You should be using the SMARTSQueryTool
SMARTSQueryTool sqt = new SMARTSQueryTool("[a]")
if (sqt.matches(mol)) {
// do stuff
}
Do you still get this error with the above code?
On Wed, Jul 28, 2010 at 12:20 PM, <[email protected]> wrote:
> Hi,
>
> I'm trying to search a substructure in a molecule by a given SMART
> pattern. So I searched for a java library which supports SMART
> patterns. CDK looks like a very professional framework, although I
> wish I could find a smaller library which just support SMART and not
> hundred features more ^^
>
> Nevertheless, I include the cdk jar file and try following code:
>
> Mol2Reader mr = new Mol2Reader(new FileReader(new File(filename)));
> final IMolecule molecule = (IMolecule)mr.read(new Molecule());
> final QueryAtomContainer query = SMARTSParser.parse("[#8]");
> final boolean b = UniversalIsomorphismTester.isSubgraph(molecule, query);
> System.out.println(b); // true
>
> It works. Next I changed the pattern into "[#8D2]". Now following
> error message occurs:
>
> Exception in thread "main" java.lang.NullPointerException
> at
> org.openscience.cdk.isomorphism.matchers.smarts.ExplicitConnectionAtom.matches(ExplicitConnectionAtom.java:60)
> at
> org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom.matches(LogicalOperatorAtom.java:82)
> at
> org.openscience.cdk.isomorphism.UniversalIsomorphismTester.isSubgraph(UniversalIsomorphismTester.java:337)
> at TestMol2.main(TestMol2.java:33)
>
> I looked in the source code and find following:
> atom.getProperty(CDKConstants.TOTAL_CONNECTIONS)
>
> This property isn't defined in my atoms. In fact, there are no
> properties defined in my atoms. So how can I load atoms which full
> property sets so that substructure search works properly?
>
> I thank you very much in advance,
> Kai
>
>
>
>
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--
Rajarshi Guha
NIH Chemical Genomics Center
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