Added a method to all Ring Finders to add the detected ring set to th…

…e respective AtomContainer as a property.

The relevant variables have been added to CDKConstants.


git-svn-id: https://cdk.svn.sourceforge.net/svnroot/cdk/trunk/cdk@5704 eb4e18e3-b210-0410-a6ab-dec725e4b171

src/org/openscience/cdk/CDKConstants.java

@@ -232,7 +232,18 @@ public class CDKConstants {
     /** A smallest set of smallest rings computed for this molecule. */
     public static final String SMALLEST_RINGS = "SmallestRings";
 
+    /** The essential rings computed for this molecule. 
+     *  The concept of Essential Rings is defined in 
+     *  SSSRFinder
+     */
+    public static final String ESSENTIAL_RINGS = "EssentialRings";
 
+    /** The relevant rings computed for this molecule. 
+     *  The concept of relevant Rings is defined in 
+     *  SSSRFinder
+     */
+    public static final String RELEVANT_RINGS = "RelevantRings";
+
 
     /****************************************
     * Some predefined property names for    *

src/org/openscience/cdk/io/JMEReader.java

@@ -37,10 +37,9 @@
 
 import org.jmol.adapter.smarter.SmarterJmolAdapter;
 import org.jmol.api.JmolAdapter;
-import org.openscience.cdk.interfaces.AtomContainer;
+import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.interfaces.IChemObject;
 import org.openscience.cdk.interfaces.IMolecule;
-import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.io.formats.IChemFormat;
 import org.openscience.cdk.io.formats.JMEFormat;
 import org.openscience.cdk.io.setting.IOSetting;

src/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java

@@ -117,7 +117,8 @@ public class UniversalIsomorphismTester {
    * @return     true if the 2 molecule are isomorph
    */
   public static boolean isIsomorph(IAtomContainer g1, IAtomContainer g2)  throws CDKException{
-    return (getIsomorphMap(g1, g2) != null);
+	  if (g2.getAtomCount() != g1.getAtomCount()) return false;
+	  return (getIsomorphMap(g1, g2) != null);
   }
 
 
@@ -237,7 +238,9 @@ public static List getSubgraphAtomsMap(IAtomContainer g1, IAtomContainer g2)  th
    * @return     true if g2 a subgraph on g1
    */
   public static boolean isSubgraph(IAtomContainer g1, IAtomContainer g2)  throws CDKException{
-    return (getSubgraphMap(g1, g2) != null);
+      if (g2.getAtomCount() > g1.getAtomCount()) return false;
+      if (!testSubgraphHeuristics(g1, g2)) return false; 
+	  return (getSubgraphMap(g1, g2) != null);
   }
 
 
@@ -785,5 +788,107 @@ private static boolean queryAdjacency(IBond a1, IBond b1, IBond a2, IBond b2) {
 
