@@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <project name="MX" default="compile" basedir=".">  - <property name="full-name" value="MX Tools for Cheminformatics" /> + <property name="full-name" value="MX - Essential Cheminformatics" /> <property name="unix-name" value="mx" /> - <property name="version" value="1.0-beta1" /> + <property name="version" value="1.0-beta-2" /> <property name="source.dir" location="src" /> <property name="resource.dir" location="resources" /> <property name="lib.dir" location="lib" /> @@ -14,10 +14,13 @@ <property name="doc.dir" location="${build.dir}/doc" /> <property name="dist.dir" location="${build.dir}/dist" /> <property name="test.dir" location="${build.dir}/test" /> + <property name="molfile.dir" location="${resource.dir}/molfiles" /> <property name="testenv.dir" location ="testenv" /> - <property name="lib-licenses.file" location="${lib.dir}/LICENSES.txt" /> - <property name="license.file" location="LICENSE.txt" /> + <property name="lib-licenses.file" location="${lib.dir}/LICENSES" /> + <property name="license.file" location="LICENSE" /> + <property name="readme.file" location="README" /> <property name="junit.lib" value="${lib.dir}/junit-4.5.jar" /> + <property name="mockito.lib" value="${lib.dir}/mockito-all-1.7.jar" /> <property name="test.class" value = "com.metamolecular.mx.test.MXTest" />  <fileset dir="${lib.dir}" id="libs"> @@ -70,7 +73,7 @@ <classpath> <fileset refid="libs" /> </classpath> - <bottom><![CDATA[<i>Copyright © 2007, 2008 <a href="http://metamolecular.com">Metamolecular, LLC</a>. All Rights Reserved.</i>]]> + <bottom><![CDATA[<i>Copyright © 2007-2009 <a href="http://metamolecular.com">Metamolecular, LLC</a> and others. All Rights Reserved.</i>]]> </bottom> </javadoc> </target> @@ -83,15 +86,21 @@ <mkdir dir="${dist.dir}/src" /> <mkdir dir="${dist.dir}/doc" /> <mkdir dir="${dist.dir}/resources" /> + <mkdir dir="${dist.dir}/resources/molfiles" /> <copy file="${junit.lib}" todir="${dist.dir}/lib" /> + <copy file="${mockito.lib}" todir="${dist.dir}/lib" /> <copy file="${lib-licenses.file}" todir="${dist.dir}/lib" /> <copy file="${license.file}" todir="${dist.dir}" /> + <copy file="${readme.file}" todir="${dist.dir}" /> <copy todir="${dist.dir}/src"> <fileset dir="${source.dir}" includes="com/metamolecular/mx/**/*.java" /> </copy> <copy todir="${dist.dir}/doc"> <fileset dir="${doc.dir}" /> </copy> + <copy todir="${dist.dir}/resources/molfiles"> + <fileset dir="${molfile.dir}" /> + </copy> <copy file="${resource.dir}/atomic_system.pdf" todir="${dist.dir}/resources" /> <copy file="${resource.dir}/atomic_system.xml" todir="${dist.dir}/resources" /> <copy file="${resource.dir}/pubchem_sample_33.sdf" todir="${dist.dir}/resources" /> build.xml @@ -1,5 +1,5 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * @@ -26,7 +26,7 @@ package com.metamolecular.mx.calc; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class DefaultMeasurement implements Measurement { src/com/metamolecular/mx/calc/DefaultMeasurement.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.calc; import com.metamolecular.mx.model.Atom; @@ -30,7 +31,7 @@ import com.metamolecular.mx.model.AtomicSystem; import com.metamolecular.mx.model.Molecule; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class MassCalculator { src/com/metamolecular/mx/calc/MassCalculator.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,10 +23,11 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.calc; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public interface Measurement { src/com/metamolecular/mx/calc/Measurement.java @@ -1,10 +1,10 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * Copyright (c) Ian Clarke * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal src/com/metamolecular/mx/fingerprint/BloomFilter.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java - * - * Copyright (c) 2007-2008 Metamolecular, LLC - * - * http://metamolecular.com + * MX - Essential Cheminformatics + * + * Copyright (c) 2007-2009 Metamolecular, LLC + * + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.fingerprint; import com.metamolecular.mx.model.Molecule; src/com/metamolecular/mx/fingerprint/Fingerprinter.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java - * - * Copyright (c) 2007-2008 Metamolecular, LLC - * - * http://metamolecular.com + * MX - Essential Cheminformatics + * + * Copyright (c) 2007-2009 Metamolecular, LLC + * + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.fingerprint; import com.metamolecular.mx.model.Atom; src/com/metamolecular/mx/fingerprint/PathFingerprinter.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,12 +23,13 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.io; import com.metamolecular.mx.model.*; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> * @author Duan Lian */ public class Molecules src/com/metamolecular/mx/io/Molecules.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.io.daylight; import com.metamolecular.mx.model.Atom; @@ -33,7 +34,7 @@ import java.util.List; import java.util.Map; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class SMILESBuilder { src/com/metamolecular/mx/io/daylight/SMILESBuilder.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.io.daylight; import com.metamolecular.mx.model.DefaultMolecule; @@ -30,7 +31,7 @@ import com.metamolecular.mx.model.Molecule; import java.util.regex.Pattern; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class SMILESReader { src/com/metamolecular/mx/io/daylight/SMILESReader.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.io.daylight; import java.util.ArrayList; @@ -32,7 +33,7 @@ import java.util.regex.Matcher; import java.util.regex.Pattern; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class SMILESTokenizer { src/com/metamolecular/mx/io/daylight/SMILESTokenizer.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -27,7 +27,7 @@ package com.metamolecular.mx.io.mdl; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class MDLStringKit { src/com/metamolecular/mx/io/mdl/MDLStringKit.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.io.mdl; import java.io.LineNumberReader; @@ -36,7 +37,7 @@ import com.metamolecular.mx.model.Molecule; import com.metamolecular.mx.model.Superatom; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class MolfileReader { src/com/metamolecular/mx/io/mdl/MolfileReader.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.io.mdl; import java.text.DecimalFormat; @@ -36,7 +37,7 @@ import com.metamolecular.mx.model.Molecule; import com.metamolecular.mx.model.Superatom; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class MolfileWriter { src/com/metamolecular/mx/io/mdl/MolfileWriter.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.io.mdl; import com.metamolecular.mx.model.Molecule; src/com/metamolecular/mx/io/mdl/SDFileReader.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.io.mdl; import com.metamolecular.mx.model.Molecule; @@ -32,7 +33,7 @@ import java.io.FileWriter; import java.io.IOException; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class SDFileWriter { src/com/metamolecular/mx/io/mdl/SDFileWriter.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.map; import com.metamolecular.mx.query.*; @@ -35,7 +36,7 @@ import java.util.Map; /** * - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class DefaultMapper implements Mapper { src/com/metamolecular/mx/map/DefaultMapper.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.map; import com.metamolecular.mx.query.*; src/com/metamolecular/mx/map/DefaultState.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.map; import com.metamolecular.mx.query.*; @@ -33,7 +34,7 @@ import java.util.Map; /** * - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public interface Mapper { src/com/metamolecular/mx/map/Mapper.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal src/com/metamolecular/mx/map/Match.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal src/com/metamolecular/mx/map/State.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -27,7 +27,7 @@ package com.metamolecular.mx.model; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public interface Atom { src/com/metamolecular/mx/model/Atom.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.model; import com.metamolecular.mx.calc.DefaultMeasurement; @@ -38,7 +39,7 @@ import org.w3c.dom.Node; import org.w3c.dom.NodeList; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class AtomicSystem { src/com/metamolecular/mx/model/AtomicSystem.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -27,7 +27,7 @@ package com.metamolecular.mx.model; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public interface Bond { src/com/metamolecular/mx/model/Bond.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.model; import java.util.ArrayList; @@ -34,7 +35,7 @@ import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> * @author Duan Lian */ public class DefaultMolecule implements Molecule src/com/metamolecular/mx/model/DefaultMolecule.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,13 +23,14 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.model; import com.metamolecular.mx.calc.Measurement; /** * - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public interface Isotope { src/com/metamolecular/mx/model/Isotope.