added substructure search benchmark

mx-cdk-substructure.xml

@@ -0,0 +1,24 @@
+<?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="10"/>
+  <param name="japex.runIterations" value="10"/>
+  <param name="japex.reportsDirectory" value="build/reports"/>
+  <driverGroup name="Ring Benchmark" xmlns="http://www.sun.com/japex/testSuite">
+    <driver name="CDK-1.2.x">
+      <param name="japex.driverClass" value="net.openmolecules.benchmark.driver.CDKSubstructureBench"/>
+      <param name="japex.classPath" value="${basedir}/lib/cdk-1.2.x-20090116.jar"/>
+      <param name="description" value="Finds all substructures in a set of hydrogen-suppressed structures."/>
+    </driver>
+    <driver name="mx-0.108.1">
+      <param name="japex.driverClass" value="net.openmolecules.benchmark.driver.MXSubstructureBench"/>
+      <param name="japex.classPath" value="${basedir}/lib/mx-0.108.1.jar"/>
+      <param name="description" value="Finds all substructures in a set of hydrogen-suppressed structures."/>
+    </driver>
+  </driverGroup>
+  <testCase name="Read 416-Record PubChem SD File and Find All Substructure Matches to Benzene in Each Hydrogen-Suppressed Structure">
+    <param name="japex.inputFile" value="data/pubchem_416_benzenes.sdf" />
+  </testCase>
+</testSuite>

src/net/openmolecules/benchmark/driver/CDKSubstructureBench.java

@@ -0,0 +1,94 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package net.openmolecules.benchmark.driver;
+
+import com.sun.japex.JapexDriverBase;
+import com.sun.japex.TestCase;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.Reader;
+import java.util.ArrayList;
+import java.util.List;
+import org.openscience.cdk.DefaultChemObjectBuilder;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.io.iterator.IteratingMDLReader;
+import org.openscience.cdk.isomorphism.UniversalIsomorphismTester;
+import org.openscience.cdk.templates.MoleculeFactory;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
+
+/**
+ *
+ * @author rich
+ */
+public class CDKSubstructureBench extends JapexDriverBase
+{
+
+  private List<IAtomContainer> molecules;
+
+  @Override
+  public void prepare(TestCase testCase)
+  {
+    molecules = new ArrayList();
+    IteratingMDLReader reader = getReader(testCase.getParam("japex.inputFile"));
+
+    while (reader.hasNext())
+    {
+      IAtomContainer molecule = (IMolecule) reader.next();
+
+      molecule = AtomContainerManipulator.removeHydrogens(molecule);
+      molecules.add(molecule);
+    }
+
+    try
+    {
+      reader.close();
+    } catch (IOException e)
+    {
+      throw new RuntimeException(e);
+    }
+  }
+
+  @Override
+  public void run(TestCase testCase)
+  {
+    IMolecule query = MoleculeFactory.makeBenzene();
+    int count = 0;
+
+    try
+    {
+      for (IAtomContainer target : molecules)
+      {
+        if (UniversalIsomorphismTester.isSubgraph(target, query))
+        {
+          count++;
+        }
+      }
+    } catch (CDKException e)
+    {
+      throw new RuntimeException(e);
+    }
+
+    System.out.println("count=" + count);
+  }
+
+  private IteratingMDLReader getReader(String filename)
+  {
+    IteratingMDLReader result = null;
+
+    try
+    {
+      Reader raw = new FileReader(filename);
+
+      result = new IteratingMDLReader(raw, DefaultChemObjectBuilder.getInstance());
+    } catch (Exception e)
+    {
+      throw new RuntimeException(e);
+    }
+
+    return result;
+  }
+}

src/net/openmolecules/benchmark/driver/MXSubstructureBench.java

@@ -0,0 +1,77 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package net.openmolecules.benchmark.driver;
+
+import com.metamolecular.mx.io.Molecules;
+import com.metamolecular.mx.io.mdl.SDFileReader;
+import com.metamolecular.mx.map.DefaultMapper;
+import com.metamolecular.mx.map.Mapper;
+import com.metamolecular.mx.model.Molecule;
+import com.sun.japex.JapexDriverBase;
+import com.sun.japex.TestCase;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ *
+ * @author rich
+ */
+public class MXSubstructureBench extends JapexDriverBase
+{
+
+  private List<Molecule> molecules;
+
+  @Override
+  public void prepare(TestCase testCase)
+  {
+    molecules = new ArrayList();
+    SDFileReader reader = createReader(testCase.getParam("japex.inputFile"));
+
+    while (reader.hasNextRecord())
+    {
+      reader.nextRecord();
+
+      Molecule molecule = reader.getMolecule(true);
+
+      molecules.add(molecule);
+    }
+
+    reader.close();
+  }
+
+  @Override
+  public void run(TestCase testCase)
+  {
+    Molecule query = Molecules.createBenzene();
+    Mapper mapper = new DefaultMapper(query);
+    int count = 0;
+
+    for (Molecule target : molecules)
+    {
+      if (mapper.hasMap(target))
+      {
+        count++;
+      }
+    }
+
+    System.out.println(count);
+  }
+
+  private SDFileReader createReader(String filename)
+  {
+    SDFileReader result = null;
+
+    try
+    {
+      result = new SDFileReader(filename);
+    } catch (IOException e)
+    {
+      throw new RuntimeException(e);
+    }
+
+    return result;
+  }
+}