Made QueryChemObject require a IChemObject builder when being constru…

…cted. This has a knock on effect that all the SMARTs atoms require the builder also. Although there are a lot of changes there's little front end API changes - the SMARTSQueryTool and PubChemFingerprinter now require a builder but other methods (e.g. descriptors and QueryAtomContainerCreator) could make use of the builder from other IChemObjects.

src/main/org/openscience/cdk/fingerprint/EStateFingerprinter.java

@@ -76,7 +76,7 @@ public IBitFingerprint getBitFingerprint(IAtomContainer atomContainer)
         int bitsetLength = PATTERNS.length;
         BitSet fingerPrint = new BitSet(bitsetLength);
 
-        SMARTSQueryTool sqt = new SMARTSQueryTool("C");
+        SMARTSQueryTool sqt = new SMARTSQueryTool("C", atomContainer.getBuilder());
         for (int i = 0; i < PATTERNS.length; i++) {
             sqt.setSmarts(PATTERNS[i]);
             boolean status = sqt.matches(atomContainer);

src/main/org/openscience/cdk/fingerprint/MACCSFingerprinter.java

@@ -97,7 +97,7 @@ public IBitFingerprint getBitFingerprint(IAtomContainer atomContainer)
         int bitsetLength = keys.length;
         BitSet fingerPrint = new BitSet(bitsetLength);
 
-        SMARTSQueryTool sqt = new SMARTSQueryTool("C");
+        SMARTSQueryTool sqt = new SMARTSQueryTool("C", atomContainer.getBuilder());
         for (int i = 0; i < keys.length; i++) {
             String smarts = keys[i].getSmarts();
             if (smarts.equals("?")) continue;

src/main/org/openscience/cdk/fingerprint/PubchemFingerprinter.java

@@ -31,6 +31,7 @@
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IRingSet;
 import org.openscience.cdk.ringsearch.SSSRFinder;
 import org.openscience.cdk.smiles.smarts.SMARTSQueryTool;
@@ -94,8 +95,8 @@
     private byte[] m_bits;
 
     private SMARTSQueryTool sqt;
-    public PubchemFingerprinter() {
-    	sqt = new SMARTSQueryTool("C");
+    public PubchemFingerprinter(IChemObjectBuilder builder) {
+    	sqt = new SMARTSQueryTool("C", builder);
         m_bits = new byte[(FP_SIZE + 7) >> 3];
     }
 
@@ -368,7 +369,9 @@ public static BitSet decode(String enc) {
                 "Input is not a proper PubChem base64 encoded fingerprint");
         }
 
-        PubchemFingerprinter pc = new PubchemFingerprinter();
+        // note the IChemObjectBuilder is passed as null because the SMARTSQueryTool
+        // isn't needed when decoding
+        PubchemFingerprinter pc = new PubchemFingerprinter(null);
         for (int i = 0; i < pc.m_bits.length; ++i) {
             pc.m_bits[i] = fp[i + 4];
         }

src/main/org/openscience/cdk/fingerprint/SubstructureFingerprinter.java

@@ -409,7 +409,7 @@ public IBitFingerprint getBitFingerprint(IAtomContainer atomContainer)
         int bitsetLength = smarts.length;
         BitSet fingerPrint = new BitSet(bitsetLength);
 
-        SMARTSQueryTool sqt = new SMARTSQueryTool("C");
+        SMARTSQueryTool sqt = new SMARTSQueryTool("C", atomContainer.getBuilder());
         for (int i = 0; i < smarts.length; i++) {
             String pattern = smarts[i];
 

src/main/org/openscience/cdk/io/MDLV2000Reader.java

@@ -721,7 +721,7 @@ private IAtomContainer readAtomContainer(IAtomContainer molecule) throws CDKExce
                 }
                 else {
                     queryBondCount++;
-                    newBond = new CTFileQueryBond();
+                    newBond = new CTFileQueryBond(molecule.getBuilder());
                     IAtom[] bondAtoms = {a1,a2};
                     newBond.setAtoms(bondAtoms);
                     newBond.setOrder(null);
@@ -741,7 +741,7 @@ private IAtomContainer readAtomContainer(IAtomContainer molecule) throws CDKExce
             if(queryBondCount==0)          
                 outputContainer = molecule;
             else {
-                outputContainer = new QueryAtomContainer();
+                outputContainer = new QueryAtomContainer(molecule.getBuilder());
             }
 
             outputContainer.setProperty(CDKConstants.TITLE, title);

src/main/org/openscience/cdk/isomorphism/matchers/CTFileQueryBond.java

@@ -24,6 +24,8 @@
 
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IChemObject;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
 
 /**
  * Captures query bond types defined in the CTFile.
@@ -51,6 +53,9 @@
         ANY
     }
 
