Followed Brian's recommendation and reduced number of hashed sequences

by two by excluding reverse pathes. git-svn-id: https://cdk.svn.sourceforge.net/svnroot/cdk/trunk/cdk@368 eb4e18e3-b210-0410-a6ab-dec725e4b171
egonw · Feb 25, 2002 · ad524ca · ad524ca
1 parent 1309364
commit ad524ca
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Showing 5 changed files with 65 additions and 12 deletions.
diff --git a/build.xml b/build.xml
@@ -1,6 +1,7 @@
 <project name="CDK" default="compile" basedir=".">
 
-        <property name="build.compiler" value="modern" />
+        <property name="build.compiler" value="javac1.1" />
+	<property name="build.target" value="1.1" />
         <property name="build" value="build" />
         <property name="sourcedist" value="sourcedist" />
         <property name="dist" value="dist" />
@@ -17,11 +18,9 @@
                 location="/usr/lib/j2sdk1.3/jre/lib/rt.jar" />
 
                 <pathelement location="." />
-
                 <fileset dir="jar">
                         <include name="*.jar" />
                 </fileset>
-
                 <fileset dir="${pathtojava3d}">
                         <include name="*.jar" />
                 </fileset>
@@ -49,9 +48,51 @@
                 <delete dir="${reports.tests}" />
         </target>
 
-        <target name="compile" depends="init">
+
+
+        <target name="compile118" depends="init">
+                <echo message="Compiling only the classes that are needed 
+		for use in a drawing applet and don't use Java3d." />
                 <echo
-                message="Compiling only the classes that don't use Java3d." />
+                message="Use 'compile-with-java3d' target for full Java3D support. " />
+                <mkdir dir="${build}" />
+
+                <javac destdir="${build}" optimize="on" debug="off" deprecation="off">
+                        <src path="." />
+                        <exclude name="${sourcedist}/**" />
+                        <exclude name="org/openscience/cdk/test/**"/>
+                        <exclude name="org/openscience/cdk/database/**"/>
+                        <exclude name="org/openscience/cdk/renderer/Molecule*.*"/>
+                        <exclude name="org/openscience/cdk/renderer/GraphRend*.*"/>
+                        <exclude name="org/openscience/cdk/renderer/AtomicTable*.*"/>
+                        <exclude name="org/openscience/cdk/io/CMLReader*.*"/>			
+
+                        <exclude
+                        name="org/openscience/cdk/applications/Viewer.java" />
+                        <exclude
+                        name="org/openscience/cdk/renderer/AcceleratedRenderer3D*" />
+                        <exclude
+                        name="org/openscience/cdk/renderer/OrbitalsRenderer3D*" />
+                        <exclude
+                        name="org/openscience/cdk/test/AcceleratedRenderer3DTest.java" />
+                        <exclude
+                        name="org/openscience/cdk/test/OrbitalsRenderer3DTest.java" />
+                        <exclude
+                        name="org/openscience/cdk/test/VisualGaussiansCalculationTest.java" />
+                        <exclude
+                        name="org/openscience/cdk/test/ZMatrixReaderTest.java" />
+
+                        <classpath refid="project.class.path" />
+                </javac>
+
+                <copy todir="${build}">
+                        <fileset dir="." includes="**/Test-*" />
+                </copy>
+        </target>
+
+
+        <target name="compile" depends="init">
+                <echo message="Compiling only the classes that don't use Java3d." />
 
                 <echo
                 message="Use 'compile-with-java3d' target for full Java3D support. " />
@@ -60,7 +101,6 @@
 
                 <javac destdir="${build}" optimize="off" debug="on" deprecation="off">
                         <src path="." />
-
                         <exclude name="${sourcedist}/**" />
                         <exclude
                         name="org/openscience/cdk/applications/Viewer.java" />
@@ -251,7 +291,7 @@
         </target>
 
