Two and a half months after the CDK milestone, the Blue Obelisk paper also reached 100 citations. Here the lucky paper is Design, Synthesis, and Preclinical Evaluation of New 5,6- (or 6,7-) Disubstituted-2-(fluorophenyl)quinolin-4-one Derivatives as Potent Antitumor Agents by Chou et al (doi:10.1021/jm100780c). The Blue Obelisk paper (doi:10.1021/ci050400b) is cited because the authors used OpenBabel. About half of the 100 citations is because OpenBabel was used, whereas OpenBabel is only mentioned as one of the Blue Obelisk-associated unprojects in the Blue Obelisk paper.
I am not sure how this habit started, but with citation practices, it is unlikely to go away. But who am I to complain....
hello,
ReplyDeleteSorry for posting this here,i had started wroking with cdk ,to write a program for descriptor calculation..the code is :
import java.util.Iterator;
import java.util.Map;
import org.openscience.cdk.*;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.qsar.descriptors.molecular.*;
import org.openscience.cdk.smiles.*;
import org.openscience.cdk.qsar.*;
import org.openscience.cdk.qsar.result.IDescriptorResult;
/**
*
* @author Hari
* @since 19-12-2010
* @version 1.0
*/
public class descr {
/**
* @param args the command line arguments
*/
public static void main(String[] args) throws CDKException {
// TODO code application logic here
BCUTDescriptor descriptor = new BCUTDescriptor();
Molecule molecule = (Molecule) new SmilesParser(DefaultChemObjectBuilder.getInstance()).parseSmiles("NC(CO)C(=O)O");
// The first program in wiki link for Descriptor Calculator
DescriptorValue value = descriptor.calculate(molecule);
IDescriptorResult theNumbers = value.getValue();
System.out.print(theNumbers.toString()+"\n\n");
// Second program
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR);
engine.process(molecule);
/**
* The function getProperties returns a Map value. Map represents a Key Value set.
* It is retrieved using an iterator. Since the key is of DescriptorSpecification class and the
* value is of type DescriptorValue we have to typecast the key and value with the same while retrieving.
* since they have not override the same to String.
*/
Map i = molecule.getProperties();
Iterator iterator = i.keySet().iterator();
/**
* The following prints the key and Value set.
*/
while(iterator. hasNext()){
String key = ((DescriptorSpecification)iterator.next()).getSpecificationReference().toString();
System.out.print(key.substring(key.lastIndexOf("#")+1)+" : ");
System.out.print(((DescriptorValue)i.get((DescriptorSpecification)iterator.next())).getValue().toString()+"\n\n");
}
}
}
the output is different for windows and linux. while i get only a bcut descriptor o/p for standalone and netbeans 6.8 in linux, around 40 descriptors are given as o/p in windows using netbeans 6.8... please advice
Hi Hari, I noted your blog, but I cannot comment there...
ReplyDeletehai egon,
ReplyDeletecould u suggest where i could blog my query?
Your blog post at http://cdkhari.blogspot.com/2011/01/cdk-varying-out-puts.html is fine. I seem now able to leave a comment.
ReplyDelete