Merge branch 'cdk-1.2.x'

egonw · Feb 26, 2010 · 5944d6a · 5944d6a
2 parents 04001b7 + e1c03fb
commit 5944d6a
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Showing 3 changed files with 103 additions and 96 deletions.
diff --git a/src/main/org/openscience/cdk/io/MDLReader.java b/src/main/org/openscience/cdk/io/MDLReader.java
@@ -319,6 +319,8 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException {
         double x = 0.0;
         double y = 0.0;
         double z = 0.0;
+        double totalX = 0.0;
+        double totalY = 0.0;
         double totalZ = 0.0;
         //int[][] conMat = new int[0][0];
         //String help;
@@ -373,7 +375,10 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException {
                 x = new Double(line.substring( 0,10).trim()).doubleValue();
                 y = new Double(line.substring(10,20).trim()).doubleValue();
                 z = new Double(line.substring(20,30).trim()).doubleValue();
-                totalZ += Math.abs(z); // *all* values should be zero, not just the sum
+                // *all* values should be zero, not just the sum
+                totalX += Math.abs(x);
+                totalY += Math.abs(y);
+                totalZ += Math.abs(z);
                 logger.debug("Coordinates: " + x + "; " + y + "; " + z);
                 String element = line.substring(31,34).trim();
 
@@ -485,7 +490,12 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException {
             }
 
             // convert to 2D, if totalZ == 0
-            if (totalZ == 0.0 && !forceReadAs3DCoords.isSet()) {
+            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);
+                }
+            } else if (totalZ == 0.0 && !forceReadAs3DCoords.isSet()) {
                 logger.info("Total 3D Z is 0.0, interpreting it as a 2D structure");
                 Iterator<IAtom> atomsToUpdate = molecule.atoms().iterator();
                 while (atomsToUpdate.hasNext()) {