Hi Egon,
Thank you for early reply.
When i use cdk-20050826, following code worked well, but cdk-20060714 gave
some troubles. Of cource import path etc are corrected well.
This is a sample code which i have trouble:
--- from here ---
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.io.iterator.IteratingSMILESReader;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.tools.HydrogenAdder;
import org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor;
import org.openscience.cdk.qsar.result.DoubleResult;
class ChemProp{
public static void main(String args[]){
if (args.length != 1){
System.out.println("Usage: ChemProp in.smi");
System.exit(1);
}
FileReader fr = null;
try {
fr = new FileReader(new File(args[0]));
} catch (FileNotFoundException e) {
System.out.println(e.toString());
System.exit(1);
}
XLogPDescriptor calcxlogp = new XLogPDescriptor();
Boolean param[] = new Boolean[2];
param[0] = Boolean.TRUE;
param[1] = Boolean.TRUE;
try {
calcxlogp.setParameters(param);
} catch (CDKException e1) {
System.out.println(e1.toString());
}
DescriptorValue dvxlogp = null;
double dtemp=0.0;
int nid = 0;
IteratingSMILESReader itr = new IteratingSMILESReader(fr);
HydrogenAdder adder = new HydrogenAdder();
while(itr.hasNext()){
Molecule mol = (Molecule)itr.next();
try {
adder.addExplicitHydrogensToSatisfyValency(mol);
dvxlogp = calcxlogp.calculate(mol);
nid++;
System.out.println(nid + ": "
+mol.getProperty("SMIdbNAME"));
dtemp=((DoubleResult)dvxlogp.getValue()).doubleValue();
System.out.println("xlogp: " + dtemp);
} catch (Exception e) {
System.out.println(e.toString());
}
}
}
}
--- end ---
Compile works well, but the following error is shown.
Exception in thread "main" java.lang.NoSuchMethodError:
org.openscience.cdk.tools.HydrogenAdder.addExplicitHydrogensToSatisfyValency
(Lorg/openscience/cdk/interfaces/IMolecule;)Lorg/openscience/cdk/interfaces/
IAtomContainer;
at ChemProp.main(ChemProp.java:50)
Exception in thread "main" java.lang.NoSuchMethodError:
org.openscience.cdk.ringsearch.AllRingsFinder.findAllRings(Lorg/openscience/
cdk/interfaces/IAtomContainer;)Lorg/openscience/cdk/interfaces/IRingSet;
at
org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor.calculate(XLo
gPDescriptor.java:198)
at ChemProp.main(ChemProp.java:51)
Changing
dvxlogp = calcxlogp.calculate(mol);
to
dvxlogp = calcxlogp.calculate((IAtomContainer)mol);
gave same results.
In addition i want to use
IAtom[] atoms= mol.getAtoms();
but it also does not work.
Do you have any idea to solve problems?
Thanks in advance.
Takayuki KOTANI
-----Original Message-----
From: Egon Willighagen [mailto:[EMAIL PROTECTED]
Sent: Thursday, August 10, 2006 6:46 PM
To: [email protected]
Cc: Takayuki KOTANI
Subject: Re: [Cdk-devel] IteratingSMILESReader
(moved this thread to [EMAIL PROTECTED])
Hi Takayuki,
On Thursday 10 August 2006 10:53, Takayuki KOTANI wrote:
> To calculate such as XLogPDescriptor, cdk-20060714 uses IAtomContainer
> class though cdk-20050826 uses AtomContainer.
> On the other hands, IteratingSMILESReader returns Molecule.
>
> I am not familiar with JAVA and CDK, I really appreciate if some one
> teach me a method for convert Molecule to IMolecule or IAtomContainer.
Java, like several other programming languages, has a concept for
interfaces.
These interfaces define the programming interface for certain types of
objects, which actually provide some implementation.
Molecule is an implementation of the IMolecule interface, and hence *is* a
IMolecule. So, there is no need to convert a Molecule into an IMolecule.
Java also is a object-oriented programming language, and therefore provide a
concept for 'extending' objects. In the CDK, the Molecule class extends the
AtomContainer class (and the IMolecule interface extends the IAtomContainer
interface).
So, there is neither the need to convert a Molecule into an AtomContainer as
it already *is* an AtomContainer (by extending it).
> Thanks in advance.
I hope this helps.
Egon
--
CUBIC
blog: http://chem-bla-ics.blogspot.com/
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