nomparser.java

化学图形处理软件

/* Generated By:JavaCC: Do not edit this line. NomParser.java */
/*
 *   Copyright (C) 2003-2007  University of Manchester
 *
 *   This library is free software; you can redistribute it and/or
 *   modify it under the terms of the GNU Lesser General Public
 *   License as published by the Free Software Foundation; either
 *   version 2.1 of the License, or (at your option) any later version.
 *
 *   This library is distributed in the hope that it will be useful,
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 *   Lesser General Public License for more details.
 *
 *   You should have received a copy of the GNU Lesser General Public
 *   License along with this library; if not, write to the Free Software
 *   Foundation, 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. 
 *   (or see http://www.gnu.org/copyleft/lesser.html)
 */
package org.openscience.cdk.iupac.parser;

import java.io.StringReader;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.exception.*;
import java.util.*;

/**
 * A class partly generated by <a href="http://javacc.dev.java.net" target="_top">JavaCC</a> which breaks down the chemical name
 * into computable subparts and passes these parts to the MoleculeBuilder.
 *
 * @author David Robinson (University of Manchester)
 * @author Bhupinder Sandhu
 * @author Stephen Tomkinson
 *
 * @cdk.keyword IUPAC name
 */
public class NomParser implements NomParserConstants {
    //private variables needed throughout the program
    private static int mainChainPrefix;
    private static boolean isMainCyclic;

    /** The tempory vector of locations the current group/substiuant is attached to */
    private static Vector tempLocation;

    /** The vector of attached functional groups, with an instance of AttachedGroup for each
     * functional group.
     */
    private static Vector attachedGroups;

    /** The vector of attached substituent, with an instance of AttachedGroup for each
     * substituent.
     */
    private static Vector attachedSubstituents;

    /**
     * Used in the build up of ancient greek style prfixes
     */
    private static int currentNumber;

    /**
     * Parses the chemical name and returns the built molecule.
     *
     * @param stringToParse A case-insensitive name of the chemical to build.
     * @return A molecule which represents the interpretatation of the name.
     * @throws ParseException Any error which occur in the parsing get wrapped
     * up in a ParseException and thrown.
     */
    public static Molecule generate (String stringToParse) throws ParseException, CDKException
    {
        isMainCyclic = false;
        tempLocation = new Vector();
        attachedSubstituents = new Vector();
        attachedGroups = new Vector();
        currentNumber = 0;

        StringReader stringReader = new StringReader (stringToParse.toLowerCase() + "\n");
        NomParser parser = new NomParser (stringReader);
        parser.completeChemicalName();

        //Scan substituents for a too high connection point
        checkConnections (attachedSubstituents.iterator());

        //Scan functional groups for a too high connection point
        checkConnections (attachedGroups.iterator());

        MoleculeBuilder moleculeBuilder = new MoleculeBuilder();
        Molecule returnedMolecule = moleculeBuilder.buildMolecule(mainChainPrefix, attachedSubstituents, attachedGroups, isMainCyclic, stringToParse);

        return returnedMolecule;
    }

    /**
     * Checks to ensure that all groups/substituents attached to the main chain
     * are connected to a valid atom which occurs on the main chain.
     *
     * @param vectorIterator An iterator which provides instances of AttachedGroup to check
     * @throws ParseException A taylored instance of ParseException so nomen can display
     * the error to the user.
     */
    private static void checkConnections (Iterator vectorIterator) throws ParseException
    {
        while (vectorIterator.hasNext())
        {
            AttachedGroup ag = (AttachedGroup) vectorIterator.next();
            Vector locations = ag.getLocations();

            Iterator locationsIterator = locations.iterator();
            while (locationsIterator.hasNext())
            {
                Token tok = (Token) locationsIterator.next();

                try
                {
                    if (Integer.parseInt(tok.image) > mainChainPrefix)
                    {
                        //Create a tiny 2D array with a single slot for data, 
                        //insert 0 into it as as to reference the first slot in the stringArray
                        int [][] intArray = new int [1][1];
                        intArray [0][0] = 0;

