Merge branch 'master' of git://github.com/cdk/cdk

danielszisz · Apr 20, 2012 · 25327de · 25327de
2 parents e49f588 + f7654cb
commit 25327de
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Showing 56 changed files with 488 additions and 369 deletions.
diff --git a/build.xml b/build.xml
@@ -539,7 +539,7 @@
             list="pdb,smiles,sdg,inchi,libiocml"/>
         <foreach target="compile-module" param="module"
             parallel="${parallel}" maxthreads="${threadCount}"
-            list="control,extra,reaction,pdbcml,libiomd"/>
+            list="control,extra,fragment,reaction,pdbcml,libiomd"/>
         <foreach target="compile-module" param="module"
             parallel="${parallel}" maxthreads="${threadCount}"
             list="charges,smarts,signature"/>
@@ -576,7 +576,7 @@
         <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-pdb,test-smiles,test-extra,test-fragment,test-atomtype,
                   test-structgen,test-iordf,test-silent"/>
         <foreach target="compile-module" param="module" trim="true"
             parallel="${parallel}" maxthreads="${threadCount}"
@@ -620,6 +620,7 @@
                     <includesfile name="${metainf}/data.libdepends"/>
                     <includesfile name="${metainf}/silent.libdepends"/>
                     <includesfile name="${metainf}/extra.libdepends"/>
+                    <includesfile name="${metainf}/fragment.libdepends"/>
                     <includesfile name="${metainf}/cip.libdepends"/>
                     <includesfile name="${metainf}/io.libdepends"/>
                     <includesfile name="${metainf}/libiocml.libdepends"/>
@@ -666,6 +667,7 @@
                     <include name="cdk-data.jar"/>
                     <include name="cdk-silent.jar"/>
                     <include name="cdk-extra.jar"/>
+                    <include name="cdk-fragment.jar"/>
                     <include name="cdk-interfaces.jar"/>
                     <include name="cdk-io.jar"/>
                     <include name="cdk-libiocml.jar"/>
@@ -743,6 +745,7 @@
                     <include name="cdk-silent.jar"/>
                     <include name="cdk-diff.jar"/>
                     <include name="cdk-extra.jar"/>
+                    <include name="cdk-fragment.jar"/>
                     <include name="cdk-interfaces.jar"/>
                     <include name="cdk-io.jar"/>
                     <include name="cdk-ioformats.jar"/>
@@ -811,6 +814,7 @@
                     <includesfile name="${metainf}/test-silent.libdepends"/>
                     <includesfile name="${metainf}/test-diff.libdepends"/>
                     <includesfile name="${metainf}/test-extra.libdepends"/>
+                    <includesfile name="${metainf}/test-fragment.libdepends"/>
                     <includesfile name="${metainf}/test-builder3d.libdepends"/>
                     <includesfile name="${metainf}/test-forcefield.libdepends"/>
                     <includesfile name="${metainf}/test-inchi.libdepends"/>
@@ -848,6 +852,7 @@
                     <include name="cdk-test-silent.jar"/>
                     <include name="cdk-test-diff.jar"/>
                     <include name="cdk-test-extra.jar"/>
+                    <include name="cdk-test-fragment.jar"/>
                     <include name="cdk-test-builder3d.jar"/>
                     <include name="cdk-test-forcefield.jar"/>
                     <include name="cdk-test-inchi.jar"/>
@@ -1080,7 +1085,7 @@
                       io,builder3d,forcefield,valencycheck,charges,reaction,
                       smarts,fingerprint,smiles,qsar,qsaratomic,qsarbond,
                       qsarmolecular,qsarionpot,qsarprotein,pdb,pcore,inchi,
-                      structgen,libiomd,libiocml,formula,render,extra,sdg,
+                      structgen,libiomd,libiocml,formula,render,extra,fragment,sdg,
                       ioformats,log4j,smsd,signature,iordf,cip,tautomer,
                       isomorphism,renderbasic,renderawt,silent"/>
         </target>

diff --git a/src/META-INF/builder3dtools.cdkdepends b/src/META-INF/builder3dtools.cdkdepends
@@ -4,7 +4,6 @@ cdk-data.jar
 cdk-silent.jar
 cdk-interfaces.jar
 cdk-io.jar
-cdk-qsar.jar
 cdk-standard.jar
 cdk-charges.jar
 cdk-forcefield.jar

diff --git a/src/META-INF/charges.cdkdepends b/src/META-INF/charges.cdkdepends
@@ -1,6 +1,5 @@
 cdk-annotation.jar
 cdk-core.jar
-cdk-data.jar
 cdk-interfaces.jar
 cdk-io.jar
 cdk-standard.jar

diff --git a/src/META-INF/fingerprint.cdkdepends b/src/META-INF/fingerprint.cdkdepends
@@ -2,7 +2,6 @@ cdk-annotation.jar
 cdk-interfaces.jar
 cdk-core.jar
 cdk-standard.jar
-cdk-io.jar
 cdk-isomorphism.jar
 cdk-valencycheck.jar
 cdk-smarts.jar

