gistfile1.txt

package gov.nih.ncgc;

import org.openscience.cdk.ChemFile;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.io.MDLV2000Reader;
import org.openscience.cdk.io.Mol2Reader;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;

import java.io.FileNotFoundException;
import java.io.FileReader;
import java.util.List;

/**
 * A one line summary.
 *
 * @author Rajarshi Guha
 */
public class Moltest {
    public static void main(String[] args) throws FileNotFoundException, CDKException {
        MDLV2000Reader reader1 = new MDLV2000Reader(new FileReader("/Users/guhar/work/fpcomp/aid692/actives.sdf"));
        IChemFile chemFile = reader1.read(new ChemFile());
        List<IAtomContainer> mols1 = ChemFileManipulator.getAllAtomContainers(chemFile);
        System.out.println("mols1.size() = " + mols1.size());

        Mol2Reader reader2 = new Mol2Reader(new FileReader("/Users/guhar/work/fpcomp/aid692/actives.sdf"));
        chemFile = (IChemFile) reader2.read(new ChemFile());
        List<IAtomContainer> mols2 = ChemFileManipulator.getAllAtomContainers(chemFile);
        System.out.println("mols2.size() = " + mols2.size());
    }
}