MDL reading and writing UP_OR_DOWN

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
cdk · May 12, 2010 · e36983b · e36983b
1 parent fd1e57c
commit e36983b
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Showing 3 changed files with 11 additions and 4 deletions.
diff --git a/src/main/org/openscience/cdk/io/MDLReader.java b/src/main/org/openscience/cdk/io/MDLReader.java
@@ -525,8 +525,11 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException {
                         // bond has no stereochemistry
                         stereo = IBond.Stereo.NONE;
                     } else if (mdlStereo == 4) {
-                        //MDL bond undefined
-                        stereo = (IBond.Stereo)CDKConstants.UNSET;
+                        //MDL up or down bond
+                        stereo = IBond.Stereo.UP_OR_DOWN;
+                    } else if (mdlStereo == 3) {
+                        //MDL e or z undefined
+                        stereo = IBond.Stereo.E_OR_Z;
                     }
                 } else {
                 	logger.warn("Missing expected stereo field at line: " + line);

diff --git a/src/main/org/openscience/cdk/io/MDLV2000Reader.java b/src/main/org/openscience/cdk/io/MDLV2000Reader.java
@@ -619,7 +619,7 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException {
                         stereo = IBond.Stereo.E_OR_Z;
                     } else if (mdlStereo == 4) {
                         //MDL bond undefined
-                        stereo = (IBond.Stereo)CDKConstants.UNSET;
+                        stereo = IBond.Stereo.UP_OR_DOWN;
                     }
                 } else {
                 	handleError(

diff --git a/src/main/org/openscience/cdk/io/MDLWriter.java b/src/main/org/openscience/cdk/io/MDLWriter.java
@@ -322,7 +322,8 @@ else if(atom.getValency()==0)
         		logger.warn("Skipping bond with more/less than two atoms: " + bond);
         	} else {
         		if (bond.getStereo() == IBond.Stereo.UP_INVERTED || 
-        				bond.getStereo() == IBond.Stereo.DOWN_INVERTED) {
+        				bond.getStereo() == IBond.Stereo.DOWN_INVERTED ||
+        				bond.getStereo() == IBond.Stereo.UP_OR_DOWN_INVERTED) {
         			// turn around atom coding to correct for inv stereo
         			line = formatMDLInt(container.getAtomNumber(bond.getAtom(1)) + 1,3);
         			line += formatMDLInt(container.getAtomNumber(bond.getAtom(0)) + 1,3);
@@ -348,6 +349,9 @@ else if(atom.getValency()==0)
         		case UP_OR_DOWN:
         			line += "4";
         			break;
+                case UP_OR_DOWN_INVERTED:
+                    line += "4";
+                    break;
            		case E_OR_Z:
           			line += "3";
           			break;