Hi John,
many thanks for your very helpful advice.
Indeed using silent builder fixed the issue! I think debug builder would
also do, however using structure diagram generator would subsequently
generate an NPE when calling atom.setPoint2D(null) (called by
StructureDiagramGenerator at line 150) because the call to logger will
fail in DebugAtom.setPoint2D (line 98).
I don't understand the linking issue, though. I have called the test
smiles program as follows:
/usr/java/bin/java -cp dist/emdchem.jar:lib/cdk-1.4.16.jar
com.emd.chemical.TestSmiles
where emdchem.jar has the following content
jar tvf dist/emdchem.jar
0 Fri Jan 04 15:32:22 CET 2013 META-INF/
366 Fri Jan 04 15:32:20 CET 2013 META-INF/MANIFEST.MF
0 Fri Jan 04 15:32:22 CET 2013 com/
0 Fri Jan 04 15:32:22 CET 2013 com/emd/
0 Fri Jan 04 15:32:22 CET 2013 com/emd/chemical/
2635 Fri Jan 04 15:32:22 CET 2013 com/emd/chemical/Chemical.class
218 Fri Jan 04 15:32:22 CET 2013 com/emd/chemical/MoleculeException.class
9661 Fri Jan 04 15:32:22 CET 2013 com/emd/chemical/MoleculeRenderer.class
1166 Fri Jan 04 15:32:22 CET 2013 com/emd/chemical/TestSmiles.class
whereby none of the other classes inside emdchem.jar are referenced by
the TestSmiles class.
Anyway it works now.
Many thanks again.
Oliver
On 01/04/2013 02:54 AM, John May wrote:
> Hi Oliver,
>
> Looks like a class path error. How are you linking the library?
>
> Also you should use the silent builder - it is much faster. Bit confusing but
> the default is only useful if you need event listeners on molecules (which
> you normally don't).
>
> J
>
> Sent from my iPhone
>
> On 3 Jan 2013, at 16:13, Oliver Karch <[email protected]> wrote:
>
>> Hello cdk gurus,
>>
>> all the best and a happy new year!
>>
>> I am currently trying to use cdk's smiles parser. Unfortunately I cannot
>> get it working. The code at the very bottom prints:
>>
>> Create Smiles parser...
>> Exception in thread "main" java.lang.NoSuchMethodError:
>> org.openscience.cdk.DefaultChemObjectBuilder.getInstance()Lorg/openscience/cdk/DefaultChemObjectBuilder;
>> at com.emd.chemical.TestSmiles.main(Unknown Source)
>>
>> If I am using the DebugChemObjectBuilder instead, it seems to work...
>> What did I wrong?
>> Any hints are warmly appreciated.
>> Many thanks.
>>
>> Oliver
>>
>> p.s. my environment
>> java version "1.7.0_02"
>> Java(TM) SE Runtime Environment (build 1.7.0_02-b13)
>> Java HotSpot(TM) 64-Bit Server VM (build 22.0-b10, mixed mode)
>> Linux cuba 2.6.37.6-24-desktop #1 SMP PREEMPT 2012-10-18 22:36:08 +0200
>> x86_64 x86_64 x86_64 GNU/Linux
>>
>> Output using DebugChemObjectBuilder
>>
>> Create Smiles parser...
>> OK.
>> Parsing smiles...