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -29,7 +29,7 @@ package com.metamolecular.mx.model; import javax.swing.event.ChangeListener; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> * @author Duan Lian */ public interface Molecule src/com/metamolecular/mx/model/Molecule.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -34,7 +34,7 @@ import com.metamolecular.mx.io.mdl.MolfileReader; import com.metamolecular.mx.io.mdl.MolfileWriter; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class MoleculeKit { src/com/metamolecular/mx/model/MoleculeKit.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal src/com/metamolecular/mx/model/Reducer.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java - * + * MX - Essential Cheminformatics + * * Copyright (c) 2007-2009 Metamolecular, LLC - * - * http://metamolecular.com + * + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,11 +23,12 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.model; /** * @author Duan Lian - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public interface Superatom { src/com/metamolecular/mx/model/Superatom.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,13 +23,14 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.model; import java.util.HashMap; import java.util.Map; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class VirtualHydrogenCounter { src/com/metamolecular/mx/model/VirtualHydrogenCounter.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal src/com/metamolecular/mx/query/AromaticAtomFilter.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal src/com/metamolecular/mx/query/AtomMatcher.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal src/com/metamolecular/mx/query/BondMatcher.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.query; import com.metamolecular.mx.model.Atom; src/com/metamolecular/mx/query/DefaultAtomMatcher.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.query; import com.metamolecular.mx.model.Atom; src/com/metamolecular/mx/query/DefaultBondMatcher.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.query; import java.util.ArrayList; src/com/metamolecular/mx/query/DefaultQuery.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal src/com/metamolecular/mx/query/Edge.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal src/com/metamolecular/mx/query/Node.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal src/com/metamolecular/mx/query/Query.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.query; /** src/com/metamolecular/mx/query/QueryCompiler.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal src/com/metamolecular/mx/query/TemplateCompiler.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -33,7 +33,7 @@ import java.util.Collection; import java.util.List; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class HanserRingFinder implements RingFinder { src/com/metamolecular/mx/ring/HanserRingFinder.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.ring; import com.metamolecular.mx.model.Atom; @@ -31,7 +32,7 @@ import java.util.Collections; import java.util.List; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class PathEdge { src/com/metamolecular/mx/ring/PathEdge.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.ring; import com.metamolecular.mx.model.Atom; @@ -33,7 +34,7 @@ import java.util.Arrays; import java.util.List; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class PathGraph { src/com/metamolecular/mx/ring/PathGraph.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal src/com/metamolecular/mx/ring/RingFilter.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -32,7 +32,7 @@ import java.util.Collection; import java.util.List; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public interface RingFinder { src/com/metamolecular/mx/ring/RingFinder.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal src/com/metamolecular/mx/test/AromaticAtomFilterTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -35,7 +35,7 @@ import javax.swing.event.ChangeListener; import junit.framework.TestCase; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class AtomTest extends TestCase { src/com/metamolecular/mx/test/AtomTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.test; import com.metamolecular.mx.model.AtomicSystem; @@ -32,7 +33,7 @@ import java.util.List; import junit.framework.TestCase; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class AtomicSystemTest extends TestCase { src/com/metamolecular/mx/test/AtomicSystemTest.java @@ -1,10 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC - * Copyright (c) Ian Clarke * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -24,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.test; import