Thanks for your help Rajarshi and Thomas .
The code here is kludgey, but I am beginning to understand how I can get
from here to something that elegantly calculates the descriptors I am
interested in .
Got calcs for two sample descriptors
Code attached
Thanks again
Hari
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.exception.InvalidSmilesException;
import org.openscience.cdk.*;
import org.openscience.cdk.smiles.*;
import org.openscience.cdk.qsar.*;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorEngine;
import org.openscience.cdk.io.iterator.IteratingMDLReader;
import java.io.*;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.qsar.IMolecularDescriptor;
public class MyDescriptorCalcExample {
public static void main(String[] args) throws FileNotFoundException{
SmilesParser smilesParser = new
SmilesParser(DefaultChemObjectBuilder.getInstance());
String smiles =
"CC1=C(C=C(C=C1)NC(=O)C2=CC=C(C=C2)CN3CCN(CC3)C)NC4=NC=CC(=N4)C5=CN=CC=C5.CS(=O)(=O)O";
DescriptorEngine engine = new
DescriptorEngine(DescriptorEngine.MOLECULAR,null);
org.openscience.cdk.interfaces.IMolecule molecule = null ;
// IteratingMDLReader iteratingMDLReader = new
IteratingMDLReader(new BufferedReader(new
FileReader("H:/Netbeans/glevec.sdf")),DefaultChemObjectBuilder.getInstance());
try {
molecule = smilesParser.parseSmiles(smiles);
} catch (InvalidSmilesException ex) {
Logger.getLogger(MyDescriptorCalcExample.class.getName()).log(Level.SEVERE,
null, ex);
}
// molecule = (IMolecule) iteratingMDLReader.next();
// System.out.println(molecule.toString());
IMolecularDescriptor descriptor = new
org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor();
DescriptorValue retval = descriptor.calculate(molecule);
System.out.println("LARGESTCHAIN:" + retval.getValue());
IMolecularDescriptor alogp = null;
try {
alogp = new
org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor();
} catch (CDKException ex) {
Logger.getLogger(MyDescriptorCalcExample.class.getName()).log(Level.SEVERE,
null, ex);
}
DescriptorValue alogp_val = alogp.calculate(molecule);
System.out.println("ALOGP:" + alogp_val.getValue());
}
}
On Mon, Feb 7, 2011 at 6:48 PM, Rajarshi Guha <rajarshi.g...@gmail.com>wrote:
> On Mon, Feb 7, 2011 at 6:41 PM, hari jayaram <hari...@gmail.com> wrote:
>
> > Now that I know it can work , i will try to calculate these using code
> and
> > the examples you have here : http://rguha.net/code/java/#desc
>
> I should point out that the code out there may be out of date
>
> > I am very rusty with my java so its been slow beginning. Wishing
> > I weren't spoiled by list comprehensions in Python.
>
> Indeed - life sucks without list comprehensions
>
> --
> Rajarshi Guha
> NIH Chemical Genomics Center
>
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