smilesvalencychecker.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) 2004-2007  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 org.openscience.cdk.CDKConstants;
import org.openscience.cdk.config.AtomTypeFactory;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.*;
import org.openscience.cdk.tools.manipulator.BondManipulator;

/**
 * Small customization of ValencyHybridChecker suggested by Todd Martin
 * specially tuned for SMILES parsing.
 *
 * @author       Egon Willighagen
 * @cdk.created  2004-06-12
 * @cdk.keyword  atom, valency
 * @cdk.module   valencycheck
 */
public class SmilesValencyChecker implements IValencyChecker, IDeduceBondOrderTool {

	private String atomTypeList = null;
	protected AtomTypeFactory structgenATF;
	protected LoggingTool logger;

	public SmilesValencyChecker() {
        this("org/openscience/cdk/config/data/hybridization_atomtypes.xml");
    }

	public SmilesValencyChecker(String atomTypeList) {
        this.atomTypeList = atomTypeList;
        logger = new LoggingTool(this);
        logger.info("Using configuration file: ", atomTypeList);
    }

	/**
	 * Saturates a molecule by setting appropriate bond orders.
	 *
	 * @cdk.keyword            bond order, calculation
     *
     * @cdk.created 2003-10-03
	 */
    public void saturate(IAtomContainer atomContainer) throws CDKException {
        logger.info("Saturating atomContainer by adjusting bond orders...");
        boolean allSaturated = allSaturated(atomContainer);
        if (!allSaturated) {
            logger.info("Saturating bond orders is needed...");
            IBond[] bonds = new IBond[atomContainer.getBondCount()];
        	for (int i=0; i<bonds.length; i++) bonds[i] = atomContainer.getBond(i);
            boolean succeeded = saturate(bonds, atomContainer);
            if (!succeeded) {
                throw new CDKException("Could not saturate this atomContainer!");
            }
        }
    }

    /**
     * Saturates a set of Bonds in an AtomContainer.
     */
    public boolean saturate(IBond[] bonds, IAtomContainer atomContainer) throws CDKException {
        logger.debug("Saturating bond set of size: ", bonds.length);
        boolean bondsAreFullySaturated = false;
        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
            logger.debug("Examining this bond: ", bond);
            if (isSaturated(bond, atomContainer)) {
                logger.debug("OK, bond is saturated, now try to saturate remaining bonds (if needed)");
                bondsAreFullySaturated = saturate(leftBonds, atomContainer);
            } else if (isUnsaturated(bond, atomContainer)) {
                logger.debug("Ok, this bond is unsaturated, and can be saturated");
                // two options now: 
                // 1. saturate this one directly
                // 2. saturate this one by saturating the rest
                logger.debug("Option 1: Saturating this bond directly, then trying to saturate rest");
                // considering organic bonds, the max order is 3, so increase twice
                double increment = 1.0;
                boolean bondOrderIncreased = saturateByIncreasingBondOrder(bond, atomContainer, increment);
                bondsAreFullySaturated = bondOrderIncreased && saturate(bonds, atomContainer);
                if (bondsAreFullySaturated) {
                    logger.debug("Option 1: worked");
                } else {
                    logger.debug("Option 1: failed. Trying option 2.");
                    logger.debug("Option 2: Saturing this bond by saturating the rest");
                    // revert the increase (if succeeded), then saturate the rest
                    if (bondOrderIncreased) unsaturateByDecreasingBondOrder(bond, increment);
                    bondsAreFullySaturated = saturate(leftBonds, atomContainer) &&
                                             isSaturated(bond, atomContainer);
                    if (!bondsAreFullySaturated) logger.debug("Option 2: failed");
                }
            } else {
                logger.debug("Ok, this bond is unsaturated, but cannot be saturated");
                // try recursing and see if that fixes things
                bondsAreFullySaturated = saturate(leftBonds, atomContainer) &&
                                         isSaturated(bond, atomContainer);
            }
        } else {
            bondsAreFullySaturated = true; // empty is saturated by default
        }
        return bondsAreFullySaturated;
    }

    public boolean unsaturateByDecreasingBondOrder(IBond bond, double decrement) {
        if (bond.getOrder() > decrement) {
            bond.setOrder(bond.getOrder() - decrement);
            return true;
        } else {
            return false;
        }
    }
    
    /**
     * Returns wether a bond is unsaturated. A bond is unsaturated if 
     * <b>all</b> Atoms in the bond are unsaturated.
     */
    public boolean isUnsaturated(IBond bond, IAtomContainer atomContainer) throws CDKException {
        logger.debug("isBondUnsaturated?: ", bond);
        IAtom[] atoms = BondManipulator.getAtomArray(bond);
        boolean isUnsaturated = true;
        for (int i=0; i<atoms.length && isUnsaturated; i++) {
            isUnsaturated = isUnsaturated && !isSaturated(atoms[i], atomContainer);
        }
        logger.debug("Bond is unsaturated?: ", isUnsaturated);
        return isUnsaturated;
    }

    /**
     * Tries to saturate a bond by increasing its bond orders by 1.0.
     *
     * @return true if the bond could be increased
     */
    public boolean saturateByIncreasingBondOrder(IBond bond, IAtomContainer atomContainer, double increment) throws CDKException {
    	IAtom[] atoms = BondManipulator.getAtomArray(bond);
    	IAtom atom = atoms[0];
    	IAtom partner = atoms[1];
        logger.debug("  saturating bond: ", atom.getSymbol(), "-", partner.getSymbol());
        IAtomType[] atomTypes1 = getAtomTypeFactory(bond.getBuilder()).getAtomTypes(atom.getSymbol());
        IAtomType[] atomTypes2 = getAtomTypeFactory(bond.getBuilder()).getAtomTypes(partner.getSymbol());
        for (int atCounter1=0; atCounter1<atomTypes1.length; atCounter1++) {
            IAtomType aType1 = atomTypes1[atCounter1];
            logger.debug("  condidering atom type: ", aType1);
            if (couldMatchAtomType(atomContainer, atom, aType1)) {
                logger.debug("  trying atom type: ", aType1);
                for (int atCounter2=0; atCounter2<atomTypes2.length; atCounter2++) {
                    IAtomType aType2 = atomTypes2[atCounter2];
                    logger.debug("  condidering partner type: ", aType1);
                    if (couldMatchAtomType(atomContainer, partner, atomTypes2[atCounter2])) {
                        logger.debug("    with atom type: ", aType2);
                        if (bond.getOrder() < aType2.getMaxBondOrder() && 
                        bond.getOrder() < aType1.getMaxBondOrder()) {
                            bond.setOrder(bond.getOrder() + increment);
                            logger.debug("Bond order now ", bond.getOrder());
                            return true;
                        }
                    }
                }
            }
        }
        return false;
    }

    /**
     * Returns wether a bond is saturated. A bond is saturated if