   }
 
+  /**
+   *  Checks some simple heuristics for whether the subgraph query can 
+   *  realistically be a subgraph of the supergraph. If, for example, the 
+   *  number of nitrogen atoms in the query is larger than that of the supergraph
+   *  it cannot be part of it.
+   *
+   * @param  ac1  the supergraph to be checked
+   * @param  ac2  the subgraph to be tested for
+   * @return    true if the subgraph ac2 has a chance to be a subgraph of ac1
+   *            
+   */
+
+  private static boolean testSubgraphHeuristics(IAtomContainer ac1, IAtomContainer ac2)
+  {
+	  int ac1SingleBondCount = 0;
+	  int ac1DoubleBondCount = 0;
+	  int ac1TripleBondCount = 0;
+	  int ac1AromaticBondCount = 0;
+	  int ac2SingleBondCount = 0;
+	  int ac2DoubleBondCount = 0;
+	  int ac2TripleBondCount = 0;
+	  int ac2AromaticBondCount = 0;
+	  int ac1SCount = 0;
+	  int ac1OCount = 0;
+	  int ac1NCount = 0;
+	  int ac1FCount = 0;
+	  int ac1ClCount = 0;
+	  int ac1BrCount = 0;
+	  int ac1ICount = 0;
+	  int ac1CCount = 0;
+
+	  int ac2SCount = 0;
+	  int ac2OCount = 0;
+	  int ac2NCount = 0;
+	  int ac2FCount = 0;
+	  int ac2ClCount = 0;
+	  int ac2BrCount = 0;
+	  int ac2ICount = 0;
+	  int ac2CCount = 0;
+
+	  IBond bond = null;
+	  IAtom atom = null;
+	  for (int i = 0; i < ac1.getBondCount(); i++)
+	  {
+		  bond = ac1.getBondAt(i);
+		  if (bond.getFlag(CDKConstants.ISAROMATIC)) ac1AromaticBondCount ++;
+		  else if (bond.getOrder() == 1) ac1SingleBondCount ++;
+		  else if (bond.getOrder() == 2) ac1DoubleBondCount ++;
+		  else if (bond.getOrder() == 3) ac1TripleBondCount ++;	  
+	  }
+	  for (int i = 0; i < ac2.getBondCount(); i++)
+	  {
+		  bond = ac2.getBondAt(i);
+		  if (bond.getFlag(CDKConstants.ISAROMATIC)) ac2AromaticBondCount ++;
+		  else if (bond.getOrder() == 1) ac2SingleBondCount ++;
+		  else if (bond.getOrder() == 2) ac2DoubleBondCount ++;
+		  else if (bond.getOrder() == 3) ac2TripleBondCount ++;	  
+	  }
+
+	  if (ac2SingleBondCount > ac1SingleBondCount) return false;
+	  if (ac2AromaticBondCount > ac1AromaticBondCount) return false;
+	  if (ac2DoubleBondCount > ac1DoubleBondCount) return false;
+	  if (ac2TripleBondCount > ac1TripleBondCount) return false;
+
+	  for (int i = 0; i < ac1.getAtomCount(); i++)
+	  {
+		  atom = ac1.getAtomAt(i);
+		  if (atom.getSymbol().equals("S")) ac1SCount ++;
+		  else if (atom.getSymbol().equals("N")) ac1NCount ++;
+		  else if (atom.getSymbol().equals("O")) ac1OCount ++;
+		  else if (atom.getSymbol().equals("F")) ac1FCount ++;
+		  else if (atom.getSymbol().equals("Cl")) ac1ClCount ++;
+		  else if (atom.getSymbol().equals("Br")) ac1BrCount ++;
+		  else if (atom.getSymbol().equals("I")) ac1ICount ++;
+		  else if (atom.getSymbol().equals("C")) ac1CCount ++;
+	  }
+	  for (int i = 0; i < ac2.getAtomCount(); i++)
+	  {
+		  atom = ac2.getAtomAt(i);
+		  if (atom.getSymbol().equals("S")) ac2SCount ++;
+		  else if (atom.getSymbol().equals("N")) ac2NCount ++;
+		  else if (atom.getSymbol().equals("O")) ac2OCount ++;
+		  else if (atom.getSymbol().equals("F")) ac2FCount ++;
+		  else if (atom.getSymbol().equals("Cl")) ac2ClCount ++;
+		  else if (atom.getSymbol().equals("Br")) ac2BrCount ++;
+		  else if (atom.getSymbol().equals("I")) ac2ICount ++;
+		  else if (atom.getSymbol().equals("C")) ac2CCount ++;
+	  }
+
+	  if (ac1SCount < ac2SCount) return false;
+	  if (ac1NCount < ac2NCount) return false;
+	  if (ac1OCount < ac2OCount) return false;
+	  if (ac1FCount < ac2FCount) return false;
+	  if (ac1ClCount < ac2ClCount) return false;
+	  if (ac1BrCount < ac2BrCount) return false;
+	  if (ac1ICount < ac2ICount) return false;
+	  if (ac1CCount < ac2CCount) return false;
+
+
+	  return true;
+  }
+
 }
 

src/org/openscience/cdk/ringsearch/AllRingsFinder.java

@@ -32,13 +32,14 @@
 import java.util.Enumeration;
 import java.util.Vector;
 
+import org.openscience.cdk.CDKConstants;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.graph.SpanningTree;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.interfaces.IRing;
 import org.openscience.cdk.interfaces.IRingSet;
-import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.graph.SpanningTree;
 
 /**
  *  Finds the Set of all Rings. This is an implementation of the algorithm
@@ -141,6 +142,7 @@ public IRingSet findAllRings(IAtomContainer atomContainer, boolean useSSSR) thro
 		{
 			doSearch(ac, pathes, ringSet);
 		}
+		atomContainer.setProperty(CDKConstants.ALL_RINGS, ringSet);
 		return ringSet;
 	}
 

src/org/openscience/cdk/ringsearch/FiguerasSSSRFinder.java

@@ -31,10 +31,11 @@
 import java.util.Vector;
 
 import org.openscience.cdk.Atom;
-import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.Molecule;
 import org.openscience.cdk.Ring;
 import org.openscience.cdk.RingSet;
+import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.tools.LoggingTool;
 
 /**
@@ -189,6 +190,7 @@ else if (smallestDegree == 3)
 		logger.debug("fullSet.size(): " + fullSet.size());				
 		logger.debug("trimSet.size(): " + trimSet.size());		
 		logger.debug("trimCounter: " + trimCounter);
+		molecule.setProperty(CDKConstants.SMALLEST_RINGS, sssr);
 	return sssr;	  
 	}
 

src/org/openscience/cdk/ringsearch/SSSRFinder.java

@@ -34,11 +34,12 @@
 import java.util.List;
 
 import org._3pq.jgrapht.UndirectedGraph;
+import org.openscience.cdk.CDKConstants;
+import org.openscience.cdk.graph.MoleculeGraphs;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IRing;
 import org.openscience.cdk.interfaces.IRingSet;
-import org.openscience.cdk.graph.MoleculeGraphs;
 import org.openscience.cdk.ringsearch.cyclebasis.CycleBasis;
 import org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle;
 
