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Also calculate FPs with CDK 1.4.0, and three object builder implement…
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…ations (see http://chem-bla-ics.blogspot.com/2011/07/data-nonotify-or-silent.html)
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@egonw
egonw committed Jul 13, 2011
1 parent 88313b5 commit 62c2e10
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36 changes: 31 additions & 5 deletions fingerprint-config.xml
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<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.warmupIterations" value="3"/>
<param name="japex.runIterations" value="10"/>
<param name="japex.reportsDirectory" value="build/reports"/>

<param name="japex.warmupsPerDriver" value="2"/>
<param name="japex.runsPerDriver" value="2"/>
<param name="japex.numberOfThreads" value="3"/>

<driverGroup name="SubgraphIsomorphism" xmlns="http://www.sun.com/japex/testSuite">
<driver name="CDK-1.2.x">
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<param name="chemObjectBuilder"
value="org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder"/>
</driver>
<driver name="CDK-trunk-13858">
<driver name="CDK-1.3.x-2009-10-08">
<param name="japex.driverClass" value="net.openmolecules.benchmark.driver.FingerprintCDKBench"/>
<param name="japex.classPath" value="${basedir}/lib/cdk-1.3.x-20091008.jar"/>
<param name="description" value="Benchmark of path based hashed fingperints based on 22 molecules
Before fingerprints, atom typing and aromaticity perception is performed"/>
<param name="chemObjectBuilder"
value="org.openscience.cdk.DefaultChemObjectBuilder"/>
</driver>
<driver name="CDK-trunk-13858-nonotify">
<driver name="CDK-1.3.x-2009-10-08-nonotify">
<param name="japex.driverClass" value="net.openmolecules.benchmark.driver.FingerprintCDKBench"/>
<param name="japex.classPath" value="${basedir}/lib/cdk-1.3.x-20091008.jar"/>
<param name="description" value="Benchmark of path based hashed fingperints based on 22 molecules
Before fingerprints, atom typing and aromaticity perception is performed"/>
<param name="chemObjectBuilder"
value="org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder"/>
</driver>
<driver name="CDK-1.4.0">
<param name="japex.driverClass" value="net.openmolecules.benchmark.driver.FingerprintCDKBench"/>
<param name="japex.classPath" value="${basedir}/lib/cdk-1.4.0.jar"/>
<param name="description" value="Benchmark of path based hashed fingperints based on 22 molecules
Before fingerprints, atom typing and aromaticity perception is performed"/>
<param name="chemObjectBuilder"
value="org.openscience.cdk.DefaultChemObjectBuilder"/>
</driver>
<driver name="CDK-1.4.0-nonotify">
<param name="japex.driverClass" value="net.openmolecules.benchmark.driver.FingerprintCDKBench"/>
<param name="japex.classPath" value="${basedir}/lib/cdk-1.4.0.jar"/>
<param name="description" value="Benchmark of path based hashed fingperints based on 22 molecules
Before fingerprints, atom typing and aromaticity perception is performed"/>
<param name="chemObjectBuilder"
value="org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder"/>
</driver>
<driver name="CDK-1.4.0-silent">
<param name="japex.driverClass" value="net.openmolecules.benchmark.driver.FingerprintCDKBench"/>
<param name="japex.classPath" value="${basedir}/lib/cdk-1.4.0.jar"/>
<param name="description" value="Benchmark of path based hashed fingperints based on 22 molecules
Before fingerprints, atom typing and aromaticity perception is performed"/>
<param name="chemObjectBuilder"
value="org.openscience.cdk.silent.SilentChemObjectBuilder"/>
</driver>
</driverGroup>

<testCase name="test1">
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