Added similarity method for Lingo's

Author: rajarshi

src/main/org/openscience/cdk/similarity/LingoSimilarity.java

@@ -0,0 +1,61 @@
+/* $Revision$ $Author$ $Date$
+ *
+ * Copyright (C) 2010  Rajarshi Guha <rajarshi.guha@gmail.com>
+ *
+ * Contact: rajarshi.guha@gmail.com
+ *
+ * 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.
+ * All I ask is that proper credit is given for my work, which includes
+ * - but is not limited to - adding the above copyright notice to the beginning
+ * of your source code files, and to any copyright notice that you may distribute
+ * with programs based on this work.
+ *
+ * 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.similarity;
+
+import org.openscience.cdk.annotations.TestClass;
+import org.openscience.cdk.annotations.TestMethod;
+
+import java.util.Map;
+import java.util.TreeSet;
+
+/**
+ * A class to evaluate the similarity between two LINGO's as described in {@cdk.cite Vidal2005}.
+ *
+ * @author Rajarshi Guha
+ * @cdk.githash
+ * @cdk.keyword lingo
+ * @cdk.keyword similarity, tanimoto
+ * @cdk.module fingerprint
+ */
+@TestClass("org.openscience.cdk.similarity.LingoTest")
+public class LingoSimilarity {
+    @TestMethod("testLingoSim")
+    public static float calculate(Map<String, Integer> features1, Map<String, Integer> features2) {
+        TreeSet<String> keys = new TreeSet<String>(features1.keySet());
+        keys.addAll(features2.keySet());
+
+        float sum = 0.0f;
+        for (String key : keys) {
+            Integer c1 = features1.get(key);
+            Integer c2 = features2.get(key);
+
+            c1 = c1 == null ? 0 : c1;
+            c2 = c2 == null ? 0 : c2;
+            sum += 1.0 - Math.abs(c1 - c2) / (c1 + c2);
+        }
+
+        return sum / keys.size();
+    }
+}

src/test/org/openscience/cdk/similarity/LingoSimilarityTest.java

@@ -0,0 +1,57 @@
+/* $Revision$ $Author$ $Date$
+ *
+ * Copyright (C) 2010  Rajarshi Guha <rajarshi.guha@gmail.com>
+ *
+ * Contact: rajarshi.guha@gmail.com
+ *
+ * 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.
+ * All I ask is that proper credit is given for my work, which includes
+ * - but is not limited to - adding the above copyright notice to the beginning
+ * of your source code files, and to any copyright notice that you may distribute
+ * with programs based on this work.
+ *
+ * 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.similarity;
+
+import org.junit.Assert;
+import org.junit.Test;
+import org.openscience.cdk.CDKTestCase;
+import org.openscience.cdk.Molecule;
+import org.openscience.cdk.fingerprint.LingoFingerprinter;
+import org.openscience.cdk.templates.MoleculeFactory;
+
+import java.util.Map;
+
+/**
+ * @cdk.module test-fingerprint
+ */
+public class LingoSimilarityTest extends CDKTestCase {
+
+    boolean standAlone = false;
+
+    @Test
+    public void testLingoSim() throws Exception {
+        Molecule mol1 = MoleculeFactory.makeIndole();
+        Molecule mol2 = MoleculeFactory.makeIndole();
+        LingoFingerprinter fingerprinter = new LingoFingerprinter();
+        Map<String, Integer> bs1 = fingerprinter.getRawFingerprint(mol1);
+        Map<String, Integer> bs2 = fingerprinter.getRawFingerprint(mol2);
+        float lingosim = LingoSimilarity.calculate(bs1, bs2);
+        if (standAlone) System.out.println("LingoSimilarity similarity: " + lingosim);
+        if (!standAlone) Assert.assertEquals(1.0, lingosim, 0.01);
+    }
+
+
+}