[Cdk-user] Re^2: [Cdk-devel] IteratingSMILESReader

[Takayuki K. <t-k...@ni...>]

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:ewi...@un...] 
Sent: Thursday, August 10, 2006 6:46 PM
To: cdk...@li...
Cc: Takayuki KOTANI
Subject: Re: [Cdk-devel] IteratingSMILESReader


(moved this thread to cdk...@li...)

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

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CUBIC
blog: http://chem-bla-ics.blogspot.com/