created fptype-config.xml + Drivers

for compairing CDK-fingerprints
egonw · Oct 13, 2009 · a9d577b · a9d577b
1 parent 6eb31fd
commit a9d577b
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diff --git a/fptype-config.xml b/fptype-config.xml
@@ -0,0 +1,94 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<testSuite name="CheminfoBench" xmlns="http://www.sun.com/japex/testSuite">
+
+  <param name="basedir" 
+         value="."/>
+  <param name="japex.classPath" 
+         value="build/classes" />
+  <param name="japex.resultUnit" 
+         value="ms" />
+  <param name="japex.warmupIterations" 
+         value="5" />
+  <param name="japex.runIterations" 
+         value="25" />
+  <param name="japex.reportsDirectory" 
+         value="build/reports" />
+
+  <driverGroup name="Fingerprints" 
+               xmlns="http://www.sun.com/japex/testSuite">
+
+    <driver name="Fingerprinter">
+      <param name="japex.driverClass" 
+             value="net.openmolecules.benchmark.driver.fingerPrinting.FingerprinterDriver" />
+      <param name="japex.classPath" 
+             value="${basedir}/lib/cdk-1.3.x-20091008.jar" />
+      <param name="description" 
+             value="" />
+      <param name="chemObjectBuilder"
+             value="org.openscience.cdk.DefaultChemObjectBuilder" />
+    </driver>
+
+    <driver name="ExtendedFingerprinter">
+      <param name="japex.driverClass" 
+             value="net.openmolecules.benchmark.driver.fingerPrinting.ExtendedFingerprinterDriver" />
+      <param name="japex.classPath" 
+             value="${basedir}/lib/cdk-1.3.x-20091008.jar" />
+      <param name="description" 
+             value="" />
+      <param name="chemObjectBuilder"
+             value="org.openscience.cdk.DefaultChemObjectBuilder" />
+    </driver>
+
+    <driver name="MACCSFingerprinter">
+      <param name="japex.driverClass" 
+             value="net.openmolecules.benchmark.driver.fingerPrinting.MACCSFingerprinterDriver" />
+      <param name="japex.classPath" 
+             value="${basedir}/lib/cdk-1.3.x-20091008.jar" />
+      <param name="description" 
+             value="" />
+      <param name="chemObjectBuilder"
+             value="org.openscience.cdk.DefaultChemObjectBuilder" />
+    </driver>
+
+    <driver name="EStateFingerprinter">
+      <param name="japex.driverClass" 
+             value="net.openmolecules.benchmark.driver.fingerPrinting.EStateFingerprinterDriver" />
+      <param name="japex.classPath" 
+             value="${basedir}/lib/cdk-1.3.x-20091008.jar" />
+      <param name="description" 
+             value="" />
+      <param name="chemObjectBuilder"
+             value="org.openscience.cdk.DefaultChemObjectBuilder" />
+    </driver>
+
+    <driver name="SubstructureFingerprinter">
+      <param name="japex.driverClass" 
+             value="net.openmolecules.benchmark.driver.fingerPrinting.SubstructureFingerprinterDriver" />
+      <param name="japex.classPath" 
+             value="${basedir}/lib/cdk-1.3.x-20091008.jar" />
+      <param name="description" 
+             value="" />
+      <param name="chemObjectBuilder"
+             value="org.openscience.cdk.DefaultChemObjectBuilder" />
+    </driver>
+
+    <driver name="PubchemFingerprinter">
+      <param name="japex.driverClass" 
+             value="net.openmolecules.benchmark.driver.fingerPrinting.PubchemFingerprinterDriver" />
+      <param name="japex.classPath" 
+             value="${basedir}/lib/cdk-1.3.x-20091008.jar" />
+      <param name="description" 
+             value="" />
+      <param name="chemObjectBuilder"
