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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