#10 GraphPotentials error for SMILES 'C2CCC(C1CC1)C2'

closed
SMILES (2)
5
2004-08-25
2004-08-24
No

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

Discussion

  • Joerg Kurt Wegner

    • status: open --> pending
     
  • Joerg Kurt Wegner

    Logged In: YES
    user_id=169818

    Dear Andreas,

    please check your classpath and ensure that you've included
    the jmat-package which should include the Matrix-class,
    which is required to calculate the GraphPotentials.
    It looks for me like an installation error and not like a
    bug. I've tested the conversion for:
    test.smi:
    C2CCC(C1CC1)C2 test
    with:
    sh convert.sh test.smi test.sdf
    and got:
    test
    -ISIS- 3D
    Used JOELib chemistry kernel (expert systems) ID is 1175941329
    6 6 0 0 0 0 0 0 0 0 1 V2000
    0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0
    0 0 0
    0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0
    0 0 0
    0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0
    0 0 0
    0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0
    0 0 0
    0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0
    0 0 0
    0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0
    0 0 0
    1 6 1 0 0 0 0
    1 2 1 0 0 0 0
    2 3 1 0 0 0 0
    3 4 1 0 0 0 0
    3 5 1 0 0 0 0
    5 6 1 0 0 0 0
    M END
    $$$$

    So all looks very fine for me.
    Please check your classpath or libraries in your
    application/applet.

    Please inform me about these checks, so i can decide to
    reopen or to close this bug request.

    Kind regards, Joerg

     
  • Joerg Kurt Wegner

    Logged In: YES
    user_id=169818

    Hi Andreas,

    i've taken a look at the sources and it looks for me like an
    installation problem and not like an implementation bug.

    Your classpath should contain the jmat-package and the
    Matrix-class, which seems not to be the case as your error
    messages show.

    Please check your classpath in your application/applet and
    inform me or give me more details. Until now i've set your
    bug request to a pending state.

    I've also tried to convert
    test.smi
    C2CCC(C1CC1)C2 test
    with:
    sh convert.sh test.smi test.sdf
    sucessfully to:
    test
    -ISIS- 3D
    Used JOELib chemistry kernel (expert systems) ID is 1175941329
    6 6 0 0 0 0 0 0 0 0 1 V2000
    0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0
    0 0 0
    0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0
    0 0 0
    0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0
    0 0 0
    0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0
    0 0 0
    0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0
    0 0 0
    0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0
    0 0 0
    1 6 1 0 0 0 0
    1 2 1 0 0 0 0
    2 3 1 0 0 0 0
    3 4 1 0 0 0 0
    3 5 1 0 0 0 0
    5 6 1 0 0 0 0
    M END
    $$$$

    So, please check again and send again more details. I can't
    reproduce this bug report in this form.

    Kind regards, Joerg

     
  • Joerg Kurt Wegner

    • status: pending --> open
     
  • Joerg Kurt Wegner

    • status: open --> pending
     
  • Joerg Kurt Wegner

    • status: pending --> closed
     
  • Joerg Kurt Wegner

    Logged In: YES
    user_id=169818

    As supposed: compiler problem.

     

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