SMILESTokenizer.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.jre.emulation.java.util.regex.Pattern;

import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
//import java.util.regex.Matcher;
//import java.util.regex.Pattern;

/**
 * @author Richard L. Apodaca
 *         Duan Lian
 */
public class SMILESTokenizer {
    private static String or = "|";
    private static String element = "[A-Z][a-z]?" + or + "[a-z]";
    private static String bond = "[-=#:\\.]";
    private static String ring = "[1-9]" + or + "\\%[1-9][0-9]";
    private static String bracket = "\\[[^\\]]*\\]";
    private static String parens = "[\\(\\)]";
    private static String regex = element + or + bracket + or + bond + or + ring + or + parens;
    private static Pattern pattern = new Pattern(regex);
    private static Pattern blacklist = new Pattern(".*[^A-Za-z0-9\\(\\)\\[\\]\\-=#:\\.\\%].*");

    private Iterator<String> iterator;

    public SMILESTokenizer(String smiles) {
        assertNoBlacklistedCharacters(smiles);

        List<String> tokens = fragment(smiles);

        this.iterator = tokens.iterator();
    }

    public boolean hasNextToken() {
        return iterator.hasNext();
    }

    public String nextToken() {
        return iterator.next();
    }

    public List<String> fragment(String string) {
//    Matcher matcher = pattern.matcher(string);
//    String[] foundStrings = new String[string.length()];
//    int foundStringCount = 0;
//    int index = 0;
//
//    while (matcher.find(index))
//    {
//      int start = matcher.start();
//      int end = matcher.end();
//
//      if (start == 0 && end == 0)
//      {
//        break;
//      }
//
//      foundStrings[foundStringCount] = string.substring(start, end);
//      index = end;
//      foundStringCount++;
//    }

        String[] foundStrings = pattern.match(string);

        List<String> result = new ArrayList<String>();

        for (int i = 0; i < foundStrings.length; i++) {
            result.add(foundStrings[i]);
        }

        return result;
    }

    private void assertNoBlacklistedCharacters(String smiles) {
        if (blacklist.matches(smiles)) {
            throw new IllegalArgumentException("Invalid SMILES character in \"" + smiles + "\"");
        }
    }
}