SMILESReader.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.daylight;

import com.chemhack.jsMolEditor.client.model.DefaultMolecule;
import com.chemhack.jsMolEditor.client.model.Molecule;
//import java.util.regex.Pattern;

/**
 * @author Richard L. Apodaca
 *         Duan Lian
 */
public class SMILESReader {
    private static SMILESReader staticReader = new SMILESReader();
    private static String SINGLE_BOND = "-";
    private static String DOUBLE_BOND = "=";
    private static String TRIPLE_BOND = "#";
//  private static Pattern atomPattern = Pattern.compile("^(([A-Z][a-z]?)|[a-z])");
//  private static Pattern bondPattern = Pattern.compile("[-=#:\\.]");
    //  private static Pattern ringIdentifierPattern = Pattern.compile("[1-9]|\\%[1-9][0-9]");
    private static String openParen = "(";
    private static String closeParen = ")";

    public SMILESReader() {

    }

    public void read(Molecule molecule, String smiles) {
        SMILESTokenizer tokenizer = new SMILESTokenizer(smiles);
        SMILESBuilder builder = new SMILESBuilder(molecule);

        while (tokenizer.hasNextToken()) {
            String token = tokenizer.nextToken();

            handleToken(token, builder);
        }
    }

    public static Molecule read(String smiles) {
        Molecule result = new DefaultMolecule();

        staticReader.read(result, smiles);

        return result;
    }

    private void handleToken(String token, SMILESBuilder builder) {
        if (token.matches("^(([A-Z][a-z]?)|[a-z])")) {
            handleAtom(token, builder);

            return;
        }

        if (token.matches("[1-9]|\\%[1-9][0-9]")) {
            handleRingIdentifier(token, builder);

            return;
        }

        if (openParen.equals(token)) {
            builder.openBranch();

            return;
        }

        if (closeParen.equals(token)) {
            builder.closeBranch();

            return;
        }

        if (token.matches("[-=#:\\.]")) {
            handleBond(token, builder);

            return;
        }

        throw new IllegalArgumentException("Unknown SMILES token \"" + token + "\"");
    }

    private void handleAtom(String token, SMILESBuilder builder) {
        builder.addHead(token);
    }

    private void handleBond(String token, SMILESBuilder builder) {
        int type = 0;

        if (SINGLE_BOND.equals(token)) {
            type = 1;
        }

        if (DOUBLE_BOND.equals(token)) {
            type = 2;
        }

        if (TRIPLE_BOND.equals(token)) {
            type = 3;
        }

        builder.addBond(type);
    }

    private void handleRingIdentifier(String token, SMILESBuilder builder) {
        builder.ring(token);
    }
}