moleculebuilder.java

化学图形处理软件

/*  $RCSfile$
 *  $Author: egonw $  
 *  $Date: 2007-01-04 18:46:10 +0100 (Thu, 04 Jan 2007) $  
 *  $Revision: 7636 $
 *
 *   Copyright (C) 2003  University of Manchester
 *   Copyright (C) 2003-2007  The Chemistry Development Kit (CDK) Project
 *
 *   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.util.Iterator;
import java.util.Vector;

import org.openscience.cdk.Atom;
import org.openscience.cdk.Bond;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.Ring;
import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.templates.MoleculeFactory;
import org.openscience.cdk.tools.HydrogenAdder;

/**
 * Takes in parsed Tokens from NomParser and contains rules
 * to convert those tokens to a Molecule.
 *
 * @see Token
 * @author David Robinson
 * @author Bhupinder Sandhu
 * @author Stephen Tomkinson
 *
 * @cdk.require ant1.6
 */
public class MoleculeBuilder
{
    /** The molecule which is worked upon throughout the class and returned at the end */
    private Molecule currentMolecule = new Molecule();
    private org.openscience.cdk.interfaces.IAtom endOfChain;
        
    /**
     * Builds the main chain which may act as a foundation for futher working groups.
     *
     * @param mainChain The parsed prefix which depicts the chain's length.
     * @param isMainCyclic A flag to show if the molecule is a ring. 0 means not a ring, 1 means is a ring.
     * @return A Molecule containing the requested chain.
     */
    private Molecule buildChain(int length, boolean isMainCyclic)
    {
        Molecule currentChain;
        if (length > 0)
        {
            //If is cyclic
            if (isMainCyclic)
            {
                //Rely on CDK's ring class constructor to generate our cyclic molecules.
                currentChain = new Molecule();
                currentChain.add(new Ring(length, "C"));
            } //Else must not be cyclic
            else
            {
                currentChain = MoleculeFactory.makeAlkane(length);
            }
        }
        else
        {
            currentChain = new Molecule();
        }
        
        return currentChain;
    }
    
    /**
     * Initiates the building of the molecules functional group(s).
     * Adds the functional group to atom 0 if only one group exists or runs
     * down the list of positions adding groups as required.
     *
     * @param attachedGroups A vector of AttachedGroup's representing functional groups.
     * @see #addFunGroup
     */
    private void buildFunGroups(Vector attachedGroups)
    {
        Iterator groupsIterator = attachedGroups.iterator();
        while (groupsIterator.hasNext())
        {
            AttachedGroup attachedGroup = (AttachedGroup) groupsIterator.next();
            
            Iterator locationsIterator = attachedGroup.getLocations().iterator();
            while (locationsIterator.hasNext())
            {
                Token locationToken = (Token) locationsIterator.next();
                addFunGroup(attachedGroup.getName(), Integer.parseInt(locationToken.image) - 1);
            }
        }
    }
    
