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);
}
------------------------------------------------------------------------------
_______________________________________________
Cdk-user mailing list
Cdk-user@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-user
