How to generate fingerprints in Java

[copied from email]





"I need generate FingerPrint from java code. I have tried your libraries, but I haven´t found any parameter settings of fingerprint or pharmacophore fingerprint descriptor in API.





Could you help me with java code?"

Here is a simple example. Save it as GenerCF.java then compile it: 'javac GenerCF.java'.





It takes three command line arguments; the first is the configuration (parameter settings) for the fingerprint (for instance you can use the default configuration by ChemAxon that is found in jchem/examples/config/cfp.xml). The second command-line parameter is your input file, which can be any molecular structure file that contains at least one structure. The third parameter specifies the name of the output file where fingerprints are stored.





This sample code generates ChemicalFingerprints for each individual structure. It can be adapted to any other MolecularDescriptor provided by ChemAxon.





I hope this helps.


Miklos

Code:

import java.io.*; import chemaxon.descriptors.*; /**  * Simple example code to demostrate the calculation of ChemicalFingerprint.  * <br>  * Takes three command-line arguments as input: config file, input SDfile,  * output descriptor file  *  * @author  Miklos Vargyas  */ public class GenerCF {     public static void main( String[] args ) {         try {             // create parameters configuration from external XML config file             CFParameters cfPar = new CFParameters( new File( args[ 0 ] ) );             // create a molecular descriptor generator for one descriptor             GenerateMD descript = new GenerateMD(1);             // set the input file for the generator             descript.setInput( args[ 1 ] );             // and tell that input is an SDfile             descript.setSDfileInput(true);             // specify the descriptor to be created: into which file, what type             // what parameters settings to be applied             descript.setDescriptor( args[ 2 ], "CF", cfPar, "" );             // initialize the generator             descript.init();             // start it and do the entire generation in one go             descript.run();             // close output file             descript.close();         }         catch ( Exception e ) {             e.printStackTrace( System.err );         }         System.exit(0);     } }

Dear Miklos,





With your famous code section, it is easy to make molecular descriptors. Thank you. That works fine with JDK1.5.0_01 and JChem3.0.8. I ran problem when I tried to compile (ok) and run (problem) with JDK1.3.1_11 and JChem2.2.1.





Exception in thread "main" java.lang.NoClassDefFoundError: javax/xml/transform/TransformerException....





I found the classes: javax.xml.transform and javax.xml.parsers. Recompiled in the classpath. At the runtime, GenerCF still complain in the following line:





CFParameters cfPar = new CFParameters();





Would you please tell me where I can get the javax.xml.*. Our webserver used JDK1.3.1_11 and JChem2.2.1. It takes a while for us to upgrade the server.





Best regards,





Tiqing

Dear Tiqing,





please find the xml parser library at this link http://java.sun.com/xml/archive.html.





Get back to the forum if you experience further difficulties.





Regards,


Miklos

Dear Miklos,





With your famous GenerCF.java, I extended this program to produce BCUT molecular descriptors. However, I tried to generate scalar descriptors with the hint from GenerCF.java (GenerateMD class) without success. It is appreciated if you can post the java codes to generate the scalar descriptors (should be seven in JChem).





Best regards,





Tiqing

Dear Tiqing,





I attached the code, it is directly derived from GenerCF.java. I also attached a suitable configuration file.


Hope this helps.





Regards,


Miklos