Merged cdk-1.4.x

cdk · Nov 24, 2011 · 7223cfb · 7223cfb
2 parents a4db4a2 + 284ff84
commit 7223cfb
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Showing 9 changed files with 274 additions and 16 deletions.
diff --git a/doc/refs/cheminf.bibx b/doc/refs/cheminf.bibx
@@ -1180,7 +1180,7 @@ Method </bibtex:title>
       <bibtex:volume>24</bibtex:volume> 
       <bibtex:number>21</bibtex:number> 
       <bibtex:pages>2518-2525</bibtex:pages> 
-      <bibtex:year>2008</bibtex:pages> 
+      <bibtex:year>2008</bibtex:year> 
       <bibtex:doi>10.1093/bioinformatics/btn479</bibtex:doi>
       <bibtex:URL>http://bioinformatics.oxfordjournals.org/content/24/21/2518.abstract</bibtex:URL> 
       <bibtex:eprint>http://bioinformatics.oxfordjournals.org/content/24/21/2518.full.pdf+html</bibtex:eprint> 

diff --git a/src/main/org/openscience/cdk/qsar/descriptors/molecular/ChiIndexUtils.java b/src/main/org/openscience/cdk/qsar/descriptors/molecular/ChiIndexUtils.java
@@ -19,6 +19,8 @@
 package org.openscience.cdk.qsar.descriptors.molecular;
 
 import org.openscience.cdk.DefaultChemObjectBuilder;
+import org.openscience.cdk.annotations.TestClass;
+import org.openscience.cdk.annotations.TestMethod;
 import org.openscience.cdk.config.IsotopeFactory;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.interfaces.IAtom;
@@ -45,6 +47,7 @@
  * @cdk.module qsarmolecular
  * @cdk.githash
  */
+@TestClass("org.openscience.cdk.qsar.descriptors.molecular.ChiIndexUtilsTest")
 class ChiIndexUtils {
 
     /**
@@ -193,7 +196,8 @@ private static int getValenceElectronCount(IAtom atom) {
      * @return The empirical delta V if it is present in one of the above
      *         environments, -1 otherwise
      */
-    private static double deltavSulphur(IAtom atom, IAtomContainer atomContainer) {
+    @TestMethod("testDeltaVSuplhurSO,testDeltaVSulphurSO2")
+    protected static double deltavSulphur(IAtom atom, IAtomContainer atomContainer) {
         if (!atom.getSymbol().equals("S")) return -1;
 
         // check whether it's a S in S-S
@@ -204,21 +208,14 @@ private static double deltavSulphur(IAtom atom, IAtomContainer atomContainer) {
                 return .89;
         }
 
-        // check whether it's a S in -SO-
-        for (IAtom connectedAtom : connected) {
-            if (connectedAtom.getSymbol().equals("O")
-                    && atomContainer.getBond(atom, connectedAtom).getOrder() == IBond.Order.DOUBLE)
-                return 1.33;
-        }
-
-        // check whether it's a S in -SO2-
         int count = 0;
         for (IAtom connectedAtom : connected) {
             if (connectedAtom.getSymbol().equals("O")
                     && atomContainer.getBond(atom, connectedAtom).getOrder() == IBond.Order.DOUBLE)
                 count++;
         }
-        if (count == 2) return 2.67;
+        if (count == 1) return 1.33; // check whether it's a S in -SO-
+        else if (count == 2) return 2.67; // check whether it's a S in -SO2-
 
         return -1;
     }

diff --git a/src/main/org/openscience/cdk/renderer/BoundsCalculator.java b/src/main/org/openscience/cdk/renderer/BoundsCalculator.java
@@ -26,6 +26,8 @@
 
 import javax.vecmath.Point2d;
 
+import org.openscience.cdk.annotations.TestClass;
+import org.openscience.cdk.annotations.TestMethod;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IAtomContainerSet;
@@ -43,6 +45,7 @@
  * @cdk.module renderbasic
  * @cdk.githash
  */
+@TestClass("org.openscience.cdk.renderer.BoundsCalculatorTest")
 public class BoundsCalculator {
 
