VirtualHydrogenCounter.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 java.util.HashMap;
import java.util.Map;

/**
 * @author Richard L. Apodaca
 */
public class VirtualHydrogenCounter {
    private Map groups;

    public VirtualHydrogenCounter() {
        groups = new HashMap();

        buildGroups();
    }

    public boolean isVirtualizableHeavyAtom(Atom atom) {
        return groups.containsKey(atom.getSymbol());
    }

    public int countVirtualHydrogens(Atom atom) {
        int group = getGroup(atom);

        if (group == -1) {
            return 0;
        }
        switch (group) {
            case 13:
                return countGroup13VirtualHydrogens(atom);
            case 14:
                return countGroup14VirtualHydrogens(atom);
            case 15:
                return countGroup15VirtualHydrogens(atom);
            case 16:
                return countGroup16VirtualHydrogens(atom);
            case 17:
                return countGroup17VirtualHydrogens(atom);
        }

        throw new RuntimeException("Unrecognized group: " + group);
    }

    private int countGroup13VirtualHydrogens(Atom atom) {
        if (atom.getCharge() != 0) {
            return 0;
        }
        return countGroup15VirtualHydrogens(atom);
    }

    private int countGroup14VirtualHydrogens(Atom atom) {
        if (atom.getValence() > 3) {
            return 0;
        }
        if (Math.abs(atom.getCharge()) > 1) {
            return 0;
        }

        return (atom.getValence() > 4) ? 0 : 4 - (atom.getValence() + Math.abs(atom.getCharge() + countRadicalElectrons(atom)));
    }

    private int countGroup15VirtualHydrogens(Atom atom) {
        if (atom.getValence() > 3) {
            return 0;
        }
        if (Math.abs(atom.getCharge()) > 1) {
            return 0;
        }

        return 3 - (atom.getValence() - atom.getCharge() + countRadicalElectrons(atom));
    }

    private int countGroup16VirtualHydrogens(Atom atom) {
        if (atom.getValence() >= 2) {
            return 0;
        }
        if (Math.abs(atom.getCharge()) >= 2) {
            return 0;
        }

        return 2 - (atom.getValence() - atom.getCharge() + countRadicalElectrons(atom));
    }

    private int countGroup17VirtualHydrogens(Atom atom) {
        if (atom.getValence() != 0) {
            return 0;
        }
        return (atom.getValence() > 1) ? 0 : 1 - (atom.getValence() - atom.getCharge() + countRadicalElectrons(atom));
    }

    private void buildGroups() {
        String[] g13 =
                {
                        "B", "Al", "Ga", "In", "Tl"
                };
        String[] g14 =
                {
                        "C", "Si", "Ge", "Sn", "Pb"
                };
        String[] g15 =
                {
                        "N", "P", "As", "Sb", "Bi"
                };
        String[] g16 =
                {
                        "O", "S", "Se", "Te", "Po"
                };
        String[] g17 =
                {
                        "F", "Cl", "Br", "I", "At"
                };

        buildGroup(g13, 13);
        buildGroup(g14, 14);
        buildGroup(g15, 15);
        buildGroup(g16, 16);
        buildGroup(g17, 17);
    }

    private void buildGroup(String[] atoms, int group) {
        Integer g = new Integer(group);

        for (int i = 0; i < atoms.length; i++) {
            groups.put(atoms[i], g);
        }
    }

    private int getGroup(Atom atom) {
        Object result = groups.get(atom.getSymbol());

        return (result == null) ? -1 : ((Integer) result).intValue();
    }

    private int countRadicalElectrons(Atom atom) {
        int result = 0;

        switch (atom.getRadical()) {
            case 1:
                result = 1;
                break;
            case 2:
                result = 2;
                break;
            case 3:
                result = 2;
                break;
        }

        return result;
    }
}