Added the Mannhold LogP descriptor

doc/refs/cheminf.bibx

@@ -401,6 +401,17 @@ obtained by accurate mass spectrometry</bibtex:title>
     </bibtex:article>
   </bibtex:entry>
 
+  <bibtex:entry id="Mannhold2009">
+    <bibtex:article>
+      <bibtex:author>Mannhold, R. and Poda, G.I. and Ostermann, C. and Tetko, I.V.</bibtex:author>
+      <bibtex:title>Calculation of molecular lipophilicity: State-of-the-art and comparison of log P methods on more than 96,000 compounds</bibtex:title>
+      <bibtex:journal>J.Pharm.Sci.</bibtex:journal>
+      <bibtex:year>2009</bibtex:year>
+      <bibtex:volume>98</bibtex:volume>
+      <bibtex:pages>861--893</bibtex:pages>
+    </bibtex:article>
+  </bibtex:entry>
+
   <bibtex:entry id="Molchanova96">
     <bibtex:article>
       <bibtex:author>Molchanova</bibtex:author>

src/main/org/openscience/cdk/qsar/descriptors/molecular/MannholdLogPDescriptor.java

@@ -0,0 +1,177 @@
+/* Copyright (C) 2009  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.,
+ * 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA. 
+ */
+package org.openscience.cdk.qsar.descriptors.molecular;
+
+import org.openscience.cdk.annotations.TestClass;
+import org.openscience.cdk.annotations.TestMethod;
+import org.openscience.cdk.config.Elements;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.qsar.DescriptorSpecification;
+import org.openscience.cdk.qsar.DescriptorValue;
+import org.openscience.cdk.qsar.IDescriptor;
+import org.openscience.cdk.qsar.IMolecularDescriptor;
+import org.openscience.cdk.qsar.result.DoubleResult;
+import org.openscience.cdk.qsar.result.DoubleResultType;
+import org.openscience.cdk.qsar.result.IDescriptorResult;
+
+/**
+ * <p>Prediction of logP based on the number of carbon and hetero atoms. The
+ * implemented equation was proposed in {@cdk.cite Mannhold2009}.
+ *
+ * @cdk.module     qsarmolecular
+ * @cdk.githash
+ * @cdk.set        qsar-descriptors
+ * @cdk.dictref    qsar-descriptors:mannholdLogP
+ *
+ * @cdk.keyword LogP
+ * @cdk.keyword descriptor
+ */
+@TestClass(
+    "org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptorTest"
+)
+public class MannholdLogPDescriptor implements IMolecularDescriptor {
+
+    private static final String[] names = {"MLogP"};
+
+    /**
+     * Gets the specification attribute of the MannholdLogPDescriptor object.
+     *
+     * @return    The specification value
+     */
+    @TestMethod("testGetSpecification")
+    public DescriptorSpecification getSpecification() {
+        return new DescriptorSpecification(
+            "http://www.blueobelisk.org/ontologies/" +
+            "chemoinformatics-algorithms/#mannholdLogP",
+            this.getClass().getName(),
+            "$Id$",
+            "The Chemistry Development Kit"
+        );
+    }
+
+    /**
+     * This {@link IDescriptor} does not have any parameters. If it had, this
+     * would have been the method to set them.
+     *
+     * @param  params            The new parameter value
+     * @exception  CDKException  Exception throw when invalid parameter values
+     *                           are passed 
+     * @see #getParameters
+     */
+    @TestMethod("testSetParameters_arrayObject")
+    public void setParameters(Object[] params) throws CDKException {
+        if (params != null && params.length > 0) {
+            throw new CDKException("MannholdLogPDescriptor has no parameters.");
+        }
+    }
+
+    /**
+     * Gets the parameters attribute of the MannholdLogPDescriptor object.
+     *
+     * @return    A zero-length Object array.
+     * @see #setParameters
+     */
+    @TestMethod("testGetParameters")
+    public Object[] getParameters() {
+        return new Object[0];
+    }
+
+    @TestMethod("testNamesConsistency")
+    public String[] getDescriptorNames() {
+        return names;
+    }
+
+    private DescriptorValue getDummyDescriptorValue(Exception e) {
+         return new DescriptorValue(getSpecification(), getParameterNames(),
+             getParameters(), new DoubleResult(Double.NaN),
+             getDescriptorNames(), e
+         );
+     }
+
+    /**
+     *  Calculates the Mannhold LogP for an atom container.
+     *
+     * @param  atomContainer      {@link IAtomContainer} to calculate the
+     *                            descriptor value for.
+     * @return A descriptor value wrapping a {@link DoubleResult}.
+     */
+    @TestMethod("testCalculate_IAtomContainer")
+    public DescriptorValue calculate(IAtomContainer atomContainer) {
+        IAtomContainer ac = null;
+        try {
+            ac = (IAtomContainer)atomContainer.clone();
+        } catch (CloneNotSupportedException e) {
+            return getDummyDescriptorValue(e);
+        }
+
+        int carbonCount = 0;
+        int heteroCount = 0;
+        for (IAtom atom : ac.atoms()) {
+            if (!Elements.HYDROGEN.getSymbol().equals(atom.getSymbol())) {
+                if (Elements.CARBON.getSymbol().equals(atom.getSymbol())) {
+                    carbonCount++;
+                } else {
+                    heteroCount++;
+                }
+            }
+        }
+        double mLogP = 1.46 + 0.11*carbonCount - 0.11*heteroCount;
+
+        return new DescriptorValue(
+            getSpecification(), getParameterNames(), getParameters(),
+            new DoubleResult(mLogP), getDescriptorNames()
+        );
+    }
+
+    /**
+     * Returns a type of return value calculated by this descriptor.
+     *
+     * @return returns a {@link DoubleResult}.
+     */
+    @TestMethod("testGetDescriptorResultType")
+    public IDescriptorResult getDescriptorResultType() {
+        return new DoubleResultType();
+    }
+
+    /**
+     * Gets the parameterNames attribute for this descriptor.
+     *
+     * @return    A zero-length String array.
+     */
+    @TestMethod("testGetParameterNames")
+    public String[] getParameterNames() {
+        return new String[0];
+    }
+
+    /**
+     * Gets the parameterType attribute for a given parameter name. It
+     * always returns null, as this descriptor does not have any parameters.
+     *
+     * @param  name  Name of the parameter for which the type is requested.
+     * @return       The parameterType of the given parameter.
+     */
+    @TestMethod("testGetParameterType_String")
+    public Object getParameterType(String name) {
+        return null;
+    }
+
+}
+

