gistfile1.java

package gov.nih.ncgc;

import chemaxon.formats.MolImporter;
import chemaxon.sss.search.MCS;
import chemaxon.struc.Molecule;

import java.io.IOException;
import java.util.ArrayList;
import java.util.List;

/**
 * Print out the MCS of a set of molecules as a SMILES string.
 *
 * @author Rajarshi Guha
 */
public class DumpMCS {
    private Molecule mcs;
    private List<Molecule> mols = null;

    public DumpMCS() {
    }

    public DumpMCS(List<Molecule> mols) {
        this.mols = new ArrayList<Molecule>(mols);
    }

    public Molecule getMCS() {
        return mcs;
    }

    public void setMols(List<Molecule> mols) {
        this.mols = new ArrayList<Molecule>(mols);
    }

    public void run() throws IOException, InterruptedException {
        if (mols == null) throw new IOException("Must set the molecules to process");
        if (mols.size() == 1) {
            mcs = mols.get(0);
            return;
        }

        List<Molecule> mcses = new ArrayList<Molecule>();
        for (int i = 0; i < mols.size(); i++) {
            for (int j = 0; j < mols.size(); j++) {
                if (i == j) continue;
                MCS mcs = new MCS();
                mcs.setMolecules(mols.get(i), mols.get(j));
                mcs.search();
                Molecule tmp = mcs.getResultAsMolecule();
                if (tmp != null)
                    mcses.add(tmp);
            }
        }

        int indexOfBiggest = -1;
        int maxSize = -1;
        int i = 0;
        for (Molecule mol : mcses) {
            if (mol.getAtomCount() > maxSize) {
                maxSize = mol.getAtomCount();
                indexOfBiggest = i;
            }
            i++;
        }
        mcs = mcses.get(indexOfBiggest);
    }

    public static void main(String[] args) throws IOException, InterruptedException {
        if (args.length != 1) {
            System.out.println("Must specify a SMILES file as the single argument");
            System.exit(-1);
        }

        List<Molecule> mols = new ArrayList<Molecule>();
        MolImporter mi = new MolImporter(args[0]);
        for (Molecule mol; (mol = mi.read()) != null;) {
            mols.add(mol);
        }
        mi.close();

        DumpMCS dmcs = new DumpMCS(mols);
        dmcs.run();
        System.out.println(dmcs.getMCS().toFormat("smiles"));
    }
}