diff --git a/src/META-INF/forcefield.cdkdepends b/src/META-INF/forcefield.cdkdepends
@@ -2,9 +2,6 @@ cdk-annotation.jar
 cdk-core.jar
 cdk-data.jar
 cdk-interfaces.jar
-cdk-qsar.jar
-cdk-qsaratomic.jar
 cdk-io.jar
 cdk-standard.jar
 cdk-charges.jar
-cdk-extra.jar
diff --git a/src/META-INF/fragment.cdkdepends b/src/META-INF/fragment.cdkdepends
@@ -0,0 +1,5 @@
+cdk-interfaces.jar
+cdk-annotation.jar
+cdk-core.jar
+cdk-standard.jar
+cdk-smiles.jar
diff --git a/src/META-INF/qsaratomic.cdkdepends b/src/META-INF/qsaratomic.cdkdepends
@@ -1,10 +1,8 @@
 cdk-annotation.jar
 cdk-interfaces.jar
-cdk-data.jar
 cdk-core.jar
 cdk-standard.jar
 cdk-valencycheck.jar
-cdk-extra.jar
 cdk-isomorphism.jar
 cdk-reaction.jar
 cdk-isomorphism.jar

diff --git a/src/META-INF/qsarbond.cdkdepends b/src/META-INF/qsarbond.cdkdepends
@@ -1,6 +1,5 @@
 cdk-annotation.jar
 cdk-interfaces.jar
-cdk-data.jar
 cdk-core.jar
 cdk-standard.jar
 cdk-valencycheck.jar

diff --git a/src/META-INF/qsarcml.cdkdepends b/src/META-INF/qsarcml.cdkdepends
@@ -1,6 +1,5 @@
 cdk-annotation.jar
 cdk-core.jar
-cdk-data.jar
 cdk-interfaces.jar
 cdk-libiocml.jar
 cdk-qsar.jar

diff --git a/src/META-INF/qsarionpot.cdkdepends b/src/META-INF/qsarionpot.cdkdepends
@@ -1,10 +1,8 @@
 cdk-annotation.jar
 cdk-interfaces.jar
-cdk-data.jar
 cdk-core.jar
 cdk-standard.jar
 cdk-valencycheck.jar
-cdk-extra.jar
 cdk-reaction.jar
 cdk-charges.jar
 cdk-qsar.jar

diff --git a/src/META-INF/qsarmolecular.cdkdepends b/src/META-INF/qsarmolecular.cdkdepends
@@ -1,10 +1,8 @@
 cdk-annotation.jar
 cdk-interfaces.jar
-cdk-data.jar
 cdk-core.jar
 cdk-standard.jar
 cdk-valencycheck.jar
-cdk-extra.jar
 cdk-reaction.jar
 cdk-charges.jar
 cdk-qsar.jar
@@ -13,3 +11,4 @@ cdk-smarts.jar
 cdk-formula.jar
 cdk-isomorphism.jar
 cdk-dict.jar
+cdk-fragment.jar
diff --git a/src/META-INF/qsarprotein.cdkdepends b/src/META-INF/qsarprotein.cdkdepends
@@ -3,8 +3,5 @@ cdk-interfaces.jar
 cdk-data.jar
 cdk-core.jar
 cdk-standard.jar
-cdk-valencycheck.jar
-cdk-reaction.jar
-cdk-charges.jar
 cdk-qsar.jar
 cdk-pdb.jar
diff --git a/src/META-INF/smarts.cdkdepends b/src/META-INF/smarts.cdkdepends
@@ -1,7 +1,6 @@
 cdk-annotation.jar
 cdk-core.jar
 cdk-interfaces.jar
-cdk-io.jar
 cdk-standard.jar
 cdk-valencycheck.jar
 cdk-isomorphism.jar
diff --git a/src/META-INF/test-fragment.cdkdepends b/src/META-INF/test-fragment.cdkdepends
@@ -0,0 +1,16 @@
+cdk-annotation.jar
+cdk-interfaces.jar
+cdk-core.jar
+cdk-data.jar
+cdk-standard.jar
+cdk-extra.jar
+cdk-smiles.jar
+cdk-test.jar
+cdk-io.jar
+cdk-silent.jar
+cdk-testdata.jar
+cdk-atomtype.jar
+cdk-valencycheck.jar
+cdk-pdb.jar
+cdk-log4j.jar
+cdk-fragment.jar
diff --git a/src/META-INF/test-fragment.devellibdepends b/src/META-INF/test-fragment.devellibdepends
@@ -0,0 +1,2 @@
+junit-4.10.jar
+
diff --git a/src/META-INF/test-fragment.libdepends b/src/META-INF/test-fragment.libdepends
@@ -0,0 +1,3 @@
+log4j*.jar
+vecmath*.jar
+jgrapht-0.6.0.jar
diff --git a/src/META-INF/test-qsarmolecular.cdkdepends b/src/META-INF/test-qsarmolecular.cdkdepends
@@ -30,3 +30,4 @@ cdk-builder3d.jar
 cdk-forcefield.jar
 cdk-sdg.jar
 cdk-ioformats.jar
+cdk-fragment.jar
diff --git a/src/main/org/openscience/cdk/EnzymeResidueLocator.java b/src/main/org/openscience/cdk/EnzymeResidueLocator.java
@@ -1,9 +1,4 @@
-/* $RCSfile$
- * $Author$
- * $Date$
- * $Revision$
- *
- * Copyright (C) 2003-2007  Egon Willighagen <egonw@users.sf.net>
+/* Copyright (C) 2003-2007  Egon Willighagen <egonw@users.sf.net>
  * 
  * Contact: cdk-devel@lists.sourceforge.net
  * 
@@ -24,14 +19,14 @@
  * You should have received a copy of the GNU Lesser General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
- *
  */
 package org.openscience.cdk;
 
 /**
  * Atom that represents part of an residue in an enzyme, like Arg255.
  *
  * @see  PseudoAtom
+ * @cdk.module pdb
  */
 public class EnzymeResidueLocator extends PseudoAtom {