Merge branch 'master' of git@github.com:cdk/cdk

cdk · May 20, 2010 · 6d1a730 · 6d1a730
2 parents d694d19 + f3f809e
commit 6d1a730
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Showing 51 changed files with 1,666 additions and 571 deletions.
diff --git a/build.xml b/build.xml
@@ -293,14 +293,16 @@
                 depends="init, check, runDoclet"/>
 
         <target id="qa-module" name="qa-module"
-                depends="check, dist.init, compile-needed-test"
-                unless="module-uptodate">
+                depends="check, dist.init">
           <echo message="Running QA for CDK's ${module} module" />
 
           <antcall target="test-module">
               <param name="module" value="${module}"/>
           </antcall>
 
+          <ant antfile="javadoc.xml" target="ojdcheck-module">
+              <property name="module" value="${module}"/>
+          </ant>
           <ant antfile="pmd.xml" target="test-module">
               <property name="pmd.test" value="custom"/>
               <property name="module" value="${module}"/>
@@ -619,6 +621,7 @@
                     <includesfile name="${metainf}/forcefield.libdepends"/>
                     <includesfile name="${metainf}/inchi.libdepends"/>
                     <includesfile name="${metainf}/smarts.libdepends"/>
+                    <includesfile name="${metainf}/smsd.libdepends"/>
                     <includesfile name="${metainf}/pcore.libdepends"/>
                     <includesfile name="${metainf}/formula.libdepends"/>
                     <includesfile name="${metainf}/isomorphism.libdepends"/>
@@ -667,6 +670,7 @@
                     <include name="cdk-formula.jar"/>
                     <include name="cdk-isomorphism.jar"/>
                     <include name="cdk-ionpot.jar"/>
+                    <include name="cdk-smsd.jar"/>
                 </fileset>
             </unjar>
 

diff --git a/src/META-INF/test-interfaces.cdkdepends b/src/META-INF/test-interfaces.cdkdepends
@@ -2,4 +2,5 @@ cdk-annotation.jar
 cdk-interfaces.jar
 cdk-core.jar
 cdk-diff.jar
+cdk-standard.jar
 cdk-test.jar
diff --git a/src/main/org/openscience/cdk/AtomContainer.java b/src/main/org/openscience/cdk/AtomContainer.java
@@ -25,20 +25,18 @@
 
 import java.io.Serializable;
 import java.util.ArrayList;
-import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.List;
-import java.util.Map;
 
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.interfaces.IAtomParity;
 import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
 import org.openscience.cdk.interfaces.IChemObjectListener;
 import org.openscience.cdk.interfaces.IElectronContainer;
 import org.openscience.cdk.interfaces.ILonePair;
 import org.openscience.cdk.interfaces.ISingleElectron;
+import org.openscience.cdk.interfaces.IStereoElement;
 import org.openscience.cdk.interfaces.IBond.Order;
 
 /**
@@ -118,10 +116,10 @@ public class AtomContainer extends ChemObject
 	 */
 	protected ISingleElectron[] singleElectrons;
 
-	/**
-	 * Internal list of atom parities.
-	 */
-	protected Map<IAtom, IAtomParity> atomParities;
+    /**
+     * Internal list of atom parities.
+     */
+    protected List<IStereoElement> stereoElements;
 
 
 	/**
@@ -150,7 +148,7 @@ public AtomContainer(IAtomContainer container)
 		this.lonePairs = new ILonePair[this.lonePairCount];
 		this.singleElectrons = new ISingleElectron[this.singleElectronCount];
 
-		atomParities = new Hashtable<IAtom, IAtomParity>(atomCount/2);
+		stereoElements = new ArrayList<IStereoElement>(atomCount/2);
 
 		for (int f = 0; f < container.getAtomCount(); f++) {
 			atoms[f] = container.getAtom(f);
@@ -192,33 +190,22 @@ public AtomContainer(int atomCount, int bondCount, int lpCount, int seCount)
 		bonds = new IBond[bondCount];
 		lonePairs = new ILonePair[lpCount];
 		singleElectrons = new ISingleElectron[seCount];
-        atomParities = new Hashtable<IAtom, IAtomParity>(atomCount/2);
+		stereoElements = new ArrayList<IStereoElement>(atomCount/2);
 	}
 
-    /**
-     * Adds an AtomParity to this container. If a parity is already given for the
-     * affected Atom, it is overwritten.
-     *
-     * @param parity The new AtomParity for this container
-     * @see   #getAtomParity
-     */
-    public void addAtomParity(IAtomParity parity) {
-        atomParities.put(parity.getAtom(), parity);
+    /** {@inheritDoc} */
+    public void addStereoElement(IStereoElement element) {
+        stereoElements.add(element);
     }
 
