Template for a class to calculate molecular volume

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>

doc/refs/cheminf.bibx

@@ -1124,6 +1124,19 @@ Method </bibtex:title>
     </bibtex:article>
   </bibtex:entry>
 
+  <bibtex:entry id="Zhao2003">
+    <bibtex:article>
+      <bibtex:author>Zhao, Yuan H. and Abraham, Michael H. and Zissimos, Andreas M.</bibtex:author>
+      <bibtex:title>Fast Calculation of van der Waals Volume as a Sum of Atomic and Bond Contributions and Its Application to Drug Compounds</bibtex:title>
+      <bibtex:journal>The Journal of Organic Chemistry</bibtex:journal>
+      <bibtex:year>2003</bibtex:year>
+      <bibtex:volume>68</bibtex:volume>
+      <bibtex:number>19</bibtex:number>
+      <bibtex:pages>7368-7373</bibtex:pages>
+      <bibtex:doi>10.1021/jo034808o</bibtex:doi>
+    </bibtex:article>
+  </bibtex:entry>
+
   <bibtex:entry id="Thalheim2010">
         <bibtex:article>
             <bibtex:author>Thalheim, T. and Vollmer, A. and Ebert, R. and Kuehne, R. and Schuurmann, G.</bibtex:author>

src/main/org/openscience/cdk/geometry/volume/VABCVolume.java

@@ -0,0 +1,46 @@
+/* Copyright (C) 2011  Egon Willighagen <egonw@users.sf.net>
+ * 
+ * Contact: cdk-devel@lists.sourceforge.net
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * 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.geometry.volume;
+
+import org.openscience.cdk.annotations.TestClass;
+import org.openscience.cdk.interfaces.IMolecule;
+
+/**
+ * Calculates the Vanderwaals volume using the method proposed
+ * in {@cdk.cite Zhao2003}. The method is limited to molecules
+ * with the folowing elements: H, C, N, O, F, Cl, Br, I,
+ * P, S, As, B, Si, Se, and Te.
+ *
+ * @cdk.module   standard
+ * @cdk.keywords volume, molecular
+ */
+@TestClass("org.openscience.cdk.geometry.volume.VABCVolumeTest")
+public class VABCVolume {
+
+    /**
+     * Calculates the volume for the given {@link IMolecule}.
+     *
+     * @param  molecule {@link IMolecule} to calculate the volume of.
+     * @return          the volume in cubic &Aring;ngstr&ouml;m.
+     */
+    public static double calculate(IMolecule molecule) {
+        return 0.0;
+    }
+
+}

src/test/org/openscience/cdk/geometry/volume/VABCVolumeTest.java

@@ -0,0 +1,51 @@
+/* Copyright (C) 2011  Egon Willighagen <egonw@users.sf.net>
+ * 
+ * Contact: cdk-devel@lists.sourceforge.net
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * 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.geometry.volume;
+
+import junit.framework.Assert;
+
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.openscience.cdk.exception.InvalidSmilesException;
+import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
+import org.openscience.cdk.smiles.SmilesParser;
+
+public class VABCVolumeTest {
+
+    private static SmilesParser smilesParser;
+
+    @BeforeClass
+    public static void setup() {
+        smilesParser = new SmilesParser(
+            NoNotificationChemObjectBuilder.getInstance()
+        );
+    }
+
+    /**
+     * Test from Table 1 from {@cdk.cite Zhao2003}.
+     */
+    @Test
+    public void testMethane() throws InvalidSmilesException {
+        IMolecule methane = smilesParser.parseSmiles("C");
+        double volume = VABCVolume.calculate(methane);
+        Assert.assertEquals(25.83, volume, 0.01);
+    }
+
+}