add basic support for O3A to Java wrapper

Code/JavaWrappers/ROMol.i

@@ -56,6 +56,7 @@
 #include <GraphMol/DistGeomHelpers/Embedder.h>
 #include <GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h>
 #include <GraphMol/MolAlign/AlignMolecules.h>
+#include <GraphMol/MolAlign/O3AAlignMolecules.h>
 #include <GraphMol/MolDrawing/MolDrawing.h>
 #include <GraphMol/MolDrawing/DrawingToSVG.h>
 
@@ -366,6 +367,23 @@
                         bool reflect=false, unsigned int maxIters=50) {
     RDKit::MolAlign::alignMolConformers(*($self), atomIds, confIds, weights, reflect, maxIters);
   }
+
+  /* From GraphMol/MolAlign/AlignMolecules */
+  std::pair<double,double> O3AAlignMol(RDKit::ROMol &refMol, 
+                     int prbCid=-1, int refCid=-1,
+                     bool reflect=false, unsigned int maxIters=50,
+                     unsigned int accuracy=0) {
+    RDKit::MMFF::MMFFMolProperties prbMP(*($self));
+    RDKit::MMFF::MMFFMolProperties refMP(refMol);
+    
+    RDKit::MolAlign::O3A o3a(*($self), refMol, &prbMP, &refMP, prbCid, refCid,
+                      reflect,maxIters,accuracy);
+    double rmsd=o3a.align();
+    double score = o3a.score();
+    return std::make_pair(rmsd,score);
+  }
+
+
 }
 
 

Code/JavaWrappers/gmwrapper/CMakeLists.txt

@@ -270,5 +270,10 @@ ADD_TEST(JavaChemTransformsTests
 	-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
 	org.RDKit.ChemTransformsTests)
 
+ADD_TEST(JavaAlignTests 
+    java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR} 
+	-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
+	org.RDKit.AlignTests)
+
 INSTALL(TARGETS GraphMolWrap 
               DESTINATION ${CMAKE_CURRENT_SOURCE_DIR} )

Code/JavaWrappers/gmwrapper/src-test/org/RDKit/AlignTests.java

@@ -0,0 +1,61 @@
+/* 
+ * $Id$
+ *
+ *  Copyright (c) 2013, Novartis Institutes for BioMedical Research Inc.
+ *  All rights reserved.
+ * 
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are
+ * met: 
+ *
+ *     * Redistributions of source code must retain the above copyright 
+ *       notice, this list of conditions and the following disclaimer.
+ *     * Redistributions in binary form must reproduce the above
+ *       copyright notice, this list of conditions and the following 
+ *       disclaimer in the documentation and/or other materials provided 
+ *       with the distribution.
+ *     * Neither the name of Novartis Institutes for BioMedical Research Inc. 
+ *       nor the names of its contributors may be used to endorse or promote 
+ *       products derived from this software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.RDKit;
+
+import static org.junit.Assert.*;
+
+import java.io.File;
+
+import org.junit.Test;
+
+public class AlignTests extends GraphMolTest {
+
+
+	@Test
+	public void testO3ABasic () {
+            String fname = new File(getRdBase(),
+                                    "Code/GraphMol/MolAlign/test_data/ref_e2_O3A.sdf").getPath();
+            SDMolSupplier sdsup = new SDMolSupplier(fname);
+            ROMol m1 = sdsup.next();
+            ROMol m2 = sdsup.next();
+            Double_Pair res = m1.O3AAlignMol(m2);
+            assertEquals(res.getFirst(),0.086,.001);
+            assertEquals(res.getSecond(),119.98,.01);
+            
+	}
+    
+	public static void main(String args[]) {
+		org.junit.runner.JUnitCore.main("org.RDKit.AlignTests");
+	}
+
+}