/*
* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2005-2007 Christian Hoppe <chhoppe@users.sf.net>
*
* 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.molecular;
import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.exception.NoSuchAtomException;
import org.openscience.cdk.graph.SpanningTree;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IRingSet;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IMolecularDescriptor;
import org.openscience.cdk.qsar.result.IDescriptorResult;
import org.openscience.cdk.qsar.result.IntegerResult;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import java.util.ArrayList;
import java.util.List;
/**
* Class that returns the number of atoms in the largest chain.
* <p/>
* <p>This descriptor uses these parameters:
* <table border="1">
* <tr>
* <td>Name</td>
* <td>Default</td>
* <td>Description</td>
* </tr>
* <tr>
* <td>checkAromaticity</td>
* <td>false</td>
* <td>True is the aromaticity has to be checked</td>
* </tr>
* <tr>
* <td>checkRingSystem</td>
* <td>false</td>
* <td>True is the CDKConstant.ISINRING has to be set</td>
* </tr>
* </table>
* <p/>
* Returns a single value named <i>nAtomLAC</i>. Note that a chain exists if there
* are two or more atoms. Thus single atom molecules will return 0
*
* @author chhoppe from EUROSCREEN
* @cdk.created 2006-1-03
* @cdk.module qsarmolecular
* @cdk.githash
* @cdk.set qsar-descriptors
* @cdk.dictref qsar-descriptors:largestChain
*/
@TestClass("org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptorTest")
public class LargestChainDescriptor implements IMolecularDescriptor {
private boolean checkAromaticity = false;
private boolean checkRingSystem = false;
private static final String[] names = {"nAtomLC"};
/**
* Constructor for the LargestChain object.
*/
public LargestChainDescriptor() {
}
/**
* Returns a <code>Map</code> which specifies which descriptor
* is implemented by this class.
* <p/>
* These fields are used in the map:
* <ul>
* <li>Specification-Reference: refers to an entry in a unique dictionary
* <li>Implementation-Title: anything
* <li>Implementation-Identifier: a unique identifier for this version of
* this class
* <li>Implementation-Vendor: CDK, JOELib, or anything else
* </ul>
*
* @return An object containing the descriptor specification
*/
@TestMethod("testGetSpecification")
public DescriptorSpecification getSpecification() {
return new DescriptorSpecification(
"http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#largestChain",
this.getClass().getName(),
"$Id$",
"The Chemistry Development Kit");
}
/**
* Sets the parameters attribute of the LargestChain object.
* <p/>
* This descriptor takes one parameter, which should be Boolean to indicate whