saturationchecker.java

化学图形处理软件

/*  $RCSfile$
 *  $Author: egonw $
 *  $Date: 2007-03-14 18:33:52 +0100 (Wed, 14 Mar 2007) $
 *  $Revision: 8121 $
 *
 *  Copyright (C) 2001-2007  The Chemistry Development Kit (CDK) project
 *
 *  Contact: [e-mail]
 *
 *  This program 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.
 *  All we ask is that proper credit is given for our work, which includes
 *  - but is not limited to - adding the above copyright notice to the beginning
 *  of your source code files, and to any copyright notice that you may distribute
 *  with programs based on this work.
 *
 *  This program 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 program; if not, write to the Free Software
 *  Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
 *
 */
package org.openscience.cdk.tools;

import java.io.IOException;
import java.util.Iterator;
import java.util.List;

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.config.AtomTypeFactory;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IPseudoAtom;
import org.openscience.cdk.interfaces.IRingSet;
import org.openscience.cdk.ringsearch.RingPartitioner;
import org.openscience.cdk.ringsearch.SSSRFinder;
import org.openscience.cdk.tools.manipulator.BondManipulator;
import org.openscience.cdk.tools.manipulator.RingSetManipulator;

/**
 * Provides methods for checking whether an atoms valences are saturated with
 * respect to a particular atom type.
 *
 * <p>Important: this class does not deal with hybridization states, which makes
 * it fail, for example, for situations where bonds are marked as aromatic (either
 * 1.5 or single an AROMATIC).
 *
 * @author     steinbeck
 * @author  Egon Willighagen
 * @cdk.created    2001-09-04
 *
 * @cdk.keyword    saturation
 * @cdk.keyword    atom, valency
 * 
 * @cdk.module     valencycheck
 */
public class SaturationChecker implements IValencyChecker, IDeduceBondOrderTool {

	AtomTypeFactory structgenATF;

	private LoggingTool logger;

	public SaturationChecker() throws IOException, ClassNotFoundException
	{
		logger = new LoggingTool(this);
	}

    /**
     * @param builder the ChemObjectBuilder implementation used to construct the AtomType's.
     */
    protected AtomTypeFactory getAtomTypeFactory(IChemObjectBuilder builder) throws CDKException {
        if (structgenATF == null) {
            try {
                structgenATF = AtomTypeFactory.getInstance(
                    "org/openscience/cdk/config/data/structgen_atomtypes.xml", 
                    builder
                );
            } catch (Exception exception) {
                logger.debug(exception);
                throw new CDKException("Could not instantiate AtomTypeFactory!", exception);
            }
        }
        return structgenATF;
    }

	public boolean hasPerfectConfiguration(IAtom atom, IAtomContainer ac) throws CDKException
	{
		double bondOrderSum = ac.getBondOrderSum(atom);
		double maxBondOrder = ac.getMaximumBondOrder(atom);
		IAtomType[] atomTypes = getAtomTypeFactory(atom.getBuilder()).getAtomTypes(atom.getSymbol());
    if(atomTypes.length==0)
      return true;
		logger.debug("*** Checking for perfect configuration ***");
		try
		{
			logger.debug("Checking configuration of atom " + ac.getAtomNumber(atom));
			logger.debug("Atom has bondOrderSum = " + bondOrderSum);
			logger.debug("Atom has max = " + bondOrderSum);
		} catch (Exception exc)
		{
		}
		for (int f = 0; f < atomTypes.length; f++)
		{
			if (bondOrderSum == atomTypes[f].getBondOrderSum() && 
                maxBondOrder == atomTypes[f].getMaxBondOrder())
			{
				try
				{
					logger.debug("Atom " + ac.getAtomNumber(atom) + " has perfect configuration");
				} catch (Exception exc)
				{
				}
				return true;
			}
		}
		try
		{
			logger.debug("*** Atom " + ac.getAtomNumber(atom) + " has imperfect configuration ***");
		} catch (Exception exc)
		{
		}
		return false;
	}