-    /**
-     * Returns the atom parity for the given Atom. If no parity is associated
-     * with the given Atom, it returns null.
-     *
-     * @param  atom   Atom for which the parity must be returned
-     * @return The AtomParity for the given Atom, or null if that Atom does
-     *         not have an associated AtomParity
-     * @see    #addAtomParity
-     */
-    public IAtomParity getAtomParity(IAtom atom) {
-        return atomParities.get(atom);
+    /** {@inheritDoc} */
+    public Iterable<IStereoElement> stereoElements() {
+        return new Iterable<IStereoElement>() {
+            public Iterator<IStereoElement> iterator() {
+                return stereoElements.iterator();
+            }
+        };
     }
-
 	/**
 	 *  Sets the array of atoms of this AtomContainer.
 	 *
@@ -1568,10 +1555,10 @@ public String toString()
 				stringContent.append(", ").append(getSingleElectron(i).toString());
 			}
 		}
-		if (atomParities.size() > 0) {
-			stringContent.append(", AP:[#").append(atomParities.size());
-            for (IAtomParity iAtomParity : atomParities.values()) {
-                stringContent.append(", ").append(iAtomParity.toString());
+		if (stereoElements.size() > 0) {
+			stringContent.append(", ST:[#").append(stereoElements.size());
+            for (IStereoElement elements : stereoElements) {
+                stringContent.append(", ").append(elements.toString());
             }
 			stringContent.append(']');
 		}

diff --git a/src/main/org/openscience/cdk/CDKConstants.java b/src/main/org/openscience/cdk/CDKConstants.java
@@ -168,14 +168,10 @@ public class CDKConstants {
     /** Flag is set if an atom could be typed.
      */
     public static final int IS_TYPEABLE = 11;
-    /** Flag is set in JCP if an arrow indicating move
-     *  should be shown.
-     */
-    public static final int SHOW_MOVE_ARRAY = 12;
     /**
      * Maximum flags array index.
      */
-    public final static int MAX_FLAG_INDEX = 13;
+    public final static int MAX_FLAG_INDEX = 12;
     /**
      * Flag used for JUnit testing the pointer functionality.
      */
@@ -295,6 +291,8 @@ public class CDKConstants {
      */
     public static final String REST_H = "cdk:RestH";
 
+    public static final String ATOM_ATOM_MAPPING = "cdk:AtomAtomMapping";
+
 
     /* **************************************
     * Some predefined property names for    *

diff --git a/src/main/org/openscience/cdk/debug/DebugAminoAcid.java b/src/main/org/openscience/cdk/debug/DebugAminoAcid.java
@@ -27,14 +27,14 @@
 import org.openscience.cdk.interfaces.IAminoAcid;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.interfaces.IAtomParity;
 import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
 import org.openscience.cdk.interfaces.IChemObjectListener;
 import org.openscience.cdk.interfaces.IElectronContainer;
 import org.openscience.cdk.interfaces.ILonePair;
-import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.ISingleElectron;
+import org.openscience.cdk.interfaces.IStereoElement;
 import org.openscience.cdk.interfaces.IBond.Order;
 import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
@@ -54,14 +54,14 @@ public class DebugAminoAcid extends AminoAcid
     ILoggingTool logger =
         LoggingToolFactory.createLoggingTool(DebugAtomContainer.class);
 
-    public void addAtomParity(IAtomParity parity) {
-		logger.debug("Adding atom parity: ", parity);
-		super.addAtomParity(parity);
+    public void addStereoElement(IStereoElement parity) {
+		logger.debug("Adding stereo element: ", parity);
+		super.addStereoElement(parity);
 	}
 
-	public IAtomParity getAtomParity(IAtom atom) {
-		logger.debug("Getting atom parity: ", atom);
-		return super.getAtomParity(atom);
+	public Iterable<IStereoElement> stereoElements() {
+		logger.debug("Getting stereo elements.");
+		return super.stereoElements();
 	}
 
 	public void setAtoms(IAtom[] atoms) {

diff --git a/src/main/org/openscience/cdk/debug/DebugAtomContainer.java b/src/main/org/openscience/cdk/debug/DebugAtomContainer.java
@@ -26,14 +26,14 @@
 import org.openscience.cdk.AtomContainer;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.interfaces.IAtomParity;
 import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
 import org.openscience.cdk.interfaces.IChemObjectListener;
 import org.openscience.cdk.interfaces.IElectronContainer;
 import org.openscience.cdk.interfaces.ILonePair;
-import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.ISingleElectron;
+import org.openscience.cdk.interfaces.IStereoElement;
 import org.openscience.cdk.interfaces.IBond.Order;
 import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
@@ -65,15 +65,15 @@ public DebugAtomContainer(IAtomContainer container) {
 		super(container);
 	}
 
-	public void addAtomParity(IAtomParity parity) {
-		logger.debug("Adding atom parity: ", parity);
-		super.addAtomParity(parity);
-	}
+    public void addStereoElement(IStereoElement parity) {
+        logger.debug("Adding stereo element: ", parity);
+        super.addStereoElement(parity);
+    }
 
