/* $Revision$ $Author$ $Date$
*
* 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.annotations.TestMethod;
import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
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.interfaces.IAtomContainerSet;
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;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
/**
* 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.githash
* @cdk.set qsar-descriptors
* @cdk.dictref qsar-descriptors:piContact
*/
public class PiContactDetectionDescriptor implements IAtomPairDescriptor {
private static final String[] names = {"piContact"};
private boolean checkAromaticity = false;
IAtomContainerSet 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(),
"$Id$",
"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];
}
/**
* 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] = checkAromaticity;
return params;
}
@TestMethod(value="testNamesConsistency")
public String[] getDescriptorNames() {
return names;
}
private DescriptorValue getDummyDescriptorValue(Exception e) {
return new DescriptorValue(
getSpecification(), getParameterNames(),
getParameters(), new BooleanResult(false),
names, e);
}
/**
* The method returns if two atoms have pi-contact.
*
* @param atomContainer AtomContainer
* @return true if the atoms have pi-contact
*/
public DescriptorValue calculate(IAtom first, IAtom second, IAtomContainer atomContainer) {
IAtomContainer ac;
try {
ac = (IAtomContainer) atomContainer.clone();
} catch (CloneNotSupportedException e) {
return getDummyDescriptorValue(e);
}
IAtom clonedFirst = ac.getAtom(atomContainer.getAtomNumber(first));
IAtom clonedSecond = ac.getAtom(atomContainer.getAtomNumber(first));
Molecule mol = new Molecule(ac);
if (checkAromaticity) {
try {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
CDKHueckelAromaticityDetector.detectAromaticity(mol);
} catch (CDKException e) {
return getDummyDescriptorValue(e);
}
}
boolean piContact = false;
int counter = 0;
if(acold!=ac){
acold=ac;
acSet = ConjugatedPiSystemsDetector.detect(mol);
}
java.util.Iterator<IAtomContainer> detected = acSet.atomContainers().iterator();
java.util.List<IAtom> neighboorsFirst = mol.getConnectedAtomsList(clonedFirst);
java.util.List<IAtom> neighboorsSecond = mol.getConnectedAtomsList(clonedSecond);
while (detected.hasNext()) {
IAtomContainer detectedAC = 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), getDescriptorNames());
}
/**
* 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 (Object neigh : neighs) {
if (ac.contains((IAtom) neigh)) {
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 true;
return null;
}
}