+             value="org.openscience.cdk.DefaultChemObjectBuilder" />
+    </driver>
+  </driverGroup>
+
+  <testCase name="test">
+    <param name="japex.inputFile" value="data/fingerprint.txt" />
+    <param name="fplength" value="1024" />
+    <param name="fpdepth" value="8" />
+    <param name="type" value="standard" />
+  </testCase>
+
+</testSuite>
diff --git a/src/net/openmolecules/benchmark/driver/fingerPrinting/AbstractFingerprintDriver.java b/src/net/openmolecules/benchmark/driver/fingerPrinting/AbstractFingerprintDriver.java
@@ -0,0 +1,70 @@
+package net.openmolecules.benchmark.driver.fingerPrinting;
+
+import java.io.FileInputStream;
+import java.lang.reflect.Method;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.fingerprint.IFingerprinter;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
+import org.openscience.cdk.io.iterator.IteratingSMILESReader;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
+
+import com.sun.japex.JapexDriverBase;
+import com.sun.japex.TestCase;
+
+
+/**
+ * @author jonalv
+ *
+ */
+public abstract class AbstractFingerprintDriver extends JapexDriverBase {
+
+    protected IFingerprinter fingerprinter;
+    protected List<IAtomContainer> mols;
+
+    @Override
+    public void prepare( TestCase testCase ) {
+
+        String fileName = testCase.getParam("japex.inputFile");
+        String chemObjectBuilder = getParam("chemObjectBuilder");
+
+        mols = new ArrayList<IAtomContainer>();
+        try {
+            Class<?> clazz = this.getClass().getClassLoader()
+                                            .loadClass(chemObjectBuilder);
+            Method getInstance = clazz.getMethod( "getInstance", 
+                                                  new Class[]{} );
+            IChemObjectBuilder builder 
+                = (IChemObjectBuilder) getInstance.invoke( new Class[]{} );
+            IteratingSMILESReader reader 
+                = new IteratingSMILESReader( new FileInputStream(fileName), 
+                                             builder );
+            while (reader.hasNext()) {
+                IAtomContainer tmp = (IAtomContainer) reader.next();
+                AtomContainerManipulator
+                    .percieveAtomTypesAndConfigureAtoms(tmp);
+                CDKHueckelAromaticityDetector.detectAromaticity(tmp);
+                mols.add(tmp);
+            }
+        } 
+        catch (Exception e) {
+            throw new RuntimeException("Exception occured", e);
+        } 
+    }
+
+    @Override
+    public void run( TestCase testCase ) {
+        for (IAtomContainer atomContainer : mols) {
+            try {
+                fingerprinter.getFingerprint(atomContainer);                
+            } 
+            catch (CDKException e) {
+                throw new RuntimeException(e);
+            }
+        }
+    }
+}
diff --git a/src/net/openmolecules/benchmark/driver/fingerPrinting/EStateFingerprinterDriver.java b/src/net/openmolecules/benchmark/driver/fingerPrinting/EStateFingerprinterDriver.java
@@ -0,0 +1,21 @@
+package net.openmolecules.benchmark.driver.fingerPrinting;
+
+import org.openscience.cdk.fingerprint.EStateFingerprinter;
+
+import com.sun.japex.TestCase;
+
+
+/**
+ * @author jonalv
+ *
+ */
+public class EStateFingerprinterDriver extends AbstractFingerprintDriver {
+
+    @Override
+    public void prepare(TestCase testCase) {
+
+        super.prepare( testCase );
+
+        fingerprinter = new EStateFingerprinter(); 
+    }
+}
diff --git a/src/net/openmolecules/benchmark/driver/fingerPrinting/ExtendedFingerprinterDriver.java b/src/net/openmolecules/benchmark/driver/fingerPrinting/ExtendedFingerprinterDriver.java
