Use Kevin's double bond location finder in the cdk.fromSMILES() method

bioclipse · Jun 21, 2012 · 8f2097d · 8f2097d
1 parent e8aecb5
commit 8f2097d
Showing 1 changed file with 11 additions and 3 deletions.
diff --git a/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/business/CDKManager.java b/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/business/CDKManager.java
@@ -149,6 +149,7 @@
 import org.openscience.cdk.silent.SilentChemObjectBuilder;
 import org.openscience.cdk.similarity.Tanimoto;
 import org.openscience.cdk.smiles.DeduceBondSystemTool;
+import org.openscience.cdk.smiles.FixBondOrdersTool;
 import org.openscience.cdk.smiles.SmilesGenerator;
 import org.openscience.cdk.smiles.SmilesParser;
 import org.openscience.cdk.smiles.smarts.SMARTSQueryTool;
@@ -969,6 +970,8 @@ public void saveMolecules( List<? extends IMolecule> molecules,
           }
       }
 
+      private FixBondOrdersTool fbot = new FixBondOrdersTool();
+
       /**
        * Create molecule from SMILES.
        *
@@ -980,14 +983,19 @@ public ICDKMolecule fromSMILES(String smilesDescription)
           SmilesParser parser
               = new SmilesParser( DefaultChemObjectBuilder.getInstance() );
 
+          org.openscience.cdk.interfaces.IMolecule molecule;
           try {
-              org.openscience.cdk.interfaces.IMolecule mol
-                  = parser.parseSmiles(smilesDescription);
-              return new CDKMolecule(mol);
+              molecule = parser.parseSmiles(smilesDescription);
           }
           catch (InvalidSmilesException e) {
               throw new BioclipseException("SMILES string is invalid. Error message said: " + e.getMessage(), e);
           }
+          try {
+        	  fbot.kekuliseAromaticRings(molecule);
+          } catch (CDKException exception) {
+        	  logger.warn("Could not figure out the double bond positions: " + exception.getMessage());
+          }
+          return new CDKMolecule(molecule);
       }
 
       /**