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Merge branch 'cdk-1.4.x' of github.com:cdk/cdk into cdk-1.4.x
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rajarshi committed Oct 5, 2012
2 parents a6ab39c + 26b13dd commit bca08c4
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Showing 84 changed files with 848 additions and 167 deletions.
2 changes: 1 addition & 1 deletion build.props
@@ -1,3 +1,3 @@
# configuration file
#
version=1.4.11.git
version=1.4.14
127 changes: 33 additions & 94 deletions build.xml
Expand Up @@ -35,21 +35,25 @@
<property name="arg3" value="" />
<property name="arg4" value="" />

<property environment="env" />
<!-- jvm arguments -->
<property name="jvmarg.cdk.debugging" value="true"
description="print debug logging statements"/>
<property name="jvmarg.cdk.stdout" value="true"/>

<!-- jar file names for libraries used for compiling -->
<property name="javaccjar" value="javacc.jar" />
<property name="antcontribjar" value="ant-contrib-1.0b3.jar" />
<property name="vecmathjar" value="vecmath1.2-1.14.jar" />
<property name="log4jjar" value="log4j.jar" />
<property name="jgraphtjar" value="jgrapht-0.6.0.jar" />
<property name="junitjar" value="junit-4.5.jar" />

<property environment="env" />

<!-- Include the ant-contrib goodies -->
<taskdef name="javancss" classname="javancss.JavancssAntTask">
<classpath>
<pathelement location="${basedir}/develjar/javacc.jar"/>
<pathelement location="${basedir}/develjar/javancss.jar"/>
<pathelement location="${basedir}/develjar/ccl.jar"/>
<pathelement location="${basedir}/develjar/jhbasic.jar"/>
</classpath>
</taskdef>
<!-- Include the JavaNCSS goodies -->
<taskdef resource="net/sf/antcontrib/antlib.xml">
<classpath>
<pathelement location="${basedir}/develjar/ant-contrib-1.0b3.jar"/>
<pathelement location="${devellib}/${antcontribjar}"/>
</classpath>
</taskdef>

Expand Down Expand Up @@ -143,11 +147,11 @@

<!-- test for optional jars -->
<available property="vecmath.present"
file="${lib}/vecmath1.2-1.14.jar"/>
file="${lib}/${vecmathjar}"/>
<available property="log4j.present"
file="${lib}/log4j.jar"/>
file="${lib}/${log4jjar}"/>
<available property="jgrapht.present"
file="${lib}/jgrapht-0.6.0.jar"/>
file="${lib}/${jgraphtjar}"/>

<!-- test for optional jars -->
<condition property="cmllibs.present">
Expand All @@ -159,7 +163,7 @@
<condition property="junit.present">
<or>
<available file="${ant.home}/lib/junit.jar"/>
<available file="${devellib}/junit-4.5.jar"/>
<available file="${devellib}/${junitjar}"/>
</or>
</condition>

Expand Down Expand Up @@ -1125,7 +1129,8 @@
-Dtestclass=&lt;class>.">
<echo message="Running test class: testclass=${testclass}"/>
<java classname="org.openscience.cdk.${testclass}" fork="yes" maxmemory="512m">
<jvmarg value="-Dcdk.debugging=true"/>
<jvmarg value="-Dcdk.debugging=${jvmarg.cdk.debugging}"/>
<jvmarg value="-Dcdk.debug.stdout=${jvmarg.cdk.stdout}"/>
<classpath>
<fileset dir="${dist}/jar/">
<include name="*.jar" />
Expand All @@ -1140,12 +1145,12 @@
</java>
</target>

<target id="junit-test" name="junit-test" depends="dist-all,test-dist-all,noJunit"
<target id="junit-test" name="junit-test" depends="dist-all,jarTestdata,test-dist-all,noJunit"
description="Runs one specific JUnit test suite (org.openscience.cdk.&lt;class>) with -Dtestclass=&lt;class>.">
<echo message="JUnit tests class: testclass=${testclass}"/>
<junit printsummary="yes" haltonfailure="no" fork="yes">
<jvmarg value="-Dcdk.debugging=true"/>
<jvmarg value="-Dcdk.debug.stdout=true"/>
<echo message="JUnit tests class: testclass=${testclass} [JVM Arguments: cdk.debugging=${cdk.debugging}, ${jvmarg.cdk.stdout}]"/>
<junit printsummary="yes" haltonfailure="no" fork="yes" maxmemory="512m">
<jvmarg value="-Dcdk.debugging=${jvmarg.cdk.debugging}"/>
<jvmarg value="-Dcdk.debug.stdout=${jvmarg.cdk.stdout}"/>
<classpath>
<fileset dir="${dist}/jar/">
<include name="*.jar" />
Expand All @@ -1171,14 +1176,13 @@
<target id="run" name="run" depends="dist-all"
description="Runs an application (org.openscience.cdk.&lt;class>) with -Drunclass=&lt;class>.">
<java classname="org.openscience.cdk.${runclass}" fork="yes" >
<!--jvmarg value="-Dcdk.debugging=true"/>
<jvmarg value="-Dcdk.debug.stdout=true"/-->

