Split a large file into smaller part using molconvert

Hi,

I'll like to know if it is possible to split a big file into 4 smaller part. e.g 4 part of 1000 compounds with molconvert ?

So far I use molconvert -m, but it will split the file according the number of molecule in there...

Many thanks,

 

Best

Hi Florent,

it is not possible to do it using molconverter but it can be done quite easily using the Chemaxon API, if you are interested I can send you a code example.

Best regards,

Zsuzsa

Sure, it can help me !

Thanks,

Hi Florent,

Below you can find the code example which generates the splitted files (it is also attached: SplitToFiles.java).

Usage: SplitToFiles <filename.extension> <number of molecules per export file>

Best regards,

Zsuzsa

package chemaxon.util;

import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;

import chemaxon.formats.MolExporter;
import chemaxon.formats.MolFormatException;
import chemaxon.formats.MolImporter;
import chemaxon.struc.Molecule;

/**
 * Exports molecules in the given file into several others with the same name a the
 * given file and indexes in the end.
 * @author Zsuzsanna Szabo
 */
public class SplitToFiles {

    /**
     * @param args program arguments: name of file(first argument) and number of molecules 
     * per export file(second argument)  
     */
    public static void main(String[] args) {
    if (args.length != 2) {
        System.out.println("Usage: SplitToFiles <filename.extension> <number of molecules per export file>\n" +
            "Name of export files <filename_<index>.extension>,\n" + 
            "Example: file Benzene.mol is exported to Benzene_1.mol, Benzene_2.mol etc.");
        System.exit(0);
    }

    String inFileName = args[0];
    int exportFileCount = Integer.parseInt(args[1]);
    if (exportFileCount < 1) {
        System.out.println("Wrong number of molecules per file: " + exportFileCount);
        System.exit(0);
    }
    try {
        splitToFiles(inFileName, exportFileCount);
    } catch (MolFormatException e) {
        System.err.println(inFileName + ": error in molecule file format.");
        e.printStackTrace();
        System.exit(1);
    } catch (FileNotFoundException e) {
        System.err.println(inFileName + ": file is not found.");
        e.printStackTrace();
        System.exit(1);
    } catch (IOException e) {
        System.err.println(inFileName + ": input/output error.");
        e.printStackTrace();
        System.exit(1);
    }
    }
    
    private static void splitToFiles(String inFileName, int exportFileCount) 
            throws MolFormatException, FileNotFoundException, IOException {
    MolImporter importer = new MolImporter(new FileInputStream(inFileName));
    Molecule mol = importer.read();
    for (int fileIndex = 1; mol != null; fileIndex++) {
        int dotIndex = inFileName.indexOf('.');
        String outFileName = inFileName.substring(0, dotIndex);
        outFileName += "_" + fileIndex;
        outFileName += inFileName.substring(dotIndex);
        System.out.println("Generating file " + outFileName);        
        MolExporter exporter = new MolExporter(
            new FileOutputStream(outFileName), importer.getFormat());
        for (int i = 0; i < exportFileCount && mol != null; i++) {
        exporter.write(mol);
        mol = importer.read();
        }
        exporter.close();
    }
    importer.close();
    }
}