Merged cdk-1.4.x

cdk · Oct 20, 2010 · 5b430d5 · 5b430d5
2 parents 3af8a8c + 1afdcdb
commit 5b430d5
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Showing 97 changed files with 3,816 additions and 44 deletions.
diff --git a/.classpath b/.classpath
@@ -5,7 +5,7 @@
 	<classpathentry excluding="**/*.class|**/*.java" including="*.javafiles" kind="src" path="build"/>
 	<classpathentry kind="src" path="src/test"/>
 	<classpathentry exported="true" kind="lib" path="jar/jgrapht-0.6.0.jar" sourcepath="cdksrc.zip"/>
-	<classpathentry exported="true" kind="lib" path="jar/jniinchi-0.5.jar" sourcepath="cdksrc.zip"/>
+	<classpathentry exported="true" kind="lib" path="jar/jniinchi-0.7.jar" sourcepath="cdksrc.zip"/>
 	<classpathentry exported="true" kind="lib" path="jar/vecmath1.2-1.14.jar" sourcepath="cdksrc.zip"/>
 	<classpathentry exported="true" kind="lib" path="jar/xom-1.1.jar" sourcepath="cdksrc.zip"/>
 	<classpathentry exported="true" kind="lib" path="jar/jama-1.0.2.jar" sourcepath="cdksrc.zip"/>
@@ -19,7 +19,16 @@
 	<classpathentry exported="true" kind="lib" path="develjar/junit-4.5.jar"/>
 	<classpathentry kind="lib" path="jar/cmlxom-2.5-b1.jar"/>
 	<classpathentry kind="lib" path="develjar/ojdcheck.jar"/>
+	<classpathentry kind="lib" path="develjar/asm-3.1.jar"/>
+	<classpathentry kind="lib" path="develjar/groovy.jar"/>
+	<classpathentry kind="lib" path="develjar/antlr.jar"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
 	<classpathentry exported="true" kind="lib" path="jar/signatures-1.0.jar"/>
+	<classpathentry kind="lib" path="jar/jena/jena.jar"/>
+	<classpathentry kind="lib" path="jar/jena/slf4j-simple-1.5.0.jar"/>
+	<classpathentry kind="lib" path="jar/jena/commons-logging-1.1.1.jar"/>
+	<classpathentry kind="lib" path="jar/jena/slf4j-api-1.5.6.jar"/>
+	<classpathentry kind="lib" path="jar/jena/iri.jar"/>
+	<classpathentry kind="lib" path="jar/jena/icu4j_3_4.jar"/>
 	<classpathentry kind="output" path="bin"/>
 </classpath>
diff --git a/build.xml b/build.xml
@@ -531,7 +531,7 @@
             list="io,structgen"/>
         <foreach target="compile-module" param="module"
             parallel="${parallel}" maxthreads="${threadCount}"
-            list="pdb,smiles,sdg,inchi,libiocml"/>
+            list="pdb,smiles,sdg,inchi,sinchi,libiocml"/>
         <foreach target="compile-module" param="module"
             parallel="${parallel}" maxthreads="${threadCount}"
             list="control,extra,reaction,pdbcml,libiomd"/>
@@ -546,7 +546,7 @@
             list="qsaratomic,qsarbond,qsarprotein,qsarcml,qsarmolecular"/>
         <foreach target="compile-module" param="module"
             parallel="${parallel}" maxthreads="${threadCount}"
-            list="forcefield,qsarionpot"/>
+            list="forcefield,qsarionpot,iordf"/>
         <foreach target="compile-module" param="module"
             parallel="${parallel}" maxthreads="${threadCount}"
             list="builder3d,builder3dtools"/>
@@ -563,13 +563,13 @@
         	      test-valencycheck,test-smarts,test-standard,test-reaction,
                   test-pcore,test-sdg,test-forcefield,test-fingerprint,
                   test-ionpot,test-qm,test-isomorphism,test-libiomd,test-dict,
-                  test-diff,test-charges,test-inchi,test-formula,
+                  test-diff,test-charges,test-inchi,test-sinchi,test-formula,
                   test-render,test-ioformats,test-log4j"/>
         <foreach target="compile-module" param="module" trim="true"
             parallel="${parallel}" maxthreads="${threadCount}"
             list="test-data,test-qsaratomic,test-qsarbond,
                   test-pdb,test-smiles,test-extra,test-atomtype,
-                  test-structgen"/>
+                  test-structgen,test-iordf"/>
         <foreach target="compile-module" param="module" trim="true"
             parallel="${parallel}" maxthreads="${threadCount}"
             list="test-qsarmolecular,test-builder3d,test-datadebug,
@@ -630,6 +630,7 @@
                     <includesfile name="${metainf}/formula.libdepends"/>
                     <includesfile name="${metainf}/isomorphism.libdepends"/>
                     <includesfile name="${metainf}/qm.libdepends"/>
+                    <includesfile name="${metainf}/iordf.libdepends"/>
                     <includesfile name="${metainf}/signature.libdepends"/>
                 </fileset>
                 <fileset dir="${dist}/jar">
@@ -677,6 +678,7 @@
                     <include name="cdk-isomorphism.jar"/>
                     <include name="cdk-ionpot.jar"/>
                     <include name="cdk-smsd.jar"/>
+                    <include name="cdk-iordf.jar"/>
                     <include name="cdk-signature.jar"/>
                     <include name="cdk-qm.jar"/>
                 </fileset>
@@ -1058,7 +1060,7 @@
                       smarts,fingerprint,smiles,qsar,qsaratomic,qsarbond,
                       qsarmolecular,qsarionpot,qsarprotein,pdb,pcore,inchi,
                       structgen,libiomd,libiocml,formula,render,extra,sdg,
-                      ioformats,log4j,smsd,signature"/>
+                      ioformats,log4j,smsd,signature,iordf"/>
         </target>
 