<arg value="${arg1}" />
<arg value="${arg2}" />
<arg value="${arg3}" />
<arg value="${arg4}" />
<classpath>
<jvmarg value="-Dcdk.debugging=${jvmarg.cdk.debugging}"/>
<jvmarg value="-Dcdk.debug.stdout=${jvmarg.cdk.stdout}"/>
<arg value="${arg1}" />
<arg value="${arg2}" />
<arg value="${arg3}" />
<arg value="${arg4}" />
<classpath>
<fileset dir="${dist}/jar">
<include name="*.jar" />
</fileset>
Expand All @@ -1189,69 +1193,4 @@
</java>
</target>

<target name="checkCopyright" id="checkCopyright" depends="check, customize">
<echo>Checking copyright info...</echo>
<mkdir dir="${build}" />
<javac includes="net/sf/cdk/tools/copyright/CheckCopyrightStatements.java"
srcdir="${src}/main/" destdir="${build}" optimize="${optimization}"
debug="${debug}" deprecation="${deprecation}"/>
<java classpath="${build}" classname="net.sf.cdk.tools.copyright.CheckCopyrightStatements">
<arg value="${src}/META-INF"/>
<arg value="${src}/main"/>
<arg value="${build}"/>
</java>
</target>

<target name="javancss" id="javancss" depends="runDoclet">
<mkdir dir="${build}" />
<echo>Calculating source statistics...</echo>
<javancss srcdir="${src}/main" includes="**/*.java"
generateReport="true"
outputfile="${build}/cdk_metrics.xml"
format="plain"
classMetrics="false"
functionMetrics="false"
/>
<javancss srcdir="${src}/test" includes="**/*.java"
generateReport="true"
outputfile="${build}/cdktest_metrics.xml"
format="plain"
classMetrics="false"
functionMetrics="false"
/>
</target>

<!-- Regenerate template fingerprints in case the fingerprint code has been updated
so that fingerprint bits are different from a previous version -->
<target name="makefp3d" id="makefp3d">
<antcall target="compile-module"><param name="module" value="builder3dtools"/></antcall>
<gunzip src="${src}/main/org/openscience/cdk/modeling/builder3d/data/ringTemplateStructures.sdf.gz"
dest="${src}/main/org/openscience/cdk/modeling/builder3d/data/" />
<java classname="org.openscience.cdk.modeling.builder3d.TemplateExtractor">
<classpath>
<pathelement location="jar/jgrapht-0.6.0.jar"/>
<pathelement location="jar/xercesImpl-2.9.0.jar"/>
<pathelement location="jar/vecmath1.2-1.14.jar"/>
<pathelement path="${dist}/jar/cdk-builder3dtools.jar" />
<pathelement path="${dist}/jar/cdk-interfaces.jar" />
<pathelement path="${dist}/jar/cdk-nonotify.jar" />
<pathelement path="${dist}/jar/cdk-standard.jar" />
<pathelement path="${dist}/jar/cdk-core.jar" />
<pathelement path="${dist}/jar/cdk-io.jar" />
<pathelement path="${dist}/jar/cdk-ioformats.jar" />
<pathelement path="${dist}/jar/cdk-data.jar" />
<pathelement path="${dist}/jar/cdk-isomorphism.jar" />
<pathelement path="${dist}/jar/cdk-fingerprint.jar" />
</classpath>
<arg value="${src}/main/org/openscience/cdk/modeling/builder3d/data/ringTemplateStructures.sdf" />
<arg value="${src}/main/org/openscience/cdk/modeling/builder3d/data/ringTemplateFingerprints.txt" />
<arg value="True" />
<arg value="True" />
</java>
<gzip src="${src}/main/org/openscience/cdk/modeling/builder3d/data/ringTemplateFingerprints.txt"
destfile="${src}/main/org/openscience/cdk/modeling/builder3d/data/ringTemplateFingerprints.txt.gz" />
<delete file="${src}/main/org/openscience/cdk/modeling/builder3d/data/ringTemplateStructures.sdf"/>
<delete file="${src}/main/org/openscience/cdk/modeling/builder3d/data/ringTemplateFingerprints.txt"/>
</target>

