Create 'aromatic' SMILES

bioclipse · Mar 12, 2012 · 78d82dd · 78d82dd
1 parent fc01345
commit 78d82dd
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Showing 3 changed files with 4 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
@@ -529,7 +529,7 @@ public void calculateSMILES(IMolecule molecule,IReturner<String> returner,
             IAtomContainer cdkMol = mol.getAtomContainer();
 
         // Create the SMILES
-        SmilesGenerator generator = new SmilesGenerator();
+        SmilesGenerator generator = new SmilesGenerator(true);
 
         // Operate on a clone with removed hydrogens
         cdkMol = AtomContainerManipulator.removeHydrogens(cdkMol);

diff --git a/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/domain/CDKMolecule.java b/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/domain/CDKMolecule.java
@@ -113,7 +113,7 @@ public String toSMILES() throws BioclipseException {
         String result = ensureFullAtomTyping(hydrogenlessClone);
         if (result.length() > 0) return result;
 
-        return new SmilesGenerator().createSMILES(hydrogenlessClone);
+        return new SmilesGenerator(true).createSMILES(hydrogenlessClone);
     }
 
 	private String ensureFullAtomTyping(IAtomContainer hydrogenlessClone) {

diff --git a/plugins/net.bioclipse.inchi/META-INF/MANIFEST.MF b/plugins/net.bioclipse.inchi/META-INF/MANIFEST.MF
@@ -9,7 +9,8 @@ Require-Bundle: org.eclipse.ui,
  net.bioclipse.core,
  org.openscience.cdk.core,
  org.openscience.cdk.interfaces,
- org.openscience.cdk.inchi
+ org.openscience.cdk.inchi,
+ org.openscience.cdk.smiles
 Bundle-ActivationPolicy: lazy
 Export-Package: net.bioclipse.inchi.business,
  net.bioclipse.inchi.ui,