MDL reading and writing atom value line, including test cases

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

src/main/org/openscience/cdk/io/MDLV2000Reader.java

@@ -813,6 +813,12 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException {
                         }
                     }
                 }
+                if (line.startsWith("V  ")) {
+                    Integer atomNumber = new Integer(line.substring(3,6).trim());
+                    IAtom atomWithComment = molecule.getAtom(atomNumber - 1);
+                    atomWithComment.setProperty(CDKConstants.COMMENT, line.substring(7));
+                }
+
                 if (!lineRead) {
                     logger.warn("Skipping line in property block: ", line);
                 }

src/main/org/openscience/cdk/io/MDLWriter.java

@@ -371,6 +371,20 @@ else if(atom.getValency()==0)
         		writer.newLine();
         	}
         }
+
+        // Write Atom Value
+        for (int i = 0; i < container.getAtomCount(); i++) {
+        	IAtom atom = container.getAtom(i);
+        	if(atom.getProperty(CDKConstants.COMMENT)!=null 
+        	&& atom.getProperty(CDKConstants.COMMENT) instanceof String
+        	&& !((String)atom.getProperty(CDKConstants.COMMENT)).trim().equals("") ) {
+                writer.write("V  ");
+                writer.write(formatMDLInt(i+1,3));
+                writer.write(" ");
+                writer.write((String)atom.getProperty(CDKConstants.COMMENT));
+                writer.newLine();
+        	}
+        }
 
         // write formal atomic charges
         for (int i = 0; i < container.getAtomCount(); i++) {

src/test/data/mdl/atomValueLines.mol

@@ -0,0 +1,10 @@
+
+  CDK     0507101526
+
+  2  1  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  2  1  2  0  0  0  0 
+V    1 Oxygen comment
+V    2 Carbon comment
+M  END

src/test/org/openscience/cdk/io/MDLV2000ReaderTest.java

@@ -796,4 +796,15 @@ private void testShortLinesForMode (IChemObjectReader.Mode mode) throws Exceptio
         Assert.assertNotNull(molOne.getAtom(0).getPoint3d());
     }
 
+    @Test public void testAtomValueLines() throws Exception {
+    	String filename = "data/mdl/atomValueLines.mol";
+    	InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+    	MDLV2000Reader reader = new MDLV2000Reader(ins);
+    	Molecule testMolecule = new Molecule();
+    	Molecule result = reader.read(testMolecule);
+    	IAtom oxygen = result.getAtom(0);
+    	Assert.assertTrue(oxygen.getSymbol().equals("O"));
+    	Assert.assertEquals(oxygen.getProperty(CDKConstants.COMMENT), "Oxygen comment");
+    }
+
 }

src/test/org/openscience/cdk/io/MDLWriterTest.java

@@ -279,4 +279,29 @@ public class MDLWriterTest extends ChemObjectIOTest {
     }
 
 
+    /**
+     * Test writing of comments made on individual atoms into an Atom Value lines. 
+     */
+    @Test public void testAtomValueLine() throws Exception {
+        IAtom carbon = builder.newInstance(IAtom.class, "C");
+        carbon.setProperty(CDKConstants.COMMENT, "Carbon comment");
+        IAtom oxygen = builder.newInstance(IAtom.class, "O");
+        oxygen.setProperty(CDKConstants.COMMENT, "Oxygen comment");
+        IBond bond = builder.newInstance(IBond.class,carbon, oxygen, CDKConstants.BONDORDER_DOUBLE);
+
+        Molecule molecule = new Molecule();
+        molecule.addAtom(oxygen);
+        molecule.addAtom(carbon);
+        molecule.addBond(bond);
+
+        StringWriter writer = new StringWriter();
+        MDLWriter mdlWriter = new MDLWriter(writer);
+        mdlWriter.write(molecule);
+        System.out.println(writer.toString());
+
+        Assert.assertTrue(writer.toString().indexOf("V    1 Oxygen comment") != -1);
+        Assert.assertTrue(writer.toString().indexOf("V    2 Carbon comment") != -1);
+
+    }
+
 }