[Joelib-help] Smiles parsing error

[Andreas M. <ma...@in...>]

Hi all,

when I try to parse the SMILES 'C2CCC(C1CC1)C2' with JOELib via

JOESmilesParser.smiToMol(mol, smiles, smiles);

where 'mol' is a JOEMol object and 'smiles' is a String I keep getting an error:

===============================================================================
Exception in thread "main" java.lang.Error: Unresolved compilation problems: 
	Matrix cannot be resolved or is not a type
	The method gMatrix(JOEMol) is undefined for the type GraphPotentials
	Matrix cannot be resolved or is not a type
	Matrix cannot be resolved or is not a type
	The method cMatrix(JOEMol) is undefined for the type GraphPotentials
	Matrix cannot be resolved or is not a type

	at joelib.desc.types.GraphPotentials.graphPotentials(GraphPotentials.java:30)
	at joelib.molecule.JOEMol.findChiralCenters(JOEMol.java:4261)
	at joelib.molecule.JOEAtom.isChiral(JOEAtom.java:609)
	at joelib.smiles.JOEMol2Smi.createSmiString(JOEMol2Smi.java:994)
	at joelib.util.database.AbstractDatabase.getSMILESHashcode(AbstractDatabase.java:173)
	at joelib.molecule.JOEMol.hashCode(JOEMol.java:4905)
	at joelib.molecule.JOEMol.reHash(JOEMol.java:5554)
	at joelib.molecule.JOEMol.endModify(JOEMol.java:3961)
	at joelib.molecule.JOEMol.endModify(JOEMol.java:3857)
	at joelib.smiles.JOESmilesParser.parseSmiles(JOESmilesParser.java:1874)
	at joelib.smiles.JOESmilesParser.smiToMol(JOESmilesParser.java:1910)
	at joelib.smiles.JOESmilesParser.smiToMol(JOESmilesParser.java:124)
	at SmilesSmartsViewer.main(SmilesSmartsViewer.java:35)
===============================================================================

I have been trying to find the reason and it appears to me that this error occurs especially when two rings are involved like in this example (however, I couldn't find a specific pattern to provoke the error and there are molecules with two rings where it works).
A fellow scientist using this routine told me the error occured in about 10% of the molecules he tried to view.

Any ideas how to fix this? As our software reaches state 'testing' we should correct this :-)
We are NOT working on the latest JOELib release due to problems with upgrading (see my last posting) but with 2004-06-21

Greetings,
Andreas