src/test/org/openscience/cdk/qsar/descriptors/molecular/MannholdLogPDescriptorTest.java

@@ -0,0 +1,84 @@
+/* Copyright (C) 2009  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.,
+ * 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA. 
+ */
+package org.openscience.cdk.qsar.descriptors.molecular;
+
+import junit.framework.Assert;
+
+import org.junit.Before;
+import org.junit.Test;
+import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
+import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
+import org.openscience.cdk.qsar.result.DoubleResult;
+import org.openscience.cdk.qsar.result.IDescriptorResult;
+
+/**
+ * TestSuite that runs unit tests.
+ *
+ * @cdk.module test-qsarmolecular
+ * @see MannholdLogPDescriptor
+ */
+public class MannholdLogPDescriptorTest extends MolecularDescriptorTest {
+
+    @Before
+    public void setUp() throws Exception {
+    	setDescriptor(MannholdLogPDescriptor.class);
+    }
+
+    @Test
+    public void testMethanol() {
+        IChemObjectBuilder builder =
+            NoNotificationChemObjectBuilder.getInstance();
+        IMolecule methanol = builder.newMolecule();
+        methanol.addAtom(builder.newAtom("C"));
+        methanol.addAtom(builder.newAtom("O"));
+        methanol.addBond(0, 1, IBond.Order.SINGLE);
+        IDescriptorResult result = descriptor.calculate(methanol).getValue();
+        Assert.assertTrue(result instanceof DoubleResult);
+        Assert.assertEquals(1.46, ((DoubleResult)result).doubleValue(), 0.01);
+    }
+
+    @Test
+    public void testMethane() {
+        IChemObjectBuilder builder =
+            NoNotificationChemObjectBuilder.getInstance();
+        IMolecule methane = builder.newMolecule();
+        methane.addAtom(builder.newAtom("C"));
+        IDescriptorResult result = descriptor.calculate(methane).getValue();
+        Assert.assertTrue(result instanceof DoubleResult);
+        Assert.assertEquals(1.57, ((DoubleResult)result).doubleValue(), 0.01);
+    }
+
+    @Test
+    public void testChloroform() {
+        IChemObjectBuilder builder =
+            NoNotificationChemObjectBuilder.getInstance();
+        IMolecule chloroform = builder.newMolecule();
+        chloroform.addAtom(builder.newAtom("C"));
+        for (int i=0; i<3; i++) {
+            chloroform.addAtom(builder.newAtom("Cl"));
+            chloroform.addBond(0, (i+1), IBond.Order.SINGLE);
+        }
+        IDescriptorResult result = descriptor.calculate(chloroform).getValue();
+        Assert.assertTrue(result instanceof DoubleResult);
+        Assert.assertEquals(1.24, ((DoubleResult)result).doubleValue(), 0.01);
+    }
+}
+