You could use setProperty and use your application-specific key On Thu, Mar 17, 2011 at 11:54 AM, Nick Vandewiele <nickvandewi...@gmail.com> wrote: > 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 > > ------------------------------------------------------------------------------ > Create and publish websites with WebMatrix > Use the most popular FREE web apps or write code yourself; > WebMatrix provides all the features you need to develop and > publish your website. http://p.sf.net/sfu/ms-webmatrix-sf > > _______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user > >
-- Rajarshi Guha NIH Chemical Genomics Center ------------------------------------------------------------------------------ Create and publish websites with WebMatrix Use the most popular FREE web apps or write code yourself; WebMatrix provides all the features you need to develop and publish your website. http://p.sf.net/sfu/ms-webmatrix-sf _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