</project>
151 changes: 151 additions & 0 deletions devel.xml
@@ -0,0 +1,151 @@
<project name="CDK" default="dist-all" basedir=".">

<property file="build.props"/>

<!-- directories -->
<property name="build" value="build" />
<property name="build.src" value="${build}/src" />
<property name="sourcedist" value="sourcedist" />
<property name="dist" value="dist" />
<property name="doc" value="doc" />
<property name="src" value="src" />
<property name="lib" value="jar" />
<property name="devellib" value="develjar" />
<property name="src.tests" value="${src}/test/org/openscience/cdk/test" />
<property name="reports.tests" value="reports" />
<property name="appjars.dir" value="${dist}/appjars" />
<property name="metainf" value="${src}/META-INF" />

<!-- jar file names for libraries used for compiling -->
<property name="javaccjar" value="javacc.jar" />
<property name="antcontribjar" value="ant-contrib-1.0b3.jar" />
<property name="vecmathjar" value="vecmath1.2-1.14.jar" />
<property name="log4jjar" value="log4j.jar" />
<property name="jgraphtjar" value="jgrapht-0.6.0.jar" />
<property name="junitjar" value="junit-4.5.jar" />
<property name="xercesjar" value="xercesImpl-2.9.0.jar" />

<property environment="env" />

<!-- Include the JavaNCSS goodies -->
<taskdef name="javancss" classname="javancss.JavancssAntTask">
<classpath>
<pathelement location="${devellib}/${javaccjar}"/>
<pathelement location="${devellib}/javancss.jar"/>
<pathelement location="${devellib}/ccl.jar"/>
<pathelement location="${devellib}/jhbasic.jar"/>
</classpath>
</taskdef>
<!-- Include the ant-contrib goodies -->
<taskdef resource="net/sf/antcontrib/antlib.xml">
<classpath>
<pathelement location="${devellib}/${antcontribjar}"/>
</classpath>
</taskdef>

<target id="info" name="info" depends="check">
<!-- Gives information about the building process. -->
<echo message="Platform:" />
<echo message=" OS: ${os.name}" />
<echo message=" Architecture: ${os.arch}" />
<echo message=" Version: ${os.version}" />
<echo message=" Mac OS/X found: ${isMacOsX}" />
<echo message="" />
<echo message="Java/Ant Environment:" />
<echo message=" Java version: ${java.version}" />
<echo message=" Java vendor: ${java.vendor}" />
<echo message=" Java dir: ${java.home}" />
<echo message=" Java ext dir: ${java.ext.dirs}" />
<echo message=" Ant version: ${ant.version}" />
<echo message=" ${ANT_HOME}: ${ant.home}" />
<echo message=" hasAnt17: ${hasAnt17}" />
<echo message="" />
<echo message="CDK Environment:" />
<echo message=" CDK version: ${version}" />
<echo message=" build.xml: $Id$" />
<echo message=" Junit found: ${junit.present}" />
<echo message=" --- required libraries ---" />
<echo message=" Vecmath found: ${vecmath.present}" />
<echo message=" Log4j found: ${log4j.present}" />
<echo message=" JGraphT found: ${jgrapht.present}" />
<echo message=" --- distributed (but optional) libraries ---" />
<echo message=" CMLDOM found: ${cmllibs.present}" />
</target>

<!-- See what platform were on -->

<target id="checkPlatforms" name="checkPlatforms">
<condition property="isMacOsX">
<and>
<os family="mac"/>
<os family="unix"/>
</and>
</condition>
</target>

<target name="checkCopyright" id="checkCopyright" depends="check, customize">
<echo>Checking copyright info...</echo>
<mkdir dir="${build}" />
<javac includes="net/sf/cdk/tools/copyright/CheckCopyrightStatements.java"
srcdir="${src}/main/" destdir="${build}" optimize="${optimization}"
debug="${debug}" deprecation="${deprecation}"/>
<java classpath="${build}" classname="net.sf.cdk.tools.copyright.CheckCopyrightStatements">
<arg value="${src}/META-INF"/>
<arg value="${src}/main"/>
<arg value="${build}"/>
</java>
</target>