                        //Put useful message in stringArray
                        String [] stringArray = new String [1];
                        stringArray [0] = " MUST BE BELOW " + (mainChainPrefix + 1) + " ";

                        tok.next = tok;

                        throw new ParseException (tok, intArray, stringArray);
                    }
                }
                catch (NumberFormatException nfe)
                {
                    //Do nothing, as this should never happen
                }
            }
        }
    }

/**
 * Stores "head tokens", the substituent prefix, in a vector of AttachedGroup objects.
 */
  void AddHeadToken() throws ParseException {
    attachedSubstituents.add (new AttachedGroup (tempLocation, currentNumber) );
    tempLocation = new Vector();
  }

  void MakeMainChainIntoSubstituent() throws ParseException {
    attachedSubstituents.add (new AttachedGroup (tempLocation, mainChainPrefix) );
    currentNumber = 0;
    mainChainPrefix = 0;
    tempLocation = new Vector();
  }

/**
 * Stores the functional groups in a vector of AttachedGroup objects.
 */
  void AddFunGroup() throws ParseException {
    Token tok;
    tok = getToken(-1);
    attachedGroups.add (new AttachedGroup (tempLocation, tok.image) );
    tempLocation = new Vector();
  }

/**
* Stores the functional group positions, the number of the atom they 
* connect to, in an array.
*/
  void AddFunGroupPos() throws ParseException {
    Token tok;
    tok = getToken(-1);
    tempLocation.add(tok);
  }

/**
* Adds to the position array a location of -1 to indicate no location was
* specified.
*/
  void AddUnknownFunGroupPos() throws ParseException {
    Token tok = new Token();
    tok.image = "-1";
    tempLocation.add(tok);
  }

/**
 * Store the mainChainPrefix token, the chain prefix of the longest carbon chain
 */
  void AddMainChain() throws ParseException {
    mainChainPrefix = currentNumber;
    currentNumber = 0;
  }

/**
 * Sets the main chain to be cyclic.
 */
  void SetMainCyclic() throws ParseException {
    isMainCyclic = true;
  }

/**
 * The general form all chemical names must follow.
 */
  final public void completeChemicalName() throws ParseException {
    if (jj_2_1(2)) {
      mainChainConstruct();
    } else {
      prefixConstruct();
      mainChainConstruct();
      jj_consume_token(EOL);
    }
  }

/**
 * Allows 1 or more prefixes
 */
  final public void prefixConstruct() throws ParseException {
    prefixType();
    label_1:
    while (true) {
      switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
      case DASH:
        ;
        break;
      default:
        jj_la1[0] = jj_gen;
        break label_1;
      }
      jj_consume_token(DASH);
      prefixType();
    }
  }

  final public void prefixType() throws ParseException {
    switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
    case CONSTANT:
      attachLocationSpecified();
      break;
    default:
      jj_la1[1] = jj_gen;
      AddUnknownFunGroupPos();
    }
    switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
    case METH:
    case ETH:
    case PROP:
    case BUT:
    case UNDEC:
    case EICOS:
    case HENICOS:
    case HEN:
    case DO:
    case TRI:
    case TETR:
    case PENT:
    case HEX:
    case HEPT:
    case OCT:
    case NON:
    case DEC:
      subChain();
      break;
    case CHLORO:
    case FLUORO:
    case BROMO:
    case IODO:
    case NITRO:
    case OXO:
    case PHENYL:
    case AMINO:
    case HYDROXY:
      functionalGroupPrefix();
      break;
    default:
      jj_la1[2] = jj_gen;
      jj_consume_token(-1);
      throw new ParseException();
    }
  }

/** The substituent part of the prefix */
  final public void subChain() throws ParseException {
    chainPrefix();
    AddHeadToken();
    jj_consume_token(YL);
  }

