data/pubchem_416_benzenes.sdf @@ -4,21 +4,21 @@ <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.runIterations" value="5"/> <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.CDKRingBench"/> <param name="japex.classPath" value="${basedir}/lib/cdk-1.2.x-20090116.jar"/> - <param name="description" value="Reads SD file, counts all rings in each structure."/> + <param name="description" value="Reads SD file, finds all rings in each hydrogen-suppressed structure."/> </driver> <driver name="mx-0.108.1"> <param name="japex.driverClass" value="net.openmolecules.benchmark.driver.MXRingBench"/> <param name="japex.classPath" value="${basedir}/lib/mx-0.108.1.jar"/> - <param name="description" value="Reads SD file, counts all rings in each structure."/> + <param name="description" value="Reads SD file, finds all rings in each hydrogen-suppressed structure."/> </driver> </driverGroup> - <testCase name="CDK and MX Read 33-Record SD File and Count Rings in Each Structure"> - <param name="japex.inputFile" value="data/steroids.sdf" /> + <testCase name="Read 416-Record PubChem SD File and Find All Rings in Each Hydrogen-Suppressed Structure"> + <param name="japex.inputFile" value="data/pubchem_416_benzenes.sdf" /> </testCase> </testSuite> \ No newline at end of file mx-cdk-ring.xml @@ -21,7 +21,6 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ - package net.openmolecules.benchmark.driver; import com.sun.japex.JapexDriverBase; @@ -45,19 +44,17 @@ import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; public class CDKRingBench extends JapexDriverBase { private List<IAtomContainer> molecules; - private AllRingsFinder finder; @Override public void prepare(TestCase testCase) { molecules = new ArrayList(); - finder = new AllRingsFinder(); IteratingMDLReader reader = getReader(testCase.getParam("japex.inputFile")); while (reader.hasNext()) { IAtomContainer molecule = (IMolecule) reader.next(); - + molecule = AtomContainerManipulator.removeHydrogens(molecule); molecules.add(molecule); } @@ -66,7 +63,6 @@ public class CDKRingBench extends JapexDriverBase { reader.close(); } - catch (IOException e) { throw new RuntimeException(e); @@ -76,20 +72,19 @@ public class CDKRingBench extends JapexDriverBase @Override public void run(TestCase testCase) { - int sum = 0; + AllRingsFinder finder = new AllRingsFinder(); for (IAtomContainer molecule : molecules) { try { - sum += finder.findAllRings(molecule).getAtomContainerCount(); - } catch (CDKException e) + finder.findAllRings(molecule); + } + catch (CDKException e) { throw new RuntimeException(e); } } - - System.out.println("sum=" + sum); } private IteratingMDLReader getReader(String filename) @@ -101,7 +96,8 @@ public class CDKRingBench extends JapexDriverBase Reader raw = new FileReader(filename); result = new IteratingMDLReader(raw, DefaultChemObjectBuilder.getInstance()); - } catch (Exception e) + } + catch (Exception e) { throw new RuntimeException(e); } src/net/openmolecules/benchmark/driver/CDKRingBench.java @@ -41,14 +41,12 @@ public class MXRingBench extends JapexDriverBase { private List<Molecule> molecules; - private RingFinder finder; @Override public void prepare(TestCase testCase) { molecules = new ArrayList(); SDFileReader reader = createReader(testCase.getParam("japex.inputFile")); - finder = new HanserRingFinder(); while (reader.hasNextRecord()) { @@ -65,14 +63,12 @@ public class MXRingBench extends JapexDriverBase @Override public void run(TestCase testCase) { - int sum = 0; + RingFinder finder = new HanserRingFinder(); for (Molecule molecule : molecules) { - sum += finder.findRings(molecule).size(); + finder.findRings(molecule); } - - System.out.println("sum=" + sum); } private SDFileReader createReader(String filename) src/net/openmolecules/benchmark/driver/MXRingBench.java a6b59dea87d931878393f2024444f296d18b127b Rich Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/cheminfbenchmark/commit/b4390dd9c4b69d331cf7bc49dd96d9e1ac415428 b4390dd9c4b69d331cf7bc49dd96d9e1ac415428 2009-01-21T08:57:45-08:00 2009-01-21T08:57:45-08:00 changed ring test data to be more representative 331d1544ed4bfc4dc111f5534745eeb9901d6aa0 Rich Apodaca rapodaca@metamolecular.com