         <target id="limitations" name="limitations" depends="noJunit, dist-all"

diff --git a/develjar/antlr.jar b/develjar/antlr.jar
diff --git a/develjar/groovy.jar b/develjar/groovy.jar
diff --git a/doc/refs/cheminf.bibx b/doc/refs/cheminf.bibx
@@ -1066,5 +1066,16 @@ Method </bibtex:title>
         </bibtex:article>
     </bibtex:entry>
 
+   <bibtex:entry id="YANG2010">
+        <bibtex:article>
+            <bibtex:author>Yang, Y. and Chen, H. and Nilsson, I. and Muresan, S. and Engkvist, O.</bibtex:author>
+            <bibtex:title>Investigation of the Relationship between Topology and Selectivity for Druglike Molecules</bibtex:title>
+            <bibtex:journal>J. Med. Chem.</bibtex:journal>
+            <bibtex:year>2010</bibtex:year>
+            <bibtex:volume>ASAP</bibtex:volume>
+            <bibtex:pages></bibtex:pages>
+        </bibtex:article>
+    </bibtex:entry>
+
 
 </bibtex:file>
diff --git a/jar/jena/commons-logging-1.1.1.jar b/jar/jena/commons-logging-1.1.1.jar
diff --git a/jar/jena/icu4j_3_4.jar b/jar/jena/icu4j_3_4.jar
diff --git a/jar/jena/iri.jar b/jar/jena/iri.jar
diff --git a/jar/jena/jena.jar b/jar/jena/jena.jar
diff --git a/jar/jena/slf4j-api-1.5.6.jar b/jar/jena/slf4j-api-1.5.6.jar
diff --git a/jar/jena/slf4j-simple-1.5.0.jar b/jar/jena/slf4j-simple-1.5.0.jar
diff --git a/jar/jniinchi-0.7.jar b/jar/jniinchi-0.7.jar
diff --git a/jar/jniinchi-0.7.jar.meta b/jar/jniinchi-0.7.jar.meta
@@ -0,0 +1,30 @@
+[jniinchi-0.7.jar]
+Library=JNI-InChI
+Version=0.7
+#Copyright=
+License=GNU Lesser General Public License
+LicenseURL=http://jni-inchi.sourceforge.net/license.html
+#Download=
+#SourceCode=
+Homepage=http://jni-inchi.sourceforge.net/
+
+[jniinchi-0.7.jar/org/apache/log4j]
+Library=Apache Log4J
+#Version=
+#Copyright=
+#License=
+#LicenseURL=
+#Download=
+#SourceCode=
+#Homepage=
+
+[jniinchi-0.7.jar/META-INF/jniinchi/1.6]
+Library=InChI Software
+Version=1.02
+#Copyright=
+License=GNU LGPL
+#LicenseURL=
+#Download=
+#SourceCode=
+Homepage=http://iupac.org/inchi/
+
diff --git a/javadoc.xml b/javadoc.xml
@@ -117,6 +117,7 @@
       <antcall target="ojdcheck-module"><param name="module" value="atomtype"/></antcall>
       <antcall target="ojdcheck-module"><param name="module" value="io"/></antcall>
       <antcall target="ojdcheck-module"><param name="module" value="ioformats"/></antcall>
+      <antcall target="ojdcheck-module"><param name="module" value="iordf"/></antcall>
       <antcall target="ojdcheck-module"><param name="module" value="inchi"/></antcall>
       <antcall target="ojdcheck-module"><param name="module" value="extra"/></antcall>
       <antcall target="ojdcheck-module"><param name="module" value="fingerprint"/></antcall>