/** 
 * An attach position has been specified using a 
 * comma seperated list followed by a dash
 */
  final public void attachLocationSpecified() throws ParseException {
    jj_consume_token(CONSTANT);
    AddFunGroupPos();
    switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
    case DASH:
      oneAttachLocation();
      break;
    case COMMA:
      twoOrThreeAttachLocations();
      break;
    default:
      jj_la1[3] = jj_gen;
      jj_consume_token(-1);
      throw new ParseException();
    }
  }

/**
 * Only one attach location specified, should be followed by a dash.
 */
  final public void oneAttachLocation() throws ParseException {
    jj_consume_token(DASH);
  }

/**
 * Two or three attach locations specidied, handle the second and if needed, the third one here.
 */
  final public void twoOrThreeAttachLocations() throws ParseException {
    jj_consume_token(COMMA);
    jj_consume_token(CONSTANT);
    AddFunGroupPos();
    switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
    case DASH:
      jj_consume_token(DASH);
      jj_consume_token(DI);
      break;
    case COMMA:
      jj_consume_token(COMMA);
      jj_consume_token(CONSTANT);
      AddFunGroupPos();
      jj_consume_token(DASH);
      jj_consume_token(TRI);
      break;
    default:
      jj_la1[4] = jj_gen;
      jj_consume_token(-1);
      throw new ParseException();
    }
  }

/**
 * A list of known tokens denoting a chain's length.
 */
  final public void chainPrefix() throws ParseException {
    switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
    case METH:
    case ETH:
    case PROP:
    case BUT:
    case UNDEC:
    case EICOS:
    case HENICOS:
    case DEC:
      specialCase();
      break;
    case HEN:
    case DO:
    case TRI:
    case TETR:
    case PENT:
    case HEX:
    case HEPT:
    case OCT:
    case NON:
      allBaseNumbers();
      switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
      case HEN:
      case DO:
      case TRI:
      case TETR:
      case PENT:
      case HEX:
      case HEPT:
      case OCT:
      case NON:
      case DEC:
      case COS:
      case CONT:
        switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
        case HEN:
        case DO:
        case TRI:
        case TETR:
        case PENT:
        case HEX:
        case HEPT:
        case OCT:
        case NON:
          tensWithUnits();
          break;
        case DEC:
        case COS:
        case CONT:
          tensNoUnits();
          break;
        default:
          jj_la1[5] = jj_gen;
          jj_consume_token(-1);
          throw new ParseException();
        }
        break;
      default:
        jj_la1[6] = jj_gen;
        ;
      }
      break;
    default:
      jj_la1[7] = jj_gen;
      jj_consume_token(-1);
      throw new ParseException();
    }
  }

/** Deal with special cases where the rules don't apply. */
  final public void specialCase() throws ParseException {
    switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
    case METH:
      jj_consume_token(METH);
              currentNumber = 1;
      break;
    case ETH:
      jj_consume_token(ETH);
             currentNumber = 2;
      break;
    case PROP:
      jj_consume_token(PROP);
              currentNumber = 3;
      break;
    case BUT:
      jj_consume_token(BUT);
             currentNumber = 4;
      break;
    case DEC:
      jj_consume_token(DEC);
             currentNumber = 10;
      break;
    case UNDEC:
      jj_consume_token(UNDEC);
               currentNumber = 11;
      break;
    case EICOS:
      jj_consume_token(EICOS);
               currentNumber = 20;
      break;
    case HENICOS:
      jj_consume_token(HENICOS);
                 currentNumber = 21;
      break;
    default:
      jj_la1[8] = jj_gen;
      jj_consume_token(-1);
      throw new ParseException();
    }
  }