-	public IAtomParity getAtomParity(IAtom atom) {
-		logger.debug("Getting atom parity: ", atom);
-		return super.getAtomParity(atom);
-	}
+    public Iterable<IStereoElement> stereoElements() {
+        logger.debug("Getting stereo elements.");
+        return super.stereoElements();
+    }
 
 	public void setAtoms(IAtom[] atoms) {
 		logger.debug("Setting atoms: ", atoms.length);

diff --git a/src/main/org/openscience/cdk/debug/DebugBioPolymer.java b/src/main/org/openscience/cdk/debug/DebugBioPolymer.java
@@ -27,16 +27,16 @@
 import org.openscience.cdk.BioPolymer;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.interfaces.IAtomParity;
 import org.openscience.cdk.interfaces.IBioPolymer;
 import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
 import org.openscience.cdk.interfaces.IChemObjectListener;
 import org.openscience.cdk.interfaces.IElectronContainer;
 import org.openscience.cdk.interfaces.ILonePair;
 import org.openscience.cdk.interfaces.IMonomer;
-import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.ISingleElectron;
+import org.openscience.cdk.interfaces.IStereoElement;
 import org.openscience.cdk.interfaces.IStrand;
 import org.openscience.cdk.interfaces.IBond.Order;
 import org.openscience.cdk.tools.ILoggingTool;
@@ -57,15 +57,15 @@ public class DebugBioPolymer extends BioPolymer
     ILoggingTool logger =
         LoggingToolFactory.createLoggingTool(DebugAtomContainer.class);
 
-    public void addAtomParity(IAtomParity parity) {
-		logger.debug("Adding atom parity: ", parity);
-		super.addAtomParity(parity);
-	}
+    public void addStereoElement(IStereoElement parity) {
+        logger.debug("Adding stereo element: ", parity);
+        super.addStereoElement(parity);
+    }
 
-	public IAtomParity getAtomParity(IAtom atom) {
-		logger.debug("Getting atom parity: ", atom);
-		return super.getAtomParity(atom);
-	}
+    public Iterable<IStereoElement> stereoElements() {
+        logger.debug("Getting stereo elements.");
+        return super.stereoElements();
+    }
 
 	public void setAtoms(IAtom[] atoms) {
 		logger.debug("Setting atoms: ", atoms.length);

diff --git a/src/main/org/openscience/cdk/debug/DebugCrystal.java b/src/main/org/openscience/cdk/debug/DebugCrystal.java
@@ -28,15 +28,15 @@
 import org.openscience.cdk.Crystal;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.interfaces.IAtomParity;
 import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
 import org.openscience.cdk.interfaces.IChemObjectListener;
 import org.openscience.cdk.interfaces.ICrystal;
 import org.openscience.cdk.interfaces.IElectronContainer;
 import org.openscience.cdk.interfaces.ILonePair;
-import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.ISingleElectron;
+import org.openscience.cdk.interfaces.IStereoElement;
 import org.openscience.cdk.interfaces.IBond.Order;
 import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
@@ -64,15 +64,15 @@ public DebugCrystal(IAtomContainer container) {
 		super(container);
 	}
 
-	public void addAtomParity(IAtomParity parity) {
-		logger.debug("Adding atom parity: ", parity);
-		super.addAtomParity(parity);
-	}
+    public void addStereoElement(IStereoElement parity) {
+        logger.debug("Adding stereo element: ", parity);
+        super.addStereoElement(parity);
+    }
 
-	public IAtomParity getAtomParity(IAtom atom) {
-		logger.debug("Getting atom parity: ", atom);
-		return super.getAtomParity(atom);
-	}
+    public Iterable<IStereoElement> stereoElements() {
+        logger.debug("Getting stereo elements.");
+        return super.stereoElements();
+    }
 
 	public void setAtoms(IAtom[] atoms) {
 		logger.debug("Setting atoms: ", atoms.length);

diff --git a/src/main/org/openscience/cdk/debug/DebugMolecule.java b/src/main/org/openscience/cdk/debug/DebugMolecule.java
@@ -26,15 +26,15 @@
 import org.openscience.cdk.Molecule;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.interfaces.IAtomParity;
 import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
 import org.openscience.cdk.interfaces.IChemObjectListener;
 import org.openscience.cdk.interfaces.IElectronContainer;
 import org.openscience.cdk.interfaces.ILonePair;
 import org.openscience.cdk.interfaces.IMolecule;
-import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.ISingleElectron;
+import org.openscience.cdk.interfaces.IStereoElement;
 import org.openscience.cdk.interfaces.IBond.Order;
 import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
@@ -66,15 +66,15 @@ public DebugMolecule(IAtomContainer container) {
 		super(container);
 	}
 
-	public void addAtomParity(IAtomParity parity) {
-		logger.debug("Adding atom parity: ", parity);
-		super.addAtomParity(parity);
-	}
+    public void addStereoElement(IStereoElement parity) {
+        logger.debug("Adding stereo element: ", parity);
+        super.addStereoElement(parity);
+    }
 
-	public IAtomParity getAtomParity(IAtom atom) {
-		logger.debug("Getting atom parity: ", atom);
-		return super.getAtomParity(atom);
-	}
+    public Iterable<IStereoElement> stereoElements() {
+        logger.debug("Getting stereo elements.");
+        return super.stereoElements();
+    }
 
 	public void setAtoms(IAtom[] atoms) {
 		logger.debug("Setting atoms: ", atoms.length);