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Perceive aromaticity before calculating molecular signature.

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olas committed Jul 23, 2010
1 parent bff58a9 commit b3ba301680becb0010731c42bee1d2c89d71ff4a
@@ -176,6 +176,14 @@ public String generateMoleculeSignature( IMolecule mol )
ICDKManager cdk = Activator.getDefault().getJavaCDKManager();
ICDKMolecule cdkmol = cdk.asCDKMolecule(mol);
+ cdkmol=cdk.perceiveAromaticity(cdkmol);
+ try {
+ cdkmol=cdk.addImplicitHydrogens(cdkmol);
+ } catch (InvocationTargetException e) {
+ throw new BioclipseException("Error adding implicit hydrogens: "
+ + e.getMessage());
+ }
+
Molecule signmol = CDKMoleculeSignatureAdapter.convert(cdkmol.getAtomContainer());
MoleculeSignature signature = new MoleculeSignature(signmol);

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