/** The usual numbers .*/
  final public void allBaseNumbers() throws ParseException {
    switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
    case HEN:
      jj_consume_token(HEN);
             currentNumber = 1;
      break;
    case DO:
      jj_consume_token(DO);
            currentNumber = 2;
      break;
    case TRI:
      jj_consume_token(TRI);
             currentNumber = 3;
      break;
    case TETR:
      jj_consume_token(TETR);
              currentNumber = 4;
      break;
    case PENT:
      jj_consume_token(PENT);
              currentNumber = 5;
      break;
    case HEX:
      jj_consume_token(HEX);
             currentNumber = 6;
      break;
    case HEPT:
      jj_consume_token(HEPT);
              currentNumber = 7;
      break;
    case OCT:
      jj_consume_token(OCT);
             currentNumber = 8;
      break;
    case NON:
      jj_consume_token(NON);
             currentNumber = 9;
      break;
    default:
      jj_la1[9] = jj_gen;
      jj_consume_token(-1);
      throw new ParseException();
    }
  }

/** Deal with fragments refering to the positioning of the base numbers (denoting their magnitude) */
  final public void tensNoUnits() throws ParseException {
    switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
    case DEC:
      jj_consume_token(DEC);
            currentNumber += 10;
      break;
    case COS:
      jj_consume_token(COS);
            currentNumber += 20;
      break;
    case CONT:
      jj_consume_token(CONT);
             currentNumber *= 10;
      break;
    default:
      jj_la1[10] = jj_gen;
      jj_consume_token(-1);
      throw new ParseException();
    }
  }

/** 
 * Deals with numbers above 30 where the base numbers set appear twice.
 * For example, in the tens and the units. */
  final public void tensWithUnits() throws ParseException {
    int tempBackup;
      tempBackup = currentNumber;
    allBaseNumbers();
    jj_consume_token(CONT);
      currentNumber *= 10; currentNumber += tempBackup;
  }

/** The functional group part of the prefix */
  final public void functionalGroupPrefix() throws ParseException {
    prefixFunctionalGroups();
    AddFunGroup();
  }

/**
 * Main chains are compulsary and consist of an optional "cyclo", a length prefix and
 * a posfix denoting functional groups.
 */
  final public void mainChainConstruct() throws ParseException {
    switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
    case CYCLO:
      cycle();
      break;
    default:
      jj_la1[11] = jj_gen;
      ;
    }
    mainChainPrefix();
    switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
    case YL:
      jj_consume_token(YL);
      AddUnknownFunGroupPos();
      MakeMainChainIntoSubstituent();
      switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
      case LITHIUM:
      case SODIUM:
      case POTASSIUM:
      case RUBIDIUM:
      case CESIUM:
      case FRANCIUM:
      case BERYLLIUM:
      case MAGNESIUM:
      case CALCIUM:
      case STRONTIUM:
      case BARIUM:
      case RADIUM:
      case SCANDIUM:
      case YTTRIUM:
      case LANTHANUM:
      case ACTINIUM:
      case TITANIUM:
      case ZIRCONIUM:
      case HAFNIUM:
      case RUTHERFORDIUM:
      case VANADIUM:
      case NIOBIUM:
      case TANTALUM:
      case DUBNIUM:
      case CHROMIUM:
      case MOLYBDENUM:
      case TUNGSTEN:
      case SEABORGIUM:
      case MANGANESE:
      case TECHNETIUM:
      case RHENIUM:
      case BOHRIUM:
      case IRON:
      case RUTHENIUM:
      case OSMIUM:
      case HASSIUM:
      case COBALT:
      case RHODIUM:
      case IRIDIUM:
      case MEITMERIUM:
      case NICKEL:
      case PALLADIUM:
      case PLATINUM:
      case COPPER:
      case SILVER:
      case GOLD:
      case ZINC:
      case CADMIUM:
      case MECURY:
      case ALUMINIUM:
      case GALLIUM:
      case INDIUM:
      case THALLIUM:
      case GERMAINIUM:
      case TIN:
      case LEAD:
      case ARSENIC:
      case ANTIMONY:
      case BISMUTH:
      case SELENIUM:
      case TELLURIUM:
      case POLONIUM:
      case CERIUM:
      case PRASEODYMIUM:
      case NEODYMIUM:
      case PROMETHIUM:
      case SANARIUM:
      case EUROPIUM:
      case GADOLINIUM: