Atom-Atom-Mapping is now read and written in MDL files. Note the read…

…ing until now was into ID field, which is not in line with description of ID field in ChemObject (Returns the identifier (ID) of this object). Also added tests for MDLWriter/Reader/2000Reader. Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
cdk · May 12, 2010 · 6b787c2 · 6b787c2
1 parent d6d6ab0
commit 6b787c2
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Showing 8 changed files with 78 additions and 3 deletions.
diff --git a/src/main/org/openscience/cdk/CDKConstants.java b/src/main/org/openscience/cdk/CDKConstants.java
@@ -291,6 +291,8 @@ public class CDKConstants {
      */
     public static final String REST_H = "cdk:RestH";
 
+    public static final String ATOM_ATOM_MAPPING = "cdk:AtomAtomMapping";
+
 
     /* **************************************
     * Some predefined property names for    *

diff --git a/src/main/org/openscience/cdk/io/MDLReader.java b/src/main/org/openscience/cdk/io/MDLReader.java
@@ -465,7 +465,7 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException {
                     try {
                         int reactionAtomID = Integer.parseInt(reactionAtomIDString);
                         if (reactionAtomID != 0) {
-                            atom.setID(reactionAtomIDString);
+                            atom.setProperty(CDKConstants.ATOM_ATOM_MAPPING, reactionAtomIDString);
                         }
                     } catch (Exception exception) {
                         logger.error("Mapping number ", reactionAtomIDString, " is not an integer.");

diff --git a/src/main/org/openscience/cdk/io/MDLV2000Reader.java b/src/main/org/openscience/cdk/io/MDLV2000Reader.java
@@ -545,7 +545,7 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException {
                     try {
                         int reactionAtomID = Integer.parseInt(reactionAtomIDString);
                         if (reactionAtomID != 0) {
-                            atom.setID(reactionAtomIDString);
+                            atom.setProperty(CDKConstants.ATOM_ATOM_MAPPING, reactionAtomID);
                         }
                     } catch (Exception exception) {
                         logger.error("Mapping number ", reactionAtomIDString, " is not an integer.");

diff --git a/src/main/org/openscience/cdk/io/MDLWriter.java b/src/main/org/openscience/cdk/io/MDLWriter.java
@@ -308,7 +308,15 @@ else if(atom.getValency()==0)
         		line += formatMDLInt(15, 3);
         	else
         		line += formatMDLInt(atom.getValency(), 3);
-        	line += "  0  0  0  0  0  0";
+        	line += "  0  0  0";
+
+        	if (container.getAtom(f).getProperty(CDKConstants.ATOM_ATOM_MAPPING) != null) {
+        	    int value = ((Integer)container.getAtom(f).getProperty(CDKConstants.ATOM_ATOM_MAPPING)).intValue();
+        	    line += formatMDLInt(value, 3);
+       	    } else {
+        	    line += formatMDLInt(0, 3);
+        	}
+      	    line += "  0  0";
         	writer.write(line);
         	writer.newLine();
         }

diff --git a/src/test/data/mdl/a-pinene-with-atom-atom-mapping.mol b/src/test/data/mdl/a-pinene-with-atom-atom-mapping.mol
@@ -0,0 +1,26 @@
+a-pinen.mol
+  ChemDraw08319810042D
+
+ 10 11  0  0  0  0  0  0  0  0  1 V2000
+   -2.0500   -1.1000    0.0000 C   0  0  0  0  0  0  0  0  0  1  0  0
+   -0.7500   -0.3500    0.0000 C   0  0  0  0  0  0  0  0  0 15  0  0
+   -0.5500   -1.1000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.7500   -1.8500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.7500   -0.3500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.8100   -1.4100    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.3625    1.1000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.0500    0.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.9375    1.8500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.6625    1.8500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  1  3  1  0  0  0  0
+  3  4  1  0  0  0  0
+  2  5  1  0  0  0  0
+  5  6  2  0  0  0  0
+  4  6  1  0  0  0  0
+  2  7  1  0  0  0  0
+  3  7  1  0  0  0  0
+  5  8  1  0  0  0  0
+  7  9  1  0  0  0  0
+  7 10  1  0  0  0  0
+M  END
diff --git a/src/test/org/openscience/cdk/io/MDLReaderTest.java b/src/test/org/openscience/cdk/io/MDLReaderTest.java
@@ -31,9 +31,11 @@
 import org.junit.Assert;
 import org.junit.BeforeClass;
 import org.junit.Test;
+import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.ChemFile;
 import org.openscience.cdk.ChemModel;
 import org.openscience.cdk.ChemObject;
+import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.Molecule;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
@@ -205,5 +207,18 @@ public class MDLReaderTest extends SimpleChemObjectReaderTest {
         Assert.assertEquals(IBond.Stereo.E_OR_Z,mol.getBond(7).getStereo());
         Assert.assertEquals(IBond.Stereo.UP_OR_DOWN,mol.getBond(11).getStereo());
     }
+
 