     /**
@@ -51,6 +54,7 @@ public class BoundsCalculator {
      * @param chemModel the chem model to use
      * @return the bounding rectangle of the chem model
      */
+    @TestMethod("testCalculateBounds_IChemModel")
     public static Rectangle2D calculateBounds(IChemModel chemModel) {
         IAtomContainerSet moleculeSet = chemModel.getMoleculeSet();
         IReactionSet reactionSet = chemModel.getReactionSet();
@@ -76,6 +80,7 @@ public static Rectangle2D calculateBounds(IChemModel chemModel) {
      * @param reactionSet the reaction set to use
      * @return the bounding rectangle of the reaction set
      */
+    @TestMethod("testCalculateBounds_IReactionSet")
     public static Rectangle2D calculateBounds(IReactionSet reactionSet) {
         Rectangle2D totalBounds = new Rectangle2D.Double();
         for (IReaction reaction : reactionSet.reactions()) {
@@ -95,6 +100,7 @@ public static Rectangle2D calculateBounds(IReactionSet reactionSet) {
      * @param reaction the reaction to use
      * @return the bounding rectangle of the reaction
      */
+    @TestMethod("testCalculateBounds_IReaction")
     public static Rectangle2D calculateBounds(IReaction reaction) {
         // get the participants in the reaction
         IMoleculeSet reactants = reaction.getReactants();
@@ -112,7 +118,8 @@ public static Rectangle2D calculateBounds(IReaction reaction) {
      * @param moleculeSet the molecule set to use
      * @return the bounding rectangle of the molecule set
      */
-    public static Rectangle2D calculateBounds(IAtomContainerSet moleculeSet) {
+    @TestMethod("testCalculateBounds_IMoleculeSet")
+    public static Rectangle2D calculateBounds(IMoleculeSet moleculeSet) {
         Rectangle2D totalBounds = new Rectangle2D.Double();
         for (int i = 0; i < moleculeSet.getAtomContainerCount(); i++) {
             IAtomContainer container = moleculeSet.getAtomContainer(i);
@@ -132,14 +139,20 @@ public static Rectangle2D calculateBounds(IAtomContainerSet moleculeSet) {
      * @param atomContainer the atom container to use
      * @return the bounding rectangle of the atom container
      */
+    @TestMethod("testCalculateBounds_IAtomContainer")
     public static Rectangle2D calculateBounds(IAtomContainer atomContainer) {
         // this is essential, otherwise a rectangle
         // of (+INF, -INF, +INF, -INF) is returned!
         if (atomContainer.getAtomCount() == 0) {
             return new Rectangle2D.Double();
         } else if (atomContainer.getAtomCount() == 1) {
-            Point2d p = atomContainer.getAtom(0).getPoint2d();
-            return new Rectangle2D.Double(p.x, p.y, 0, 0);
+            Point2d point = atomContainer.getAtom(0).getPoint2d();
+            if (point == null) {
+                throw new IllegalArgumentException(
+                    "Cannot calculate bounds when 2D coordinates are missing."
+                );
+            }
+            return new Rectangle2D.Double(point.x, point.y, 0, 0);
         }
 
         double xmin = Double.POSITIVE_INFINITY;
@@ -149,6 +162,11 @@ public static Rectangle2D calculateBounds(IAtomContainer atomContainer) {
 
         for (IAtom atom : atomContainer.atoms()) {
             Point2d point = atom.getPoint2d();
+            if (point == null) {
+                throw new IllegalArgumentException(
+                    "Cannot calculate bounds when 2D coordinates are missing."
+                );
+            }
             xmin = Math.min(xmin, point.x);
             xmax = Math.max(xmax, point.x);
             ymin = Math.min(ymin, point.y);

diff --git a/src/main/org/openscience/cdk/tools/ProteinBuilderTool.java b/src/main/org/openscience/cdk/tools/ProteinBuilderTool.java
@@ -104,7 +104,7 @@ public static BioPolymer addAminoAcidAtCTerminus(
 
