
getGraph()
Deprecated.
Returns the graph object of this CDKRGraph.
|
int |
getSecondGraphSize()
Deprecated.
Returns the size of the second of the two
compared graphs.
|
List<BitSet> |
getSolutions()
Deprecated.
Returns the list of solutions.
|
void |
parse(BitSet sourceBitSet,
BitSet targetBitSet,
boolean findAllStructure,
boolean findAllMap,
TimeManager timeManager)
Deprecated.
Parsing of the CDKRGraph.
|
BitSet |
projectG1(BitSet set)
Deprecated.
Projects a CDKRGraph bitset on the source graph G1.
|
BitSet |
projectG2(BitSet set)
Deprecated.
Projects a CDKRGraph bitset on the source graph G2.
|
void |
setAllMap(boolean findAllMap)
Deprecated.
Sets the 'finAllMap' option.
|
void |
setAllStructure(boolean findAllStructure)
Deprecated.
Sets the 'AllStructres' option.
|
void |
setFirstGraphSize(int graphSize)
Deprecated.
Sets the size of the first of the two
compared graphs.
|
void |
setMaxIteration(int maxIterator)
Deprecated.
Sets the maxIteration for the CDKRGraph parsing.
|
void |
setSecondGraphSize(int graphSize)
Deprecated.
Returns the size of the second of the two
compared graphs.
|
String |
toString()
Deprecated.
Returns a string representation of the CDKRGraph.
|
public CDKRGraph()
public int getFirstGraphSize()
public int getSecondGraphSize()
public void setFirstGraphSize(int graphSize)
graphSize
- The size of the second of the two compared graphspublic void setSecondGraphSize(int graphSize)
graphSize
- The size of the second of the two compared graphspublic void clear()
public List<CDKRNode> getGraph()
public void addNode(CDKRNode newNode)
newNode
- The node to add to the graphpublic void parse(BitSet sourceBitSet, BitSet targetBitSet, boolean findAllStructure, boolean findAllMap, TimeManager timeManager) throws CDKException
sourceBitSet
- constrain on the graph G1targetBitSet
- constrain on the graph G2findAllStructure
- true if we want all results to be generatedfindAllMap
- true is we want all possible 'mappings'timeManager
- CDKException
public List<BitSet> getSolutions()
public List<CDKRMap> bitSetToRMap(BitSet set)
set
- the BitSetpublic void setAllStructure(boolean findAllStructure)
findAllStructure
- public void setAllMap(boolean findAllMap)
findAllMap
- public void setMaxIteration(int maxIterator)
maxIterator
- The new maxIteration valuepublic String toString()
public BitSet projectG1(BitSet set)
set
- CDKRGraph BitSet to projectCopyright © 2021. All rights reserved.