+    @Test public void testReadAtomAtomMapping() throws Exception {
+        String filename = "data/mdl/a-pinene-with-atom-atom-mapping.mol";
+        logger.info("Testing: " + filename);
+        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+        MDLV2000Reader reader = new MDLV2000Reader(ins);
+
+        IMolecule mol = reader.read(new Molecule()); 
+        Assert.assertNotNull(mol);
+        Assert.assertEquals(1, ((Integer)mol.getAtom(0).getProperty(CDKConstants.ATOM_ATOM_MAPPING)).intValue());
+        Assert.assertEquals(15, ((Integer)mol.getAtom(1).getProperty(CDKConstants.ATOM_ATOM_MAPPING)).intValue());
+        Assert.assertNull(mol.getAtom(2).getProperty(CDKConstants.ATOM_ATOM_MAPPING));
+    }
 }
diff --git a/src/test/org/openscience/cdk/io/MDLV2000ReaderTest.java b/src/test/org/openscience/cdk/io/MDLV2000ReaderTest.java
@@ -772,4 +772,16 @@ private void testShortLinesForMode (IChemObjectReader.Mode mode) throws Exceptio
         Assert.assertEquals(mol.getAtomCount(), 5);
         Assert.assertEquals(mol.getBondCount(), 4);
     }
+
+    @Test public void testReadAtomAtomMapping() throws Exception {
+        String filename = "data/mdl/a-pinene-with-atom-atom-mapping.mol";
+        logger.info("Testing: " + filename);
+        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+        MDLV2000Reader reader = new MDLV2000Reader(ins);
+        IMolecule mol = reader.read(new Molecule());
+        Assert.assertNotNull(mol);
+        Assert.assertEquals(1, ((Integer)mol.getAtom(0).getProperty(CDKConstants.ATOM_ATOM_MAPPING)).intValue());
+        Assert.assertEquals(15, ((Integer)mol.getAtom(1).getProperty(CDKConstants.ATOM_ATOM_MAPPING)).intValue());
+        Assert.assertNull(mol.getAtom(2).getProperty(CDKConstants.ATOM_ATOM_MAPPING));
+    }
 }
diff --git a/src/test/org/openscience/cdk/io/MDLWriterTest.java b/src/test/org/openscience/cdk/io/MDLWriterTest.java
@@ -120,6 +120,18 @@ public class MDLWriterTest extends ChemObjectIOTest {
         Assert.assertTrue(output.indexOf("0  0  0  0  0 15  0  0  0  0  0  0") != -1);
     }
 
+    @Test public void testWriteAtomAtomMapping() throws Exception {
+        StringWriter writer = new StringWriter();
+        Molecule molecule = MoleculeFactory.makeAlphaPinene();
+        molecule.getAtom(0).setProperty(CDKConstants.ATOM_ATOM_MAPPING,1);
+        molecule.getAtom(1).setProperty(CDKConstants.ATOM_ATOM_MAPPING,15);
+        MDLWriter mdlWriter = new MDLWriter(writer);
+        mdlWriter.write(molecule);
+        String output = writer.toString();
+        Assert.assertTrue(output.indexOf("0  0  0  0  0  0  0  0  0  1  0  0") != -1);
+        Assert.assertTrue(output.indexOf("0  0  0  0  0  0  0  0  0 15  0  0") != -1);
+    }
+
     /**
      * Test for bug #1778479 "MDLWriter writes empty PseudoAtom label string".
      * When a molecule contains an IPseudoAtom without specifying the atom label