    /**
     * Determines of all atoms on the AtomContainer are saturated.
     */
	public boolean isSaturated(IAtomContainer container) throws CDKException {
        return allSaturated(container);
    }
	public boolean allSaturated(IAtomContainer ac) throws CDKException
	{
        logger.debug("Are all atoms saturated?");
        for (int f = 0; f < ac.getAtomCount(); f++) {
            if (!isSaturated(ac.getAtom(f), ac)) {
                return false;
            }
        }
        return true;
    }

    /**
     * Returns wether a bond is unsaturated. A bond is unsaturated if 
     * <b>both</b> Atoms in the bond are unsaturated.
     */
    public boolean isUnsaturated(IBond bond, IAtomContainer atomContainer) throws CDKException {

    	IAtom[] atoms = BondManipulator.getAtomArray(bond);
        boolean isUnsaturated = true;
        for (int i=0; i<atoms.length; i++) {
            isUnsaturated = isUnsaturated && !isSaturated(atoms[i], atomContainer);
        }
        return isUnsaturated;
    }
    
    /**
     * Returns wether a bond is saturated. A bond is saturated if 
     * <b>both</b> Atoms in the bond are saturated.
     */
    public boolean isSaturated(IBond bond, IAtomContainer atomContainer) throws CDKException {
    	IAtom[] atoms = BondManipulator.getAtomArray(bond);
        boolean isSaturated = true;
        for (int i=0; i<atoms.length; i++) {
            isSaturated = isSaturated && isSaturated(atoms[i], atomContainer);
        }
        return isSaturated;
    }
    
    /**
     * Checks wether an Atom is saturated by comparing it with known AtomTypes.
     */
	public boolean isSaturated(IAtom atom, IAtomContainer ac) throws CDKException {
		IAtomType[] atomTypes = getAtomTypeFactory(atom.getBuilder()).getAtomTypes(atom.getSymbol());
        if(atomTypes.length==0)
          return true;
        double bondOrderSum = ac.getBondOrderSum(atom);
        double maxBondOrder = ac.getMaximumBondOrder(atom);
        int hcount = atom.getHydrogenCount();
        int charge = atom.getFormalCharge();
        try {
            logger.debug("*** Checking saturation of atom ", atom.getSymbol(), "" + ac.getAtomNumber(atom) + " ***");
            logger.debug("bondOrderSum: " + bondOrderSum);
            logger.debug("maxBondOrder: " + maxBondOrder);
            logger.debug("hcount: " + hcount);
        } catch (Exception exc) {
            logger.debug(exc);
        }
        for (int f = 0; f < atomTypes.length; f++) {
            if (bondOrderSum - charge + hcount == atomTypes[f].getBondOrderSum() && 
                maxBondOrder <= atomTypes[f].getMaxBondOrder()) {
                    logger.debug("*** Good ! ***");
                    return true;
                }
        }
        logger.debug("*** Bad ! ***");
        return false;
    }

	/**
	 * Checks if the current atom has exceeded its bond order sum value.
	 *
	 * @param  atom The Atom to check
	 * @param  ac   The atomcontainer context
	 * @return      oversaturated or not
	 */
	public boolean isOverSaturated(IAtom atom, IAtomContainer ac) throws CDKException
	{
		IAtomType[] atomTypes = getAtomTypeFactory(atom.getBuilder()).getAtomTypes(atom.getSymbol());
    if(atomTypes.length==0)
      return false;
		double bondOrderSum = ac.getBondOrderSum(atom);
		double maxBondOrder = ac.getMaximumBondOrder(atom);
		int hcount = atom.getHydrogenCount();
		int charge = atom.getFormalCharge();
		try
		{
			logger.debug("*** Checking saturation of atom " + ac.getAtomNumber(atom) + " ***");
			logger.debug("bondOrderSum: " + bondOrderSum);
			logger.debug("maxBondOrder: " + maxBondOrder);
			logger.debug("hcount: " + hcount);
		} catch (Exception exc)
		{
		}
		for (int f = 0; f < atomTypes.length; f++)
		{
			if (bondOrderSum - charge + hcount > atomTypes[f].getBondOrderSum())
			{
				logger.debug("*** Good ! ***");
				return true;
			}
		}
		logger.debug("*** Bad ! ***");
		return false;
	}
    
