Hi, I found strange behaviour of the CDKConstants.VISITED flag after running the SMARTSQueryTool on cyclic species.
-Normal behavior for linear alkanes such as n-decane: IMolecule mol = MoleculeFactory.makeAlkane(10); Boolean test = mol.getAtom(4).getFlag(CDKConstants.VISITED); System.out.println(test); String smartsQuery = "[#6]"; SMARTSQueryTool querytool = new SMARTSQueryTool(smartsQuery); boolean status = querytool.matches(mol); test = mol.getAtom(4).getFlag(CDKConstants.VISITED); The VISITED flag returns 'false'. -Non-consistent behavior for cyclic species, like benzene: IMolecule mol = MoleculeFactory.makeBenzene(); Boolean test = mol.getAtom(4).getFlag(CDKConstants.VISITED); System.out.println(test); String smartsQuery = "[#6]"; SMARTSQueryTool querytool = new SMARTSQueryTool(smartsQuery); boolean status = querytool.matches(mol); test = mol.getAtom(4).getFlag(CDKConstants.VISITED); The VISITED flag returns 'true'... I guess this should be made consistent. I ran into this problem when i wanted to label atoms that had been visited by my algorithm. What other way would you suggest to label individual atoms arbitrarily? I am using CDK 1.3.4 and haven't tested other (newer) versions. regards, Nick
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