com.metamolecular.mx.fingerprint.BloomFilter; src/com/metamolecular/mx/test/BloomFilterTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.test; import com.metamolecular.mx.model.Atom; @@ -32,7 +33,7 @@ import com.metamolecular.mx.model.Molecule; import junit.framework.TestCase; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class BondTest extends TestCase { src/com/metamolecular/mx/test/BondTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.test; import com.metamolecular.mx.io.Molecules; src/com/metamolecular/mx/test/DefaultAtomMatcherTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal src/com/metamolecular/mx/test/DefaultBondMatcherTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,10 +23,10 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.test; import com.metamolecular.mx.io.Molecules; -import com.metamolecular.mx.io.daylight.SMILESReader; import com.metamolecular.mx.model.Atom; import com.metamolecular.mx.model.DefaultMolecule; import com.metamolecular.mx.model.Molecule; @@ -40,7 +40,7 @@ import junit.framework.TestCase; /** * - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class DefaultMapperTest extends TestCase { src/com/metamolecular/mx/test/DefaultMapperTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal src/com/metamolecular/mx/test/DefaultStateTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.test; import com.metamolecular.mx.model.Atom; src/com/metamolecular/mx/test/DefaultStepTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.test; import com.metamolecular.mx.model.Atom; src/com/metamolecular/mx/test/DefaultWalkerTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -35,7 +35,7 @@ import java.util.List; import junit.framework.TestCase; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class HanserRingFinderTest extends TestCase { src/com/metamolecular/mx/test/HanserRingFinderTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -30,7 +30,7 @@ import junit.framework.TestSuite; import junit.textui.TestRunner; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class MXTest { src/com/metamolecular/mx/test/MXTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.test; import com.metamolecular.mx.calc.MassCalculator; @@ -31,7 +32,7 @@ import com.metamolecular.mx.model.Molecule; import junit.framework.TestCase; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class MassCalculatorTest extends TestCase { src/com/metamolecular/mx/test/MassCalculatorTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.test; import com.metamolecular.mx.io.Molecules; @@ -31,7 +32,7 @@ import com.metamolecular.mx.model.MoleculeKit; import junit.framework.TestCase; /** - * @author Richard Apodaca + * @author Richard Apodaca <rapodaca at metamolecular.com> */ public class MoleculeKitTest extends TestCase { src/com/metamolecular/mx/test/MoleculeKitTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.test; import com.metamolecular.mx.model.Atom; @@ -34,7 +35,7 @@ import javax.swing.event.ChangeListener; import junit.framework.TestCase; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class MoleculeTest extends TestCase { src/com/metamolecular/mx/test/MoleculeTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -34,7 +34,7 @@ import com.metamolecular.mx.model.Bond; import junit.framework.TestCase; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class MolfileReaderTest extends TestCase { src/com/metamolecular/mx/test/MolfileReaderTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java - * + * MX - Essential Cheminformatics + * * Copyright (c) 2007-2009 Metamolecular, LLC - * - * http://metamolecular.com + * + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.test; import junit.framework.TestCase; @@ -33,6 +34,7 @@ import java.io.*; /** * @author Duan Lian + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class MolfileWriterTest extends TestCase { src/com/metamolecular/mx/test/MolfileWriterTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.test; import com.metamolecular.mx.io.Molecules; @@ -32,7 +33,7 @@ import java.util.Arrays; import junit.framework.TestCase; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class PathEdgeTest extends TestCase { src/com/metamolecular/mx/test/PathEdgeTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java - * - * Copyright (c) 2007-2008 Metamolecular, LLC - * - * http://metamolecular.com + * MX - Essential Cheminformatics + * + * Copyright (c) 2007-2009 Metamolecular, LLC + * + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.test; import com.metamolecular.mx.fingerprint.PathFingerprinter; src/com/metamolecular/mx/test/PathFingerprinterTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.test; import