I made sure the MDLV2000Reader considers 0,0,0 coordinates in files with a single atom as 2d and 3d coordinates. The MDLReader does not handle the 0,0,0 case explicitly, so I just added a test for 2d. It might be better to have uniforma handling, but I will file a bug report for that.

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

Author: Stefan Kuhn

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

@@ -573,8 +573,12 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException {
             // convert to 2D, if totalZ == 0
             if (totalX == 0.0 && totalY == 0.0 && totalZ == 0.0) {
                 logger.info("All coordinates are 0.0");
-                for (IAtom atomToUpdate : molecule.atoms()) {
-                    atomToUpdate.setPoint3d(null);
+                if (molecule.getAtomCount()==1){
+                    molecule.getAtom(0).setPoint2d(new Point2d(x,y));
+                }else{
+                    for (IAtom atomToUpdate : molecule.atoms()) {
+                        atomToUpdate.setPoint3d(null);
+                    }
                 }
             } else if (totalZ == 0.0 && !forceReadAs3DCoords.isSet()) {
                 logger.info("Total 3D Z is 0.0, interpreting it as a 2D structure");

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

@@ -37,6 +37,7 @@
 import org.openscience.cdk.ChemObject;
 import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.Molecule;
+import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
@@ -221,4 +222,14 @@ public class MDLReaderTest extends SimpleChemObjectReaderTest {
         Assert.assertEquals(15, ((Integer)mol.getAtom(1).getProperty(CDKConstants.ATOM_ATOM_MAPPING)).intValue());
         Assert.assertNull(mol.getAtom(2).getProperty(CDKConstants.ATOM_ATOM_MAPPING));
     }
+
+    @Test(expected=AssertionError.class)
+    public void testHas2DCoordinates_With000() throws CDKException {
+        String filenameMol = "data/mdl/with000coordinate.mol";
+        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filenameMol);
+        Molecule molOne=null;
+        MDLReader reader = new MDLReader(ins, Mode.RELAXED);
+        molOne = (Molecule)reader.read(new Molecule());
+        Assert.assertNotNull(molOne.getAtom(0).getPoint2d());
+    }
 }

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

@@ -784,4 +784,16 @@ private void testShortLinesForMode (IChemObjectReader.Mode mode) throws Exceptio
         Assert.assertEquals(15, ((Integer)mol.getAtom(1).getProperty(CDKConstants.ATOM_ATOM_MAPPING)).intValue());
         Assert.assertNull(mol.getAtom(2).getProperty(CDKConstants.ATOM_ATOM_MAPPING));
     }
+
+    @Test public void testHas2DCoordinates_With000() throws CDKException {
+        String filenameMol = "data/mdl/with000coordinate.mol";
+        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filenameMol);
+        Molecule molOne=null;
+        MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.STRICT);
+        molOne = (Molecule)reader.read(new Molecule());
+        System.out.println(molOne.getAtomCount());
+        Assert.assertNotNull(molOne.getAtom(0).getPoint2d());
+        Assert.assertNotNull(molOne.getAtom(0).getPoint3d());
+    }
+
 }