@@ -0,0 +1,25 @@
+package net.openmolecules.benchmark.driver.fingerPrinting;
+
+import org.openscience.cdk.fingerprint.ExtendedFingerprinter;
+import org.openscience.cdk.fingerprint.Fingerprinter;
+
+import com.sun.japex.TestCase;
+
+
+/**
+ * @author jonalv
+ *
+ */
+public class ExtendedFingerprinterDriver extends AbstractFingerprintDriver {
+
+    @Override
+    public void prepare(TestCase testCase) {
+
+        super.prepare( testCase );
+
+        int length = Integer.parseInt( testCase.getParam("fplength") );
+        int depth  = Integer.parseInt( testCase.getParam("fpdepth")  );
+
+        fingerprinter = new ExtendedFingerprinter( length, depth ); 
+    }
+}
diff --git a/src/net/openmolecules/benchmark/driver/fingerPrinting/FingerprinterDriver.java b/src/net/openmolecules/benchmark/driver/fingerPrinting/FingerprinterDriver.java
@@ -0,0 +1,24 @@
+package net.openmolecules.benchmark.driver.fingerPrinting;
+
+import org.openscience.cdk.fingerprint.Fingerprinter;
+
+import com.sun.japex.TestCase;
+
+
+/**
+ * @author jonalv
+ *
+ */
+public class FingerprinterDriver extends AbstractFingerprintDriver {
+
+    @Override
+    public void prepare(TestCase testCase) {
+
+        super.prepare( testCase );
+
+        int length = Integer.parseInt( testCase.getParam("fplength") );
+        int depth  = Integer.parseInt( testCase.getParam("fpdepth")  );
+
+        fingerprinter = new Fingerprinter( length, depth ); 
+    }
+}
diff --git a/src/net/openmolecules/benchmark/driver/fingerPrinting/MACCSFingerprinterDriver.java b/src/net/openmolecules/benchmark/driver/fingerPrinting/MACCSFingerprinterDriver.java
@@ -0,0 +1,22 @@
+package net.openmolecules.benchmark.driver.fingerPrinting;
+
+import org.openscience.cdk.fingerprint.Fingerprinter;
+import org.openscience.cdk.fingerprint.MACCSFingerprinter;
+
+import com.sun.japex.TestCase;
+
+
+/**
+ * @author jonalv
+ *
+ */
+public class MACCSFingerprinterDriver extends AbstractFingerprintDriver {
+
+    @Override
+    public void prepare(TestCase testCase) {
+
+        super.prepare( testCase );
+
+        fingerprinter = new MACCSFingerprinter(); 
+    }
+}
diff --git a/src/net/openmolecules/benchmark/driver/fingerPrinting/PubchemFingerprinterDriver.java b/src/net/openmolecules/benchmark/driver/fingerPrinting/PubchemFingerprinterDriver.java
@@ -0,0 +1,22 @@
+package net.openmolecules.benchmark.driver.fingerPrinting;
+
+import org.openscience.cdk.fingerprint.MACCSFingerprinter;
+
+import com.sun.japex.TestCase;
+
+
+/**
+ * @author jonalv
+ *
+ */
+public class PubchemFingerprinterDriver extends AbstractFingerprintDriver {
+
+    @Override
+    public void prepare(TestCase testCase) {
+
+        super.prepare( testCase );
+
+        throw new RuntimeException("Not yet implemented");
+//        fingerprinter = new PubchemFingerprinter(); 
+    }
+}
diff --git a/src/net/openmolecules/benchmark/driver/fingerPrinting/SubstructureFingerprinterDriver.java b/src/net/openmolecules/benchmark/driver/fingerPrinting/SubstructureFingerprinterDriver.java
@@ -0,0 +1,20 @@
+package net.openmolecules.benchmark.driver.fingerPrinting;
+
+import org.openscience.cdk.fingerprint.SubstructureFingerprinter;
+
+import com.sun.japex.TestCase;
+
+
+/**
+ * @author jonalv
+ *
+ */
+public class SubstructureFingerprinterDriver extends AbstractFingerprintDriver {
+
+    @Override
+    public void prepare(TestCase testCase) {
+
+        super.prepare( testCase );
+        fingerprinter = new SubstructureFingerprinter(); 
+    }
+}