/* $Revision: 9202 $ $Author: egonw $ $Date: 2007-10-25 11:54:10 +0200 (Thu, 25 Oct 2007) $ * * Copyright (C) 2004-2007  The Chemistry Development Kit (CDK) project * * Contact: cdk-devel@lists.sourceforge.net * * 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. * * 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.qsar.descriptors.atompair;import org.openscience.cdk.Molecule;import org.openscience.cdk.AtomContainerSet;import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;import org.openscience.cdk.exception.CDKException;import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector;import org.openscience.cdk.interfaces.IAtom;import org.openscience.cdk.interfaces.IAtomContainer;import org.openscience.cdk.qsar.DescriptorSpecification;import org.openscience.cdk.qsar.DescriptorValue;import org.openscience.cdk.qsar.IAtomPairDescriptor;import org.openscience.cdk.qsar.result.BooleanResult;/** * This class checks if two atoms have pi-contact (this is true when there is * one and the same conjugated pi-system which contains both atoms, or directly * linked neighboors of the atoms). * * <p>This descriptor uses these parameters: * <table border="1"> *   <tr> *     <td>Name</td> *     <td>Default</td> *     <td>Description</td> *   </tr> *   <tr> *     <td>firstAtom</td> *     <td>0</td> *     <td>The position of the first atom</td> *   </tr> *   <tr> *     <td>secondAtom</td> *     <td>0</td> *     <td>The position of the second atom</td> *   </tr> *   <tr> *     <td>checkAromaticity</td> *     <td>false</td> *     <td>True is the aromaticity has to be checked</td> *   </tr> * </table> * * @author         mfe4 * @cdk.created    2004-11-03 * @cdk.module     qsar * @cdk.set        qsar-descriptors * @cdk.dictref    qsar-descriptors:piContact */public class PiContactDetectionDescriptor implements IAtomPairDescriptor {    private boolean checkAromaticity = false;    AtomContainerSet acSet = null;    private IAtomContainer acold=null;    /**     * Constructor for the PiContactDetectionDescriptor object.     */    public PiContactDetectionDescriptor() { }    /**     * Gets the specification attribute of the PiContactDetectionDescriptor object.     *     * @return    The specification value     */    public DescriptorSpecification getSpecification() {        return new DescriptorSpecification(                "http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#piContact",                this.getClass().getName(),                "$Id: PiContactDetectionDescriptor.java 9202 2007-10-25 09:54:10Z egonw $",                "The Chemistry Development Kit");    }    /**     * Sets the parameters attribute of the PiContactDetectionDescriptor object.     *     * @param  params Parameters contains a     *                boolean (true if is needed a checkAromaticity)     * @exception     CDKException  Description of the Exception     */    public void setParameters(Object[] params) throws CDKException {        if (params.length != 1) {            throw new CDKException("PiContactDetectionDescriptor expects 1 parameters");        }        if (!(params[0] instanceof Boolean)) {            throw new CDKException("The first parameter must be of type Boolean");        }        checkAromaticity = ((Boolean) params[0]).booleanValue();    }    /**     * Gets the parameters attribute of the PiContactDetectionDescriptor object.     *     * @return    The parameters value     */    public Object[] getParameters() {        // return the parameters as used for the descriptor calculation        Object[] params = new Object[1];        params[0] = new Boolean(checkAromaticity);        return params;    }    /**     * The method returns if two atoms have pi-contact.     *     * @param  atomContainer                AtomContainer     * @return                   true if the atoms have pi-contact     * @exception  CDKException  Possible Exceptions     */    public DescriptorValue calculate(IAtom first, IAtom second, IAtomContainer atomContainer) throws CDKException {        IAtomContainer ac;        try {            ac = (IAtomContainer) atomContainer.clone();        } catch (CloneNotSupportedException e) {            throw new CDKException("Error during clone");        }        IAtom clonedFirst = ac.getAtom(atomContainer.getAtomNumber(first));        IAtom clonedSecond = ac.getAtom(atomContainer.getAtomNumber(first));        Molecule mol = new Molecule(ac);        if (checkAromaticity) {            HueckelAromaticityDetector.detectAromaticity(mol);        }        boolean piContact = false;        int counter = 0;        if(acold!=ac){          acold=ac;          acSet = ConjugatedPiSystemsDetector.detect(mol);        }        java.util.Iterator detected = acSet.atomContainers();        java.util.List neighboorsFirst = mol.getConnectedAtomsList(clonedFirst);        java.util.List neighboorsSecond = mol.getConnectedAtomsList(clonedSecond);        while (detected.hasNext()) {        	IAtomContainer detectedAC = (IAtomContainer)detected.next();            if (detectedAC.contains(clonedFirst) && detectedAC.contains(clonedSecond)) {                counter += 1;                break;            }            if (isANeighboorsInAnAtomContainer(neighboorsFirst, detectedAC) && isANeighboorsInAnAtomContainer(neighboorsSecond, detectedAC)) {                counter += 1;                break;            }        }        if (counter > 0) {            piContact = true;        }        return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new BooleanResult(piContact));    }    /**     * Gets if neighboors of an atom are in an atom container.     *     * @param  neighs  array of atoms     * @param  ac      AtomContainer     * @return         The boolean result     */    private boolean isANeighboorsInAnAtomContainer(java.util.List neighs, IAtomContainer ac) {        boolean isIn = false;        int count = 0;        for (int i = 0; i < neighs.size(); i++) {            if (ac.contains((IAtom)neighs.get(i))) {                count += 1;            }        }        if (count > 0) {            isIn = true;        }        return isIn;    }    /**     * Gets the parameterNames attribute of the PiContactDetectionDescriptor     * object.     *     * @return    The parameterNames value     */    public String[] getParameterNames() {        String[] params = new String[1];        params[0] = "checkAromaticity";        return params;    }    /**     * Gets the parameterType attribute of the PiContactDetectionDescriptor object.     *     * @param  name  Description of the Parameter     * @return       The parameterType value     */    public Object getParameterType(String name) {        if (name.equals("checkAromaticity")) return new Boolean(true);        return null;    }}