Updated javadocs and added extra unit test

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Sep 7, 2010 · ac211ce · ac211ce
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commit ac211ce
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Showing 3 changed files with 35 additions and 31 deletions.
diff --git a/src/main/org/openscience/cdk/dict/data/descriptor-algorithms.owl b/src/main/org/openscience/cdk/dict/data/descriptor-algorithms.owl
@@ -2493,7 +2493,7 @@
         <dc:contributor rdf:resource="#rguha"/>
         <dc:date>2010-08-31</dc:date>
         <definition rdf:parseType='Literal'>
-            Characterizes molecular complexity in terms of carbon hybridization states
+            Characterizes molecular complexity in terms of carbon hybridization states.
         </definition>
         <description rdf:parseType='Literal'>
             This descriptor is designed to give a simple characterization of molecular

diff --git a/src/main/org/openscience/cdk/qsar/descriptors/molecular/HybridizationRatioDescriptor.java b/src/main/org/openscience/cdk/qsar/descriptors/molecular/HybridizationRatioDescriptor.java
@@ -1,10 +1,7 @@
 /*
- *  $RCSfile$
- *  $Author$
- *  $Date$
- *  $Revision$
  *
- *  Copyright (C) 2004-2007  The Chemistry Development Kit (CDK) project
+ *
+ *  Copyright (C) 2010 Rajarshi Guha <rajarshi.guha@gmail.com> 
  *
  *  Contact: cdk-devel@lists.sourceforge.net
  *
@@ -38,7 +35,7 @@
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 
 /**
- * IDescriptor that reports the fraction of sp3 carbons to sp2 carbons.
+ * {@link IDescriptor} that reports the fraction of sp3 carbons to sp2 carbons.
  * <p/>
  * Note that it only considers carbon atoms and rather than use a simple ratio
  * it reports the value of N<sub>sp3</sub>/ (N<sub>sp3</sub> + N<sub>sp2</sub>).
@@ -56,23 +53,15 @@
 public class HybridizationRatioDescriptor implements IMolecularDescriptor {
 
     /**
-     * Constructor for the WeightDescriptor object.
+     * Constructor for the HybridizationRatioDescriptor object.
      */
     public HybridizationRatioDescriptor() {
     }
 
     /**
-     * Returns a <code>Map</code> which specifies which descriptor is implemented by this class.
-     * <p/>
-     * These fields are used in the map:
-     * <ul>
-     * <li>Specification-Reference: refers to an entry in a unique dictionary
-     * <li>Implementation-Title: anything
-     * <li>Implementation-Identifier: a unique identifier for this version of
-     * this class
-     * <li>Implementation-Vendor: CDK, JOELib, or anything else
-     * </ul>
+     * Returns a {@link Map} which specifies which descriptor is implemented by this class.
      *
+     * @inheritDoc     
      * @return An object containing the descriptor specification
      */
     @TestMethod("testGetSpecification")
@@ -85,7 +74,7 @@ public DescriptorSpecification getSpecification() {
     }
 
     /**
-     * Sets the parameters attribute of the WeightDescriptor object.
+     * Sets the parameters attribute of the HybridizationRatioDescriptor object.
      *
      * @param params The new parameters value
      * @throws org.openscience.cdk.exception.CDKException
@@ -99,7 +88,9 @@ public void setParameters(Object[] params) throws CDKException {
 
 
     /**
-     * Gets the parameters attribute of the WeightDescriptor object.
+     * Gets the parameters attribute of the HybridizationRatioDescriptor object.
+     *
+     * This descriptor takes no parameters
      *
      * @return The parameters value
      * @see #setParameters
@@ -114,17 +105,23 @@ public String[] getDescriptorNames() {
         return new String[]{"HybRatio"};
     }
 
+    /**
+     * @inheritDoc
+     * 
+     * @param e
+     * @return
+     */
     private DescriptorValue getDummyDescriptorValue(Exception e) {
         return new DescriptorValue(getSpecification(), getParameterNames(),
                 getParameters(), new DoubleResult(Double.NaN), getDescriptorNames(), e);
     }
 
 
     /**
-     * Calculate the weight of specified element type in the supplied {@link org.openscience.cdk.interfaces.IAtomContainer}.
+     * Calculate sp3/sp2 hybridization ratio in the supplied {@link org.openscience.cdk.interfaces.IAtomContainer}.
      *
      * @param container The AtomContainer for which this descriptor is to be calculated.
-     * @return The total weight of atoms of the specified element type
+     * @return The ratio of sp3 to sp2 carbons
      */
     @TestMethod("testCalculate_IAtomContainer")
     public DescriptorValue calculate(IAtomContainer container) {
@@ -166,7 +163,9 @@ public IDescriptorResult getDescriptorResultType() {
 
 
     /**
-     * Gets the parameterNames attribute of the WeightDescriptor object.
+     * Gets the parameterNames attribute of the HybridizationRatioDescriptor object.
+     *
+     * This descriptor takes no parameters
      *
      * @return The parameterNames value
      */
@@ -179,7 +178,9 @@ public String[] getParameterNames() {
     /**
      * Gets the parameterType attribute of the HybridizationRatioDescriptor object.
      *
-     * @param name Description of the Parameter
+     * This descriptor takes no parameters
+     *
+     * @param name the parameter name
      * @return An Object whose class is that of the parameter requested
      */
     @TestMethod("testGetParameterType_String")

diff --git a/...test/org/openscience/cdk/qsar/descriptors/molecular/HybridizationRatioDescriptorTest.java b/...test/org/openscience/cdk/qsar/descriptors/molecular/HybridizationRatioDescriptorTest.java
@@ -1,9 +1,5 @@
-/* $RCSfile$
- * $Author$
- * $Date$
- * $Revision$
- * 
- * Copyright (C) 2004-2007  The Chemistry Development Kit (CDK) project
+/*
+ * Copyright (C) 2010 Rajarshi Guha <rajarshi.guha@gmail.com>
  * 
  * Contact: cdk-devel@lists.sourceforge.net
  * 
@@ -32,7 +28,7 @@
 import org.openscience.cdk.smiles.SmilesParser;
 
 /**
- * TestSuite that runs a test for the HybridizationRatioDescriptor.
+ * TestSuite that runs a test for the {@link HybridizationRatioDescriptor}.
  *
  * @cdk.module test-qsarmolecular
  */
@@ -59,4 +55,11 @@ public void testHybRatioDescriptor2() throws Exception {
         IAtomContainer mol = sp.parseSmiles("c1ccccc1");
         Assert.assertEquals(0.0, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1);
     }
+
+    @Test
+    public void testHybRatioDescriptor3() throws Exception {
+        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
+        IAtomContainer mol = sp.parseSmiles("[H]C#N");
+        Assert.assertEquals(Double.NaN, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1);
+    }
 }