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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