MoleculeKit.java

/*
 * MX Cheminformatics Tools for Java
 * 
 * Copyright (c) 2007, 2008 Metamolecular, LLC
 * 
 * http://metamolecular.com
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */

package com.chemhack.jsMolEditor.client.model;

import com.chemhack.jsMolEditor.client.calc.MassCalculator;
import java.util.ArrayList;
import java.util.List;

import com.chemhack.jsMolEditor.client.io.mdl.MolfileReader;
import com.chemhack.jsMolEditor.client.io.mdl.MolfileWriter;

/**
 * @author Richard L. Apodaca
 */
public class MoleculeKit {
    private static MolfileReader reader;
    private static MolfileWriter writer;
    private static VirtualHydrogenCounter hydrogenCounter;
    private static String hydrogen = "H";
    private static MassCalculator massCalculator;

    static {
        reader = new MolfileReader();
        writer = new MolfileWriter();
        massCalculator = new MassCalculator();
        hydrogenCounter = new VirtualHydrogenCounter();
    }

    /**
     *
     */
    private MoleculeKit() {

    }

    public static double getMass(Molecule molecule) {
        return massCalculator.findAveragedMass(molecule);
    }

    public static Molecule readMolfile(String molfile) {
        Molecule result = new DefaultMolecule();

        reader.read(result, molfile.replaceAll("\\\\n", "\n"));

        return result;
    }

    public static Molecule readMolfile(String molfile, boolean virtualizeHydrogens) {
        Molecule mol = readMolfile(molfile);

        if (virtualizeHydrogens) {
            virtualizeHydrogens(mol);
        }

        return mol;
    }

    public static String writeMolfile(Molecule molecule) {
        return writer.write(molecule);
    }

    public static void virtualizeHydrogens(Molecule molecule) {
        List toStrip = new ArrayList();

        for (int i = 0; i < molecule.countAtoms(); i++) {
            Atom atom = molecule.getAtom(i);

            recordVirtualizableHydrogens(atom, toStrip);
        }

        if (toStrip.isEmpty()) return;

        molecule.beginModify();

        for (int i = 0; i < toStrip.size(); i++) {
            Atom atom = (Atom) toStrip.get(i);

            molecule.removeAtom(atom);
        }

        molecule.endModify();
    }

    public static boolean isVirtualizableHydrogen(Atom atom) {
        if (!hydrogen.equals(atom.getSymbol())) {
            return false;
        }

        if (atom.hasSingleIsotope() || atom.countNeighbors() != 1) {
            return false;
        }

        Bond[] bonds = atom.getBonds();

        return bonds[0].getStereo() == 0 && bonds[0].getType() == 1;
    }

    public static boolean isVirtualizableHydrogenBond(Bond bond) {
        if (!(hydrogen.equals(bond.getSource().getSymbol()) || hydrogen.equals(bond.getTarget().getSymbol()))) {
            return false;
        }

        if (hydrogen.equals(bond.getSource().getSymbol()) && hydrogen.equals(bond.getTarget().getSymbol())) {
            return false;
        }

        return bond.getStereo() == 0 && bond.getType() == 1;
    }

    private static void recordVirtualizableHydrogens(Atom atom, List toStrip) {
        if (!hydrogenCounter.isVirtualizableHeavyAtom(atom)) return;

        Bond[] bonds = atom.getBonds();

        for (int i = 0; i < bonds.length; i++) {
            Bond bond = bonds[i];
            Atom neighbor = bond.getMate(atom);

            if (hydrogen.equals(neighbor.getSymbol())) {
                if (neighbor.hasSingleIsotope()) continue;
                if (bond.getStereo() != 0) continue;

                toStrip.add(neighbor);
            }
        }
    }
}