diff --git a/pmd-unused.xml b/pmd-unused.xml
@@ -57,6 +57,7 @@
       <antcall target="test-module"><param name="module" value="diff"/></antcall>
       <antcall target="test-module"><param name="module" value="qm"/></antcall>
       <antcall target="test-module"><param name="module" value="smsd"/></antcall>
+      <antcall target="test-module"><param name="module" value="iordf"/></antcall>
       <antcall target="test-module"><param name="module" value="signature"/></antcall>
       <!-- the test modules -->
       <antcall target="test-module"><param name="module" value="test-core"/></antcall>
@@ -80,6 +81,7 @@
       <antcall target="test-module"><param name="module" value="test-qsarmolecular"/></antcall>
       <antcall target="test-module"><param name="module" value="test-qsarprotein"/></antcall>
       <antcall target="test-module"><param name="module" value="test-diff"/></antcall>
+      <antcall target="test-module"><param name="module" value="test-iordf"/></antcall>
       <antcall target="test-module"><param name="module" value="test-qm"/></antcall>
       <antcall target="test-module"><param name="module" value="test-smsd"/></antcall>
       <antcall target="test-module"><param name="module" value="test-signature"/></antcall>

diff --git a/pmd.xml b/pmd.xml
@@ -64,6 +64,7 @@
       <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="charges"/></antcall>
       <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="diff"/></antcall>
       <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="smsd"/></antcall>
+      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="iordf"/></antcall>
       <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="signature"/></antcall>
       <antcall target="test-module"><param name="pmd.test" value="custom-qm"/><param name="module" value="qm"/></antcall>
       <!-- the test modules -->
@@ -92,6 +93,7 @@
       <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-smsd"/></antcall>
       <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-log4j"/></antcall>
       <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-signature"/></antcall>
+      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-iordf"/></antcall>
     </target>
 
     <target id="test-module" name="test-module"

diff --git a/src/META-INF/iordf.cdkdepends b/src/META-INF/iordf.cdkdepends
@@ -0,0 +1,7 @@
+cdk-annotation.jar
+cdk-interfaces.jar
+cdk-ioformats.jar
+cdk-core.jar
+cdk-standard.jar
+cdk-atomtype.jar
+cdk-io.jar
diff --git a/src/META-INF/iordf.libdepends b/src/META-INF/iordf.libdepends
@@ -0,0 +1,7 @@
+vecmath1.2-1.14.jar
+jena/commons-logging-1.1.1.jar
+jena/icu4j_3_4.jar
+jena/iri.jar
+jena/jena.jar
+jena/slf4j-api-1.5.6.jar
+jena/slf4j-simple-1.5.0.jar
diff --git a/src/META-INF/sinchi.cdkdepends b/src/META-INF/sinchi.cdkdepends
@@ -0,0 +1,6 @@
+cdk-annotation.jar
+cdk-core.jar
+cdk-interfaces.jar
+cdk-io.jar
+cdk-standard.jar
+cdk-valencycheck.jar
diff --git a/src/META-INF/sinchi.libdepends b/src/META-INF/sinchi.libdepends
@@ -0,0 +1,4 @@
+vecmath1.2-1.14.jar
+xom-1.1.jar
+jniinchi-0.5.jar
+cmlxom-2.5-b1.jar
diff --git a/src/META-INF/test-extra.cdkdepends b/src/META-INF/test-extra.cdkdepends
@@ -25,3 +25,4 @@ cdk-test-core.jar
 cdk-test-io.jar
 cdk-testdata.jar
 cdk-diff.jar
+cdk-dict.jar
diff --git a/src/META-INF/test-formula.cdkdepends b/src/META-INF/test-formula.cdkdepends
@@ -9,3 +9,4 @@ cdk-formula.jar
 cdk-extra.jar
 cdk-smiles.jar
 cdk-valencycheck.jar
+cdk-io.jar
diff --git a/src/META-INF/test-io.devellibdepends b/src/META-INF/test-io.devellibdepends
@@ -1,2 +1,4 @@
 junit-4.5.jar
-
+groovy.jar
+asm-3.1.jar
+antlr.jar
diff --git a/src/META-INF/test-ioformats.cdkdepends b/src/META-INF/test-ioformats.cdkdepends
@@ -4,6 +4,7 @@ cdk-interfaces.jar
 cdk-core.jar
 cdk-standard.jar
 cdk-io.jar
+cdk-iordf.jar
 cdk-smiles.jar
 cdk-pdb.jar
 cdk-libiocml.jar

