Added control 'isref' creating a CML with reaction and listmolecules

egonw · Feb 27, 2010 · d9d20c2 · d9d20c2
1 parent 5944d6a
commit d9d20c2
Showing 1 changed file with 13 additions and 11 deletions.
diff --git a/src/main/org/openscience/cdk/libio/cml/Convertor.java b/src/main/org/openscience/cdk/libio/cml/Convertor.java
@@ -511,17 +511,19 @@ private CMLMolecule cdkAtomContainerToCMLMolecule(IAtomContainer structure, bool
         	ident.setCMLValue(structure.getProperty(CDKConstants.INCHI).toString());
           cmlMolecule.appendChild(ident);
         }
-        for (int i = 0; i < structure.getAtomCount(); i++) {
-            IAtom cdkAtom = structure.getAtom(i);
-            CMLAtom cmlAtom = cdkAtomToCMLAtom(structure, cdkAtom);
-            if (structure.getConnectedSingleElectronsCount(cdkAtom) > 0) {
-                cmlAtom.setSpinMultiplicity(structure.getConnectedSingleElectronsCount(cdkAtom) + 1);
-            }
-            cmlMolecule.addAtom(cmlAtom);
-        }
-        for (int i = 0; i < structure.getBondCount(); i++) {
-            CMLBond cmlBond = cdkBondToCMLBond(structure.getBond(i));
-            cmlMolecule.addBond(cmlBond);
+        if(!isRef){
+	        for (int i = 0; i < structure.getAtomCount(); i++) {
+	            IAtom cdkAtom = structure.getAtom(i);
+	            CMLAtom cmlAtom = cdkAtomToCMLAtom(structure, cdkAtom);
+	            if (structure.getConnectedSingleElectronsCount(cdkAtom) > 0) {
+	                cmlAtom.setSpinMultiplicity(structure.getConnectedSingleElectronsCount(cdkAtom) + 1);
+	            }
+	            cmlMolecule.addAtom(cmlAtom);
+	        }
+	        for (int i = 0; i < structure.getBondCount(); i++) {
+	            CMLBond cmlBond = cdkBondToCMLBond(structure.getBond(i));
+	            cmlMolecule.addBond(cmlBond);
+	        }
         }
 
         // ok, output molecular properties, but not TITLE, INCHI, or DictRef's