	/**
	 * Returns the currently maximum formable bond order for this atom.
	 *
	 * @param  atom  The atom to be checked
	 * @param  ac    The AtomContainer that provides the context
	 * @return       the currently maximum formable bond order for this atom
	 */
	public double getCurrentMaxBondOrder(IAtom atom, IAtomContainer ac) throws CDKException
	{
		IAtomType[] atomTypes = getAtomTypeFactory(atom.getBuilder()).getAtomTypes(atom.getSymbol());
    if(atomTypes.length==0)
      return 0;
		double bondOrderSum = ac.getBondOrderSum(atom);
		int hcount = atom.getHydrogenCount();
		double max = 0;
		double current = 0;
		for (int f = 0; f < atomTypes.length; f++)
		{
			current = hcount + bondOrderSum;
			if (atomTypes[f].getBondOrderSum() - current > max)
			{
				max = atomTypes[f].getBondOrderSum() - current;
			}
		}
		return max;
	}


    /**
     * Resets the bond orders of all atoms to 1.0.
     */
    public void unsaturate(IAtomContainer atomContainer) {
    	Iterator bonds = atomContainer.bonds();
    	while (bonds.hasNext()) {
    		((IBond)bonds.next()).setOrder(CDKConstants.BONDORDER_SINGLE);
    	}
    }
    
    /**
     * Resets the bond order of the Bond to 1.0.
     */
    public void unsaturateBonds(IAtomContainer container) {
    	Iterator bonds = container.bonds();
        while (bonds.hasNext()) ((IBond)bonds.next()).setOrder(1.0);
    }

	/**
	 * Saturates a molecule by setting appropriate bond orders.
	 * This method is known to fail, especially on pyrolle-like compounts.
	 * Consider using import org.openscience.cdk.smiles.DeduceBondSystemTool, which should work better
	 *
	 * @cdk.keyword bond order, calculation
     * @cdk.created 2003-10-03
	 */
    public void newSaturate(IAtomContainer atomContainer) throws CDKException {
        logger.info("Saturating atomContainer by adjusting bond orders...");
        boolean allSaturated = allSaturated(atomContainer);
        if (!allSaturated) {
        	IBond[] bonds = new IBond[atomContainer.getBondCount()];
        	for (int i=0; i<bonds.length; i++) bonds[i] = atomContainer.getBond(i);
            boolean succeeded = newSaturate(bonds, atomContainer);
            for(int i=0;i<bonds.length;i++){
              if(bonds[i].getOrder()==2 && bonds[i].getFlag(CDKConstants.ISAROMATIC) && (bonds[i].getAtom(0).getSymbol().equals("N") && bonds[i].getAtom(1).getSymbol().equals("N"))){
                int atomtohandle=0;
                if(bonds[i].getAtom(0).getSymbol().equals("N"))
                  atomtohandle=1;
                java.util.List bondstohandle=atomContainer.getConnectedBondsList(bonds[i].getAtom(atomtohandle));
                for(int k=0;k<bondstohandle.size();k++){
                	IBond bond = (IBond)bondstohandle.get(k);
                  if(bond.getOrder()==1 && bond.getFlag(CDKConstants.ISAROMATIC)){
                    bond.setOrder(2);
                    bonds[i].setOrder(1);
                    break;
                  }
                }
              }
            }
            if (!succeeded) {
                throw new CDKException("Could not saturate this atomContainer!");
            }
        }
    }

    /**
     * Saturates a set of Bonds in an AtomContainer.
	 * This method is known to fail, especially on pyrolle-like compounts.
	 * Consider using import org.openscience.cdk.smiles.DeduceBondSystemTool, which should work better
     */
    public boolean newSaturate(IBond[] bonds, IAtomContainer atomContainer) throws CDKException {
        logger.debug("Saturating bond set of size: " + bonds.length);
        boolean bondsAreFullySaturated = true;
        if (bonds.length > 0) {
        	IBond bond = bonds[0];

            // determine bonds left
            int leftBondCount = bonds.length-1;
            IBond[] leftBonds = new IBond[leftBondCount];
            System.arraycopy(bonds, 1, leftBonds, 0, leftBondCount);

            // examine this bond
            if (isUnsaturated(bond, atomContainer)) {
                // either this bonds should be saturated or not