first java wrappers of pdb stuff

Code/JavaWrappers/MonomerInfo.i

@@ -0,0 +1,42 @@
+/* 
+* $Id$
+*
+*  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.
+*/
+
+%include "std_string.i"
+
+%{
+#include <GraphMol/MonomerInfo.h>
+%}
+
+%include <GraphMol/MonomerInfo.h>
+
+

Code/JavaWrappers/gmwrapper/CMakeLists.txt

@@ -269,6 +269,10 @@ ADD_TEST(JavaChemTransformsTests
     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.ChemTransformsTests)
+ADD_TEST(JavaPDBTests 
+    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.PDBTests)
 
 INSTALL(TARGETS GraphMolWrap 
               DESTINATION ${CMAKE_CURRENT_SOURCE_DIR} )

Code/JavaWrappers/gmwrapper/GraphMolJava.i

@@ -155,6 +155,7 @@ typedef unsigned long long int	uintmax_t;
 %include "../QueryAtom.i"
 %include "../QueryBond.i"
 %include "../QueryOps.i"
+%include "../MonomerInfo.i"
 %include "../PeriodicTable.i"
 %include "../SanitException.i"
 %include "../SmilesParse.i"

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

@@ -0,0 +1,76 @@
+/* 
+ * $Id: ForceFieldsTests.java 131 2011-01-20 22:01:29Z ebakke $
+ *
+ *  Copyright (c) 2010, 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 PDBTests extends GraphMolTest {
+
+	File testDataDir = new File(getRdBase(), 
+	"Code/GraphMol/FileParsers/test_data");
+
+	@Test
+	public void testPDBReadBasic () {
+            File molFile = new File(testDataDir, "1CRN.pdb");
+            ROMol m = RWMol.MolFromPDBFile(molFile.getPath());
+            assertEquals(327, m.getNumAtoms());
+            assertEquals(337, m.getNumBonds());
+            AtomMonomerInfo mi=new AtomMonomerInfo(m.getAtomWithIdx(0).getMonomerInfo());
+            assert(mi instanceof AtomPDBResidueInfo);
+            // FIX: need to actually test this
+	}
+
+	@Test
+	public void testPDBWriteBasic () {
+            File molFile = new File(testDataDir, "1CRN.pdb");
+            ROMol m = RWMol.MolFromPDBFile(molFile.getPath());
+            String mb = new String(m.MolToPDBBlock());
+            ROMol m2 = RWMol.MolFromPDBBlock(mb);
+            assertEquals(327, m2.getNumAtoms());
+            assertEquals(337, m2.getNumBonds());
+            AtomMonomerInfo mi=new AtomMonomerInfo(m2.getAtomWithIdx(0).getMonomerInfo());
+            assert(mi instanceof AtomPDBResidueInfo);
+            // FIX: need to actually test this
+            
+	}
+
+
+	public static void main(String args[]) {
+            org.junit.runner.JUnitCore.main("org.RDKit.PDBTests");
+	}
+
+}