diff --git a/src/META-INF/test-iordf.cdkdepends b/src/META-INF/test-iordf.cdkdepends
@@ -0,0 +1,16 @@
+cdk-annotation.jar
+cdk-interfaces.jar
+cdk-ioformats.jar
+cdk-core.jar
+cdk-standard.jar
+cdk-atomtype.jar
+cdk-io.jar
+cdk-iordf.jar
+cdk-diff.jar
+cdk-data.jar
+cdk-nonotify.jar
+cdk-test.jar
+cdk-test-io.jar
+cdk-datadebug.jar
+cdk-testdata.jar
+cdk-iordf.jar
diff --git a/src/META-INF/test-iordf.devellibdepends b/src/META-INF/test-iordf.devellibdepends
@@ -0,0 +1,2 @@
+junit-4.5.jar
+
diff --git a/src/META-INF/test-iordf.libdepends b/src/META-INF/test-iordf.libdepends
@@ -0,0 +1,9 @@
+vecmath1.2-1.14.jar
+log4j.jar
+xercesImpl-2.9.0.jar
+jena/commons-logging-1.1.1.jar
+jena/icu4j_3_4.jar
+jena/iri.jar
+jena/jena.jar
+jena/slf4j-api-1.5.6.jar
+jena/slf4j-simple-1.5.0.jar
diff --git a/src/META-INF/test-sinchi.cdkdepends b/src/META-INF/test-sinchi.cdkdepends
@@ -0,0 +1,10 @@
+cdk-annotation.jar
+cdk-data.jar
+cdk-core.jar
+cdk-interfaces.jar
+cdk-io.jar
+cdk-render.jar
+cdk-standard.jar
+cdk-valencycheck.jar
+cdk-test.jar
+cdk-sinchi.jar
diff --git a/src/META-INF/test-sinchi.devellibdepends b/src/META-INF/test-sinchi.devellibdepends
@@ -0,0 +1,2 @@
+junit-4.5.jar
+
diff --git a/src/META-INF/test-sinchi.libdepends b/src/META-INF/test-sinchi.libdepends
@@ -0,0 +1,5 @@
+vecmath1.2-1.14.jar
+xom-1.1.jar
+jniinchi-0.7.jar
+cmlxom-2.5-b1.jar
+log4j.jar
diff --git a/src/main/org/openscience/cdk/dict/data/descriptor-algorithms.owl b/src/main/org/openscience/cdk/dict/data/descriptor-algorithms.owl
@@ -1069,6 +1069,27 @@
         <isClassifiedAs rdf:resource="#geometricalDescriptor"/>
         <isClassifiedAs rdf:resource="#molecularDescriptor"/>
 
+    </Descriptor>
+
+     <Descriptor rdf:ID="fmf">
+        <rdfs:label>FMF</rdfs:label>
+        <annotation>
+            <documentation>
+                <dc:contributor rdf:resource="#rguha"/>
+                <dc:date>2004-11-24</dc:date>
+            </documentation>
+        </annotation>
+        <definition rdf:parseType='Literal'>
+            Descriptor characterizing molecular complexity in terms of its Murcko framework
+        </definition>
+        <description rdf:parseType='Literal'>
+            This descriptor is described by Yang et al
+            <bibtex:cite ref="YANG2010"/> and is the ratio of heavy atoms in the Murcko
+            framework of a molecule to the total number of heavy atoms in the molecule.
+        </description>
+        <isClassifiedAs rdf:resource="#topologicalDescriptor"/>
+        <isClassifiedAs rdf:resource="#molecularDescriptor"/>
+
     </Descriptor>
 
     <Descriptor rdf:ID="gravitationalIndex_SquareAndCubeRoots">

diff --git a/src/main/org/openscience/cdk/fragment/MurckoFragmenter.java b/src/main/org/openscience/cdk/fragment/MurckoFragmenter.java
@@ -149,14 +149,16 @@ private void run(IAtomContainer atomContainer) throws CDKException {
         // only add this in if there is actually a framework
         // in some cases we might just have rings and sidechains
         if (hasframework(currentFramework)) {
-            smiles = smilesGenerator.createSMILES(clone);
+            smiles = smilesGenerator.createSMILES(currentFramework);
 
             // if we only want the single framework according to Murcko, then
             // it was the first framework that is added, since subsequent recursive
             // calls will work on substructures of the original framework
             if (singleFrameworkOnly) {
-                if (frameMap.size() == 0) frameMap.put(smiles, clone);
-            } else frameMap.put(smiles, clone);
+                if (frameMap.size() == 0) {
+                    frameMap.put(smiles, currentFramework);
+                }
+            } else frameMap.put(smiles, currentFramework);
         }
 
         // extract ring systems - we also delete pseudo linker bonds as described by