Molecules.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.io;

import com.chemhack.jsMolEditor.client.model.Atom;
import com.chemhack.jsMolEditor.client.model.DefaultMolecule;
import com.chemhack.jsMolEditor.client.model.Molecule;

/**
 * @author Richard L. Apodaca
 */
public class Molecules {
    private Molecules() {
    }

    public static Molecule createMethane() {
        Molecule result = new DefaultMolecule();
        Atom c0 = result.addAtom("C");

        return result;
    }

    public static Molecule createPropane() {
        Molecule result = new DefaultMolecule();
        Atom c0 = result.addAtom("C");
        Atom c1 = result.addAtom("C");
        Atom c2 = result.addAtom("C");

        result.connect(c0, c1, 1);
        result.connect(c1, c2, 1);

        return result;
    }

    public static Molecule createCyclopropane() {
        Molecule result = new DefaultMolecule();
        Atom c0 = result.addAtom("C");
        Atom c1 = result.addAtom("C");
        Atom c2 = result.addAtom("C");

        result.connect(c0, c1, 1);
        result.connect(c1, c2, 1);
        result.connect(c2, c0, 1);

        return result;
    }

    public static Molecule createHexane() {
        Molecule result = new DefaultMolecule();
        Atom c0 = result.addAtom("C");
        Atom c1 = result.addAtom("C");
        Atom c2 = result.addAtom("C");
        Atom c3 = result.addAtom("C");
        Atom c4 = result.addAtom("C");
        Atom c5 = result.addAtom("C");

        result.connect(c0, c1, 1);
        result.connect(c1, c2, 1);
        result.connect(c2, c3, 1);
        result.connect(c3, c4, 1);
        result.connect(c4, c5, 1);

        return result;
    }

    public static Molecule createCyclohexane() {
        Molecule result = new DefaultMolecule();
        Atom c0 = result.addAtom("C");
        Atom c1 = result.addAtom("C");
        Atom c2 = result.addAtom("C");
        Atom c3 = result.addAtom("C");
        Atom c4 = result.addAtom("C");
        Atom c5 = result.addAtom("C");

        result.connect(c0, c1, 1);
        result.connect(c1, c2, 1);
        result.connect(c2, c3, 1);
        result.connect(c3, c4, 1);
        result.connect(c4, c5, 1);
        result.connect(c5, c0, 1);

        return result;
    }

    public static Molecule createBenzene() {
        Molecule result = new DefaultMolecule();
        Atom c1 = result.addAtom("C");
        Atom c2 = result.addAtom("C");
        Atom c3 = result.addAtom("C");
        Atom c4 = result.addAtom("C");
        Atom c5 = result.addAtom("C");
        Atom c6 = result.addAtom("C");

        result.connect(c1, c2, 1);
        result.connect(c2, c3, 2);
        result.connect(c3, c4, 1);
        result.connect(c4, c5, 2);
        result.connect(c5, c6, 1);
        result.connect(c6, c1, 2);

        return result;
    }

    public static Molecule createPyridine() {
        Molecule result = new DefaultMolecule();
        Atom c1 = result.addAtom("C");
        Atom c2 = result.addAtom("C");
        Atom c3 = result.addAtom("C");
        Atom c4 = result.addAtom("C");
        Atom c5 = result.addAtom("C");
        Atom c6 = result.addAtom("N");

        result.connect(c1, c2, 1);
        result.connect(c2, c3, 2);
        result.connect(c3, c4, 1);
        result.connect(c4, c5, 2);
        result.connect(c5, c6, 1);
        result.connect(c6, c1, 2);

        return result;
    }

    public static Molecule createToluene() {
        Molecule result = new DefaultMolecule();
        Atom c1 = result.addAtom("C");
        Atom c2 = result.addAtom("C");
        Atom c3 = result.addAtom("C");
        Atom c4 = result.addAtom("C");
        Atom c5 = result.addAtom("C");
        Atom c6 = result.addAtom("C");
        Atom c7 = result.addAtom("C");

        result.connect(c1, c2, 1);
        result.connect(c2, c3, 2);
        result.connect(c3, c4, 1);
        result.connect(c4, c5, 2);
        result.connect(c5, c6, 1);
        result.connect(c6, c1, 2);
        result.connect(c7, c1, 1);

        return result;
    }

    public static Molecule createPhenol() {
        Molecule result = new DefaultMolecule();
        Atom c1 = result.addAtom("C");
        Atom c2 = result.addAtom("C");
        Atom c3 = result.addAtom("C");
        Atom c4 = result.addAtom("C");
        Atom c5 = result.addAtom("C");
        Atom c6 = result.addAtom("C");
        Atom c7 = result.addAtom("O");

        result.connect(c1, c2, 1);
        result.connect(c2, c3, 2);
        result.connect(c3, c4, 1);
        result.connect(c4, c5, 2);
        result.connect(c5, c6, 1);
        result.connect(c6, c1, 2);
        result.connect(c7, c1, 1);

        return result;
    }

    public static Molecule createNaphthalene() {
        Molecule result = new DefaultMolecule();
        Atom c0 = result.addAtom("C");
        Atom c1 = result.addAtom("C");
        Atom c2 = result.addAtom("C");
        Atom c3 = result.addAtom("C");
        Atom c4 = result.addAtom("C");
        Atom c5 = result.addAtom("C");
        Atom c6 = result.addAtom("C");
        Atom c7 = result.addAtom("C");
        Atom c8 = result.addAtom("C");
        Atom c9 = result.addAtom("C");

        result.connect(c0, c1, 1);
        result.connect(c1, c2, 2);
        result.connect(c2, c3, 1);
        result.connect(c3, c4, 2);
        result.connect(c4, c5, 1);
        result.connect(c5, c0, 2);
        result.connect(c4, c6, 1);
        result.connect(c6, c7, 2);
        result.connect(c7, c8, 1);
        result.connect(c8, c9, 2);
        result.connect(c9, c5, 1);

        return result;
    }

    public static Molecule createAcetone() {
        Molecule result = new DefaultMolecule();
        Atom c0 = result.addAtom("C");
        Atom c1 = result.addAtom("C");
        Atom c2 = result.addAtom("C");
        Atom o3 = result.addAtom("O");

        result.connect(c0, c1, 1);
        result.connect(c1, c2, 1);
        result.connect(c1, o3, 2);

        return result;
    }

    public static Molecule createNeopentane() {
        Molecule result = new DefaultMolecule();
        Atom c0 = result.addAtom("C");
        Atom c1 = result.addAtom("C");
        Atom c2 = result.addAtom("C");
        Atom c3 = result.addAtom("C");
        Atom c4 = result.addAtom("C");

        result.connect(c0, c1, 1);
        result.connect(c0, c2, 1);
        result.connect(c0, c3, 1);
        result.connect(c0, c4, 1);

        return result;
    }
}