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Create 'aromatic' SMILES

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commit 78d82ddb213bd998d62fdb54f38df390e201fa1e 1 parent fc01345
@egonw egonw authored
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2  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);
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2  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) {
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3  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,
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