    /**
     * Adds a functional group to a given atom in the current molecule.
     *
     * @param funGroupToken The token which denotes this specific functional group.
     * @param addPos The atom to add the group to.
     */
    private void addFunGroup(String funGroupToken, int addPos)
    {
        //BOND MODIFICATION
        //Alkanes - Single bond
        if (funGroupToken == "an")
        {
            //Do nothing since all bonds are single by default.
        }
        //Alkenes - Double bond
        else if (funGroupToken == "en")
        {
            //If functional group hasn't had a location specified:
            if (addPos < 0)
            {
                //Set the first bond to an order of 2 (i.e. a double bond)
                currentMolecule.getBond(0).setOrder(2.0);
            }
            else
            {
                //Set the addPos'th bond to an order of 2 (i.e. a double bond)
                currentMolecule.getBond(addPos).setOrder(2.0);
            }
        }
        //Alkynes - Tripple bond
        else if (funGroupToken == "yn")
        {
            //If functional group hasn't had a location specified:
            if (addPos < 0)
            {
                //Set the first bond to an order of 3 (i.e. a tripple bond)
                currentMolecule.getBond(0).setOrder(3.0);
            }
            else
            {
                //Set the addPos'th bond to an order of 3 (i.e. a tripple bond)
                currentMolecule.getBond(addPos).setOrder(3.0);
            }
        }
        //FUNCTIONAL GROUP SUFFIXES
        //Ending "e"
        else if (funGroupToken == "e")
        {
            //Do nothing, since the "e" is found at the end of chain names
            //with a bond modifer but no functional groups.
        }
        //Alcohols
        else if (funGroupToken == "ol" || funGroupToken == "hydroxy")
        {
            //If functional group hasn't had a location specified:
            if (addPos < 0)
            {
                addAtom("O", endOfChain, 1.0, 1);
            }
            else
            {
                addAtom("O", currentMolecule.getAtom(addPos), 1.0, 1);
            }
        }
        //Aldehydes
        else if (funGroupToken == "al")
        {
            addAtom("O", endOfChain, 2.0, 0);
        }
        //Carboxylic acid
        else if (funGroupToken == "oic acid")
        {
            addAtom("O", endOfChain, 2.0, 0);
            addAtom("O", endOfChain, 1.0, 1);
        }
        //Carboxylic Acid Chloride
        else if (funGroupToken == "oyl chloride")
        {
            addAtom("O", endOfChain, 2.0, 0);
            addAtom("Cl", endOfChain, 1.0, 0);
        }
        //PREFIXES
        //Halogens
        //Chlorine
        else if (funGroupToken == "chloro")
        {
            //If functional group hasn't had a location specified:
            if (addPos < 0)
            {
                addAtom("Cl", currentMolecule.getFirstAtom(), 1.0, 0);
            }
            else
            {
                addAtom("Cl", currentMolecule.getAtom(addPos), 1.0, 0);
            }
        }
        //Fluorine
        else if (funGroupToken == "fluoro")
        {
            //If functional group hasn't had a location specified:
            if (addPos < 0)
            {
                addAtom("F", currentMolecule.getFirstAtom(), 1.0, 0);
            }
            else
            {
                addAtom("F", currentMolecule.getAtom(addPos), 1.0, 0);
            }
        }
        //Bromine
        else if (funGroupToken == "bromo")
        {
            //If functional group hasn't had a location specified:
            if (addPos < 0)
            {
                addAtom("Br", currentMolecule.getFirstAtom(), 1.0, 0);
            }
            else
            {
                addAtom("Br", currentMolecule.getAtom(addPos), 1.0, 0);
            }
        }
        //Iodine
        else if (funGroupToken == "iodo")
        {
            //If functional group hasn't had a location specified:
            if (addPos < 0)
            {
                addAtom("I", currentMolecule.getFirstAtom(), 1.0, 0);
            }
            else
            {
                addAtom("I", currentMolecule.getAtom(addPos), 1.0, 0);
            }
        }
        //Nitro
        else if (funGroupToken == "nitro")
        {
            //If functional group hasn't had a location specified:
            if (addPos < 0)
            {
                addAtom("N", currentMolecule.getFirstAtom(), 1.0, 0);
            }
            else
            {
                addAtom("N", currentMolecule.getAtom(addPos), 1.0, 0);
            }
            
            //Stuff which applied no matter where the N atom is:
            org.openscience.cdk.interfaces.IAtom nitrogenAtom = currentMolecule.getLastAtom();
            nitrogenAtom.setFormalCharge(+1);
            addAtom("O", nitrogenAtom, 1.0, 0);
            currentMolecule.getLastAtom().setFormalCharge(-1);
            addAtom("O", nitrogenAtom, 2.0, 0);
        }
        //Oxo
        else if (funGroupToken == "oxo")
        {
            //If functional group hasn't had a location specified:
            if (addPos < 0)
            {
                addAtom("O", currentMolecule.getFirstAtom(), 2.0, 0);
            }