<target name="javancss" id="javancss" depends="runDoclet">
<mkdir dir="${build}" />
<echo>Calculating source statistics...</echo>
<javancss srcdir="${src}/main" includes="**/*.java"
generateReport="true"
outputfile="${build}/cdk_metrics.xml"
format="plain"
classMetrics="false"
functionMetrics="false"
/>
<javancss srcdir="${src}/test" includes="**/*.java"
generateReport="true"
outputfile="${build}/cdktest_metrics.xml"
format="plain"
classMetrics="false"
functionMetrics="false"
/>
</target>

<!-- Regenerate template fingerprints in case the fingerprint code has been updated
so that fingerprint bits are different from a previous version -->
<target name="makefp3d" id="makefp3d">
<antcall target="compile-module"><param name="module" value="builder3dtools"/></antcall>
<gunzip src="${src}/main/org/openscience/cdk/modeling/builder3d/data/ringTemplateStructures.sdf.gz"
dest="${src}/main/org/openscience/cdk/modeling/builder3d/data/" />
<java classname="org.openscience.cdk.modeling.builder3d.TemplateExtractor">
<classpath>
<pathelement location="jar/${jgraphtjar}"/>
<pathelement location="jar/${xercesjar}"/>
<pathelement location="jar/${vecmathjar}"/>
<pathelement path="${dist}/jar/cdk-builder3dtools.jar" />
<pathelement path="${dist}/jar/cdk-interfaces.jar" />
<pathelement path="${dist}/jar/cdk-nonotify.jar" />
<pathelement path="${dist}/jar/cdk-standard.jar" />
<pathelement path="${dist}/jar/cdk-core.jar" />
<pathelement path="${dist}/jar/cdk-io.jar" />
<pathelement path="${dist}/jar/cdk-ioformats.jar" />
<pathelement path="${dist}/jar/cdk-data.jar" />
<pathelement path="${dist}/jar/cdk-isomorphism.jar" />
<pathelement path="${dist}/jar/cdk-fingerprint.jar" />
</classpath>
<arg value="${src}/main/org/openscience/cdk/modeling/builder3d/data/ringTemplateStructures.sdf" />
<arg value="${src}/main/org/openscience/cdk/modeling/builder3d/data/ringTemplateFingerprints.txt" />
<arg value="True" />
<arg value="True" />
</java>
<gzip src="${src}/main/org/openscience/cdk/modeling/builder3d/data/ringTemplateFingerprints.txt"
destfile="${src}/main/org/openscience/cdk/modeling/builder3d/data/ringTemplateFingerprints.txt.gz" />
<delete file="${src}/main/org/openscience/cdk/modeling/builder3d/data/ringTemplateStructures.sdf"/>
<delete file="${src}/main/org/openscience/cdk/modeling/builder3d/data/ringTemplateFingerprints.txt"/>
</target>

</project>
54 changes: 54 additions & 0 deletions doxygen.xml
@@ -0,0 +1,54 @@
<project name="CDK" default="html" basedir=".">

<property file="build.props"/>

<!-- $Id$ -->

<property name="vecmath.src" value="gcj/vecmath" />
<property name="vecmath.javadoc.dir" value="doc/vecmath/api" />

<property name="src" value="src" />
<property name="javadoc.dir" value="doc/cdk-javadoc-${version}" />
<property name="doxygen.dir" value="doc/doxygen" />

<property name="pathtojava3d" value="" />

<!-- directories -->
<property name="build" value="build" />
<property name="lib" value="jar" />
<property name="devellib" value="develjar" />
<property name="dist" value="dist" />
<property name="metainf" value="${src}/META-INF" />

<!-- Used in the html task to properly link to java library classes -->
<property name="javaURL" value="http://java.sun.com/j2se/1.5.0/docs/api/"/>

<path id="project.class.path">
<pathelement location="." />
<fileset dir="jar">
<include name="*.jar" />
</fileset>
<fileset dir="${pathtojava3d}">
<include name="*.jar" />
</fileset>
</path>

<taskdef name="doxygen" classname="org.doxygen.tools.DoxygenTask"
classpath="develjar/ant_doxygen.jar" />

<target name="doxygen" id="doxygen">
<mkdir dir="${doxygen.dir}" />
<doxygen>
<property name="INPUT" value="src/" />
<property name="PROJECT_NAME" value="The Chemistry Development Kit" />
<property name="OUTPUT_DIRECTORY" value="${doxygen.dir}" />
<property name="OPTIMIZE_OUTPUT_JAVA" value="YES" />
<property name="UML_LOOK" value="YES" />
<property name="ALIASES" value='"cdk.module=Is part of the CDK module:"' />
</doxygen>
</target>

</project>



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