Re: [Joelib-help] Smiles parsing error

[Joerg K. W. <we...@in...>]

Hi Andreas,

i've changed the bug request to 'pending', because i can't reproduce 
this bug. Please send more informations and recheck your classpath if it 
contains the jmat-package.

https://sourceforge.net/tracker/?func=detail&atid=425969&aid=1015117&group_id=39708

Kind regards, Joerg

> 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
> 
> 
> 
> 
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-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
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