com.metamolecular.mx.io.Molecules; @@ -34,7 +35,7 @@ import java.util.List; import junit.framework.TestCase; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class PathGraphTest extends TestCase { src/com/metamolecular/mx/test/PathGraphTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.test; import com.metamolecular.mx.walk.PathWriter; src/com/metamolecular/mx/test/PathWriterTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.test; import com.metamolecular.mx.query.BondMatcher; src/com/metamolecular/mx/test/QueryTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal src/com/metamolecular/mx/test/ReducerTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal src/com/metamolecular/mx/test/RingFilterTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.test; import com.metamolecular.mx.io.mdl.SDFileReader; src/com/metamolecular/mx/test/SDFileReaderTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.test; import com.metamolecular.mx.io.Molecules; @@ -32,7 +33,7 @@ import java.io.File; import junit.framework.TestCase; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class SDFileWriterTest extends TestCase { src/com/metamolecular/mx/test/SDFileWriterTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.test; import com.metamolecular.mx.io.daylight.SMILESBuilder; @@ -31,7 +32,7 @@ import com.metamolecular.mx.model.Molecule; import junit.framework.TestCase; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class SMILESBuilderTest extends TestCase { src/com/metamolecular/mx/test/SMILESBuilderTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.test; import com.metamolecular.mx.io.daylight.SMILESReader; @@ -32,7 +33,7 @@ import com.metamolecular.mx.model.Molecule; import junit.framework.TestCase; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class SMILESReaderTest extends TestCase { src/com/metamolecular/mx/test/SMILESReaderTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,13 +23,14 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.test; import com.metamolecular.mx.io.daylight.SMILESTokenizer; import junit.framework.TestCase; /** - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class SMILESTokenizerTest extends TestCase { src/com/metamolecular/mx/test/SMILESTokenizerTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.test; import com.metamolecular.mx.model.Molecule; @@ -38,7 +39,7 @@ import javax.swing.event.ChangeEvent; /** * @author Duan Lian - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class SuperatomTest extends TestCase { src/com/metamolecular/mx/test/SuperatomTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal src/com/metamolecular/mx/test/TemplateCompilerTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.test; import com.metamolecular.mx.model.Atom; @@ -34,7 +35,7 @@ import junit.framework.TestCase; /** * - * @author Richard L. Apodaca + * @author Richard L. Apodaca <rapodaca at metamolecular.com> */ public class VirtualHydrogenCounterTest extends TestCase { src/com/metamolecular/mx/test/VirtualHydrogenCounterTest.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.walk; import com.metamolecular.mx.model.Atom; src/com/metamolecular/mx/walk/DefaultStep.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.walk; import com.metamolecular.mx.model.Atom; src/com/metamolecular/mx/walk/DefaultWalker.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java - * - * Copyright (c) 2007-2008 Metamolecular, LLC - * - * http://metamolecular.com + * MX - Essential Cheminformatics + * + * Copyright (c) 2007-2009 Metamolecular, LLC + * + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal @@ -23,6 +23,7 @@ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ + package com.metamolecular.mx.walk; import com.metamolecular.mx.model.Atom; src/com/metamolecular/mx/walk/PathWriter.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal src/com/metamolecular/mx/walk/Reporter.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal src/com/metamolecular/mx/walk/Step.java @@ -1,9 +1,9 @@ /* - * MX Cheminformatics Tools for Java + * MX - Essential Cheminformatics * * Copyright (c) 2007-2009 Metamolecular, LLC * - * http://metamolecular.com + * http://metamolecular.com/mx * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal src/com/metamolecular/mx/walk/Walker.java 8e39ba03e98b8a24706f496bc1e19facd27026e0 Rich Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/9542b28b7bba586573552b7abb47269b7462a664 9542b28b7bba586573552b7abb47269b7462a664

2009-07-01T17:43:30-07:00

updated copyright notice, email addresses, build file, bumped release eaea98830abdc1f8bb9895c3bab4b27266a7ce8b Rich Apodaca rapodaca@metamolecular.com