Of the top of my head, I think you need to perform ring perception
explicitly. In general, RingAtom is used by the SMARTS parser, which
performs ring perception during initialization
On Mar 27, 2009, at 10:38 AM, P D wrote:
> Hi, I'm using cdk 1.2 and I think I'm having a simple problem, tho I
> can't figure out how to fix it.
>
> I'm reading in a test molfile containing cycloheptane (code below)
> and iterating through each atom trying to find which atoms are
> members of a ring (they all should be considered members of a ring).
>
> I've removed the try/catch blocks, but when this code is run I get a
> NPE when calling the "matches()" method of the RingAtom class.
> The NPE disappears if i remove the line
> "CDKHueckelAromaticityDetector.detectAromaticity(cphep);", but then
> the atoms are all mis-characterized as not being part of a ring.
>
> the specific error trace is this: java.lang.NullPointerException at
> org
> .openscience
> .cdk.isomorphism.matchers.smarts.RingAtom.matches(RingAtom.java:66)
>
> Strangely (at least to me), AliphaticAtom.matches() and
> AromaticAtom.matches() work properly, but not RingAtom.
>
> Any ideas as to what I'm doing wrong?
>
> TIA!
>
> //////////////////////// begin
> code //////////////////////////////////////
> MolReader mr = new MolReader("C:\\cycloheptane.mol"); //MolReader is
> a home-built class
> MDMolecule cphep = mr.getMDMolecule(); //home-built method
>
> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(cphep);
> CDKHueckelAromaticityDetector.detectAromaticity(cphep);
>
> Iterator a = cphep.atoms().iterator();
>
> while (a.hasNext()) {
>
> IAtom qa = (IAtom) a.next();
> int j = 7;
> RingAtom ra = new RingAtom(j);
> boolean b = ra.matches(qa); // <== ********NPE is thrown here
> ***********
> System.out.println(b);
> }
>
>
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Rajarshi Guha <[email protected]>
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