         <target name="run" depends="dist">
-                <java classname="org.openscience.cdk.test.Renderer2DTest" fork="yes">
+                <java classname="org.openscience.cdk.test.FingerprinterTest" fork="yes">
                         <classpath>
                                 <pathelement
                                 location="${dist}/jar/cdk.jar" />
@@ -280,3 +320,4 @@
 </project>
 
 
+
diff --git a/org/openscience/cdk/fingerprint/Fingerprinter.java b/org/openscience/cdk/fingerprint/Fingerprinter.java
@@ -50,7 +50,8 @@ public class Fingerprinter implements CDKConstants
 	static int defaultSize = 1024;
 	static int searchDepth = 7;
 	static Hashtable pathes;
-
+	static boolean debug = true;
+	static int debugCounter = 0;
 
 	/**
 	 *  Generates a fingerprint of the default size for the given AtomContainer
@@ -96,6 +97,7 @@ public static BitSet getFingerprint(AtomContainer ac, int size)
 	static void findPathes(AtomContainer ac)
 	{
 		pathes = new Hashtable();
+		debugCounter = 0;
 		for (int f = 0; f < ac.getAtomCount(); f++)
 		{
 			for (int g = 0; g < ac.getAtomCount(); g++)
@@ -122,16 +124,23 @@ static void depthFirstSearch(AtomContainer ac, Atom root, String currentPath, in
 		root.flags[VISITED] = true;
 		currentDepth++;
 		String newPath = new String(currentPath);
+		String reversePath = null;
+		StringBuffer strBuff = null;
 		for (int f = 0; f < bonds.length; f++)
 		{
 			nextAtom = bonds[f].getConnectedAtom(root);
 			if (!nextAtom.flags[VISITED])
 			{
 				newPath += nextAtom.getSymbol();
-				if (!pathes.containsKey(newPath))
+				reversePath = new StringBuffer(newPath).reverse().toString();
+				if (!pathes.containsKey(newPath) && !pathes.containsKey(reversePath))
 				{
 					pathes.put(newPath, newPath);
-					System.out.println(newPath + ", Hash: " + newPath.hashCode());
+					if (debug)
+					{
+						debugCounter ++;
+						System.out.println("Path no. " + debugCounter + ": " + newPath + ", Hash: " + newPath.hashCode());
+					}
 				}
 				if (currentDepth == searchDepth)
 				{

diff --git a/org/openscience/cdk/io/cml/cdopi/CDOAcceptedObjects.java b/org/openscience/cdk/io/cml/cdopi/CDOAcceptedObjects.java
@@ -35,7 +35,7 @@ public CDOAcceptedObjects () {
   }
 
   public void add(String object) {
-    objects.add(object);
+    objects.addElement(object);
   }
 
   public boolean contains(String object) {

diff --git a/org/openscience/cdk/test/FingerprinterTest.java b/org/openscience/cdk/test/FingerprinterTest.java
@@ -42,7 +42,9 @@ public static boolean test()
 	{
 		Molecule mol = MoleculeFactory.makeAlphaPinene();
 		BitSet bs = Fingerprinter.getFingerprint(mol);
+		System.out.println("Resulting BitSet looks like:");
 		System.out.println(bs);
+		System.out.println("(Numbers indicate position of '1' Bits)");
 		return false;
 	}
 

diff --git a/org/openscience/cdk/tools/LoggingTool.java b/org/openscience/cdk/tools/LoggingTool.java
@@ -43,7 +43,8 @@ public LoggingTool(String classname) {
             // configure Log4J
             URL url = getClass().getClassLoader().getResource("org/openscience/cdk/config/log4j.properties");
             // debug(url.toString());
-            (org.apache.log4j.PropertyConfigurator).configure(url);
+            //(org.apache.log4j.PropertyConfigurator).configure(url);
+	    org.apache.log4j.PropertyConfigurator.configure(url);
         } catch (NoClassDefFoundError e) {
             tostdout = true;
         } catch (NullPointerException e) {