     /**
      * Creates a BioPolymer from a sequence of amino acid as identified by a
-     * the sequence of there one letter codes.
+     * the sequence of their one letter codes.
      *
      * <p>For example:
      * <pre>

diff --git a/src/main/org/openscience/cdk/tools/diff/AtomContainerDiff.java b/src/main/org/openscience/cdk/tools/diff/AtomContainerDiff.java
@@ -36,6 +36,7 @@
  * 
  * @author     egonw
  * @cdk.module diff
+ * @cdk.githash
  */
 @TestClass("org.openscience.cdk.tools.diff.AtomContainerDiffTest")
 public class AtomContainerDiff {

diff --git a/src/test/org/openscience/cdk/coverage/CoverageAnnotationTest.java b/src/test/org/openscience/cdk/coverage/CoverageAnnotationTest.java
@@ -90,6 +90,7 @@ protected boolean runCoverageTest() {
     private int checkClass(String className) {
         Class coreClass = loadClass(getClassName(className));
         if (coreClass.isInterface()) return 0;
+        if (Modifier.isAbstract(coreClass.getModifiers())) return 0;
 
         int missingTestCount = 0;
         HashMap<String, TestMethod> methodAnnotations = new HashMap<String, TestMethod>();

diff --git a/src/test/org/openscience/cdk/modulesuites/MrenderbasicTests.java b/src/test/org/openscience/cdk/modulesuites/MrenderbasicTests.java
@@ -23,6 +23,7 @@
 import org.junit.runners.Suite.SuiteClasses;
 import org.openscience.cdk.coverage.RenderbasicCoverageTest;
 import org.openscience.cdk.renderer.AtomContainerRendererTest;
+import org.openscience.cdk.renderer.BoundsCalculatorTest;
 import org.openscience.cdk.renderer.elements.ArrowElementTest;
 import org.openscience.cdk.renderer.elements.AtomSymbolElementTest;
 import org.openscience.cdk.renderer.elements.GeneralPathTest;
@@ -69,6 +70,7 @@
 	LineToTest.class,
 	CubicToTest.class,
 	MoveToTest.class,
-	QuadToTest.class
+	QuadToTest.class,
+	BoundsCalculatorTest.class
 })
 public class MrenderbasicTests {}
diff --git a/src/test/org/openscience/cdk/qsar/descriptors/molecular/ChiIndexUtilsTest.java b/src/test/org/openscience/cdk/qsar/descriptors/molecular/ChiIndexUtilsTest.java
@@ -20,12 +20,66 @@
  */
 package org.openscience.cdk.qsar.descriptors.molecular;
 
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
 import org.openscience.cdk.CDKTestCase;
+import org.openscience.cdk.DefaultChemObjectBuilder;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IMolecule;
 
 /**
  * @cdk.module test-qsarmolecular
  */
 public class ChiIndexUtilsTest extends CDKTestCase {
 
+    DefaultChemObjectBuilder builder;
+
+    public ChiIndexUtilsTest() {
+    }
+
+    @Before
+    public void setup() {
+        builder = (DefaultChemObjectBuilder) DefaultChemObjectBuilder.getInstance();
+    }
+
+    @Test
+    public void testDeltaVSulphurSO() {
+        IAtom s = builder.newInstance(IAtom.class, "S");
+        IAtom o = builder.newInstance(IAtom.class, "O");
+        IBond b = builder.newInstance(IBond.class, s, o);
+        b.setOrder(IBond.Order.DOUBLE);
+
+        IMolecule m = builder.newInstance(IMolecule.class);
+        m.addAtom(s);
+        m.addAtom(o);
+        m.addBond(b);
+
+        double deltav = ChiIndexUtils.deltavSulphur(s, m);
+        Assert.assertEquals(1.33, deltav, 0.01);
+    }
+
+    @Test
+    public void testDeltaVSulphurSO2() {
+        IAtom s = builder.newInstance(IAtom.class, "S");
+        IAtom o1 = builder.newInstance(IAtom.class, "O");
+        IAtom o2 = builder.newInstance(IAtom.class, "O");
+        IBond b1 = builder.newInstance(IBond.class, s, o1);
+        IBond b2 = builder.newInstance(IBond.class, s, o2);
+        b1.setOrder(IBond.Order.DOUBLE);
+        b2.setOrder(IBond.Order.DOUBLE);
+
+        IMolecule m = builder.newInstance(IMolecule.class);
+        m.addAtom(s);
+        m.addAtom(o1);
+        m.addBond(b1);
+        m.addAtom(o2);
+        m.addBond(b2);
+
+        double deltav = ChiIndexUtils.deltavSulphur(s, m);
+        Assert.assertEquals(2.67, deltav, 0.01);
+    }
+
 }