@@ -94,7 +95,8 @@ public IRingSet findSSSR() {
 		if (atomContainer==null) {
 			return null;
 		}
-
+		IRingSet ringSet = toRingSet(atomContainer, cycleBasis().cycles());
+		atomContainer.setProperty(CDKConstants.SMALLEST_RINGS, ringSet);
 		return toRingSet(atomContainer, cycleBasis().cycles());	  
 
 	}
@@ -110,6 +112,8 @@ public IRingSet findEssentialRings() {
 		if (atomContainer==null) {
 			return null;
 		}
+		IRingSet ringSet = toRingSet(atomContainer, cycleBasis().cycles());
+		atomContainer.setProperty(CDKConstants.ESSENTIAL_RINGS, ringSet);
 
 		return toRingSet(atomContainer, cycleBasis().essentialCycles());	  
 
@@ -127,6 +131,9 @@ public IRingSet findRelevantRings() {
 			return null;
 		}
 
+		IRingSet ringSet = toRingSet(atomContainer, cycleBasis().cycles());
+		atomContainer.setProperty(CDKConstants.RELEVANT_RINGS, ringSet);
+
 		return toRingSet(atomContainer, cycleBasis().relevantCycles().keySet());	  
 
 	}

src/org/openscience/cdk/structgen/SingleStructureRandomGenerator.java

@@ -66,7 +66,7 @@ public class SingleStructureRandomGenerator
 {
 	AtomContainer atomContainer;
 	SaturationChecker satCheck;
-	final static boolean debug = false;
+	final static boolean debug = true;
 	Random random = null;
 
 	/**
@@ -125,15 +125,18 @@ public Molecule generate() throws CDKException
 						if (partner != null)
 						{
 							cmax1 = satCheck.getCurrentMaxBondOrder(atom, atomContainer);
+
 							cmax2 = satCheck.getCurrentMaxBondOrder(partner, atomContainer);
 							max = Math.min(cmax1, cmax2);
 							order = Math.min(Math.max(1.0, random.nextInt((int)Math.round(max))), 3.0);
+							if (debug) System.out.println("Forming bond of order " + order);
 							atomContainer.addBond(new Bond(atom, partner, order));
 							bondFormed = true;
 						}
 					}
 				}
 			} while (bondFormed);
+			//System.out.println("Blaeh");
 			if (ConnectivityChecker.isConnected(atomContainer) && satCheck.allSaturated(atomContainer))
 			{
 				structureFound = true;

src/org/openscience/cdk/templates/MoleculeFactory.java

@@ -458,6 +458,54 @@ public static Molecule makeEthylPropylPhenantren()
 		return mol;
 	}
 
+	public static Molecule makeSteran()
+	{
+		Molecule mol = new Molecule();
+		mol.addAtom(new Atom("C")); // 0
+		mol.addAtom(new Atom("C")); // 1
+		mol.addAtom(new Atom("C")); // 2
+		mol.addAtom(new Atom("C")); // 3
+		mol.addAtom(new Atom("C")); // 4
+		mol.addAtom(new Atom("C")); // 5
+		mol.addAtom(new Atom("C")); // 6
+		mol.addAtom(new Atom("C")); // 7
+		mol.addAtom(new Atom("C")); // 8
+		mol.addAtom(new Atom("C")); // 9
+		mol.addAtom(new Atom("C")); // 10
+		mol.addAtom(new Atom("C")); // 11
+		mol.addAtom(new Atom("C")); // 12
+		mol.addAtom(new Atom("C")); // 13
+		mol.addAtom(new Atom("C")); // 14
+		mol.addAtom(new Atom("C")); // 15
+		mol.addAtom(new Atom("C")); // 16
+
+
+		mol.addBond(0, 1, 1.0); // 1
+		mol.addBond(1, 2,1.0); // 2
+		mol.addBond(2, 3, 1.0); // 3
+		mol.addBond(3, 4,1.0); // 4
+		mol.addBond(4, 5, 1.0); // 5
+		mol.addBond(5, 6,1.0); // 6
+		mol.addBond(6, 7, 1.0); // 8
+		mol.addBond(7, 8,1.0); // 9
+		mol.addBond(8, 9, 1.0); // 10
+		mol.addBond(9, 0,1.0); // 11		
+		mol.addBond(9, 4, 1.0); // 12
+		mol.addBond(8, 10, 1.0); // 13
+		mol.addBond(10, 11,1.0); // 14
+		mol.addBond(11, 12, 1.0); // 15
+		mol.addBond(12, 13,1.0); // 16
+		mol.addBond(13, 7, 1.0); // 17
+		mol.addBond(13, 14, 1.0); // 18
+		mol.addBond(14, 15, 1.0); // 19
+		mol.addBond(15, 16, 1.0); // 20
+		mol.addBond(16, 12, 1.0); // 21
+
+		configureAtoms(mol);
+		return mol;
+	}
+
+
 	public static Molecule makeAzulene()
 	{
 		Molecule mol = new Molecule();