+    public CTFileQueryBond(IChemObjectBuilder builder){
+        super(builder);
+    }
     /**
      * The type of this bond.
      */

src/main/org/openscience/cdk/isomorphism/matchers/InverseSymbolSetQueryAtom.java

@@ -23,6 +23,7 @@
 import java.util.Set;
 
 import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
 
 /**
  *  A QueryAtom that matches all symbols but those in this container. You may
@@ -45,7 +46,9 @@
     /**
      *  Constructor for the InverseSymbolSetQueryAtom object
      */
-    public InverseSymbolSetQueryAtom() { }
+    public InverseSymbolSetQueryAtom(IChemObjectBuilder builder) {
+        super(builder);
+    }
     public void setOperator(String str){}
 
     /**

src/main/org/openscience/cdk/isomorphism/matchers/OrderQueryBond.java

@@ -26,6 +26,7 @@
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
 
 /**
  * @cdk.module isomorphism
@@ -35,11 +36,12 @@
 
     private static final long serialVersionUID = 2292654937621883661L;
 
-    public OrderQueryBond() {
+    public OrderQueryBond(IChemObjectBuilder builder) {
+        super(builder);
     }
 
-    public OrderQueryBond(IQueryAtom atom1, IQueryAtom atom2, IBond.Order order) {
-        super(atom1, atom2, order);
+    public OrderQueryBond(IQueryAtom atom1, IQueryAtom atom2, IBond.Order order, IChemObjectBuilder builder) {
+        super(atom1, atom2, order, builder);
     }
     
 	public boolean matches(IBond bond) {

src/main/org/openscience/cdk/isomorphism/matchers/OrderQueryBondOrderOnly.java

@@ -25,6 +25,7 @@
 
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
 
 /**
  * <code>IQueryBond</code> that matches IBond object only based on bond order, and
@@ -37,11 +38,12 @@
 
     private static final long serialVersionUID = 2292654937621883661L;
 
-    public OrderQueryBondOrderOnly() {
+    public OrderQueryBondOrderOnly(IChemObjectBuilder builder) {
+        super(builder);
     }
 
-    public OrderQueryBondOrderOnly(IQueryAtom atom1, IQueryAtom atom2, IBond.Order order) {
-        super(atom1, atom2, order);
+    public OrderQueryBondOrderOnly(IQueryAtom atom1, IQueryAtom atom2, IBond.Order order, IChemObjectBuilder builder) {
+        super(atom1, atom2, order, builder);
     }
     
 	public boolean matches(IBond bond) {

src/main/org/openscience/cdk/isomorphism/matchers/QueryAtom.java

@@ -25,6 +25,7 @@
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.interfaces.IAtomType;
 import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
 
 /**
  * @cdk.module  isomorphism
@@ -127,11 +128,14 @@
     /** The atomic number for this element giving their position in the periodic table. */
     protected Integer atomicNumber = (Integer) CDKConstants.UNSET;
 
-    public QueryAtom(String symbol) {
+    public QueryAtom(String symbol, IChemObjectBuilder builder) {
+        this(builder);
         this.symbol = symbol;
     }
 
-    public QueryAtom() {}
+    public QueryAtom(IChemObjectBuilder builder) {
+        super(builder);
+    }
 
     /**
      *  Sets the partial charge of this atom.

src/main/org/openscience/cdk/isomorphism/matchers/QueryAtomContainer.java

@@ -26,6 +26,7 @@
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.interfaces.IBond.Order;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
 import org.openscience.cdk.interfaces.IElectronContainer;
 import org.openscience.cdk.interfaces.ILonePair;
@@ -117,8 +118,9 @@ public String toString() {
     /**
      *  Constructs an empty AtomContainer.
      */
-    public QueryAtomContainer() {
-        this(10, 10, 0, 0);
+    public QueryAtomContainer(IChemObjectBuilder builder) {
+        this(10, 10, 0, 0,
+             builder);
     }
 
 
@@ -129,8 +131,9 @@ public QueryAtomContainer() {
      *
      * @param  container  An AtomContainer to copy the atoms and electronContainers from
      */
-    public QueryAtomContainer(IAtomContainer container)
+    public QueryAtomContainer(IAtomContainer container, IChemObjectBuilder builder)
     {
+        super(builder);
         this.atomCount = container.getAtomCount();
         this.bondCount = container.getBondCount();
         this.lonePairCount = container.getLonePairCount();
@@ -172,8 +175,10 @@ public QueryAtomContainer(IAtomContainer container)
      *@param  seCount          Number of single electrons to be in this container
      *
      */
-    public QueryAtomContainer(int atomCount, int bondCount, int lpCount, int seCount)
+    public QueryAtomContainer(int atomCount, int bondCount, int lpCount, int seCount,
+                              IChemObjectBuilder builder)
     {
+        super(builder);
         this.atomCount = 0;
         this.bondCount = 0;
         this.lonePairCount = 0;