>> Molecule: Molecule(576464345, AtomContainer(576464345, #A:6,
>> Atom(599974635, S:C, H:1, AtomType(599974635, N:C.sp2, FC:0, H:SP2,
>> NC:3, EV:4, Isotope(599974635, Element(599974635, S:C, AN:6)))),
>> Atom(958113357, S:C, H:1, AtomType(958113357, N:C.sp2, FC:0, H:SP2,
>> NC:3, EV:4, Isotope(958113357, Element(958113357, S:C, AN:6)))),
>> Atom(388841694, S:C, H:1, AtomType(388841694, N:C.sp2, FC:0, H:SP2,
>> NC:3, EV:4, Isotope(388841694, Element(388841694, S:C, AN:6)))),
>> Atom(469613237, S:C, H:1, AtomType(469613237, N:C.sp2, FC:0, H:SP2,
>> NC:3, EV:4, Isotope(469613237, Element(469613237, S:C, AN:6)))),
>> Atom(787271534, S:C, H:1, AtomType(787271534, N:C.sp2, FC:0, H:SP2,
>> NC:3, EV:4, Isotope(787271534, Element(787271534, S:C, AN:6)))),
>> Atom(1025922771, S:C, H:1, AtomType(1025922771, N:C.sp2, FC:0, H:SP2,
>> NC:3, EV:4, Isotope(1025922771, Element(1025922771, S:C, AN:6)))), #B:6,
>> Bond(2049480620, #O:SINGLE, #S:NONE, #A:2, Atom(958113357, S:C, H:1,
>> AtomType(958113357, N:C.sp2, FC:0, H:SP2, NC:3, EV:4, Isotope(958113357,
>> Element(958113357, S:C, AN:6)))), Atom(599974635, S:C, H:1,
>> AtomType(599974635, N:C.sp2, FC:0, H:SP2, NC:3, EV:4, Isotope(599974635,
>> Element(599974635, S:C, AN:6)))), ElectronContainer(2049480620EC:0)),
>> Bond(1282230271, #O:SINGLE, #S:NONE, #A:2, Atom(388841694, S:C, H:1,
>> AtomType(388841694, N:C.sp2, FC:0, H:SP2, NC:3, EV:4, Isotope(388841694,
>> Element(388841694, S:C, AN:6)))), Atom(958113357, S:C, H:1,
>> AtomType(958113357, N:C.sp2, FC:0, H:SP2, NC:3, EV:4, Isotope(958113357,
>> Element(958113357, S:C, AN:6)))), ElectronContainer(1282230271EC:0)),
>> Bond(1583882228, #O:SINGLE, #S:NONE, #A:2, Atom(469613237, S:C, H:1,
>> AtomType(469613237, N:C.sp2, FC:0, H:SP2, NC:3, EV:4, Isotope(469613237,
>> Element(469613237, S:C, AN:6)))), Atom(388841694, S:C, H:1,
>> AtomType(388841694, N:C.sp2, FC:0, H:SP2, NC:3, EV:4, Isotope(388841694,
>> Element(388841694, S:C, AN:6)))), ElectronContainer(1583882228EC:0)),
>> Bond(101317784, #O:SINGLE, #S:NONE, #A:2, Atom(787271534, S:C, H:1,
>> AtomType(787271534, N:C.sp2, FC:0, H:SP2, NC:3, EV:4, Isotope(787271534,
>> Element(787271534, S:C, AN:6)))), Atom(469613237, S:C, H:1,
>> AtomType(469613237, N:C.sp2, FC:0, H:SP2, NC:3, EV:4, Isotope(469613237,
>> Element(469613237, S:C, AN:6)))), ElectronContainer(101317784EC:0)),
>> Bond(445767052, #O:SINGLE, #S:NONE, #A:2, Atom(1025922771, S:C, H:1,
>> AtomType(1025922771, N:C.sp2, FC:0, H:SP2, NC:3, EV:4,
>> Isotope(1025922771, Element(1025922771, S:C, AN:6)))), Atom(787271534,
>> S:C, H:1, AtomType(787271534, N:C.sp2, FC:0, H:SP2, NC:3, EV:4,
>> Isotope(787271534, Element(787271534, S:C, AN:6)))),
>> ElectronContainer(445767052EC:0)), Bond(2130566107, #O:SINGLE, #S:NONE,
>> #A:2, Atom(1025922771, S:C, H:1, AtomType(1025922771, N:C.sp2, FC:0,
>> H:SP2, NC:3, EV:4, Isotope(1025922771, Element(1025922771, S:C,
>> AN:6)))), Atom(599974635, S:C, H:1, AtomType(599974635, N:C.sp2, FC:0,
>> H:SP2, NC:3, EV:4, Isotope(599974635, Element(599974635, S:C, AN:6)))),
>> ElectronContainer(2130566107EC:0))))
>>
>> The code:
>>
>> import org.openscience.cdk.DefaultChemObjectBuilder;
>> import org.openscience.cdk.debug.DebugChemObjectBuilder;
>> import org.openscience.cdk.exception.InvalidSmilesException;
>>
>> import org.openscience.cdk.interfaces.IMolecule;
>> import org.openscience.cdk.smiles.SmilesParser;
>>
>> public class TestSmiles {
>>
>> public static void main( String[] argv ) {
>> try {
>> System.out.println( "Create Smiles parser...");
>> SmilesParser sp = new
>> SmilesParser(DefaultChemObjectBuilder.getInstance());
>> // SmilesParser sp = new
>> SmilesParser(DebugChemObjectBuilder.getInstance());
>> System.out.println( "OK." );
>> System.out.println( "Parsing smiles...");
>> IMolecule m = sp.parseSmiles("c1ccccc1");
>> System.out.println( "Molecule: "+m );
>> } catch (InvalidSmilesException ise) {
>> ise.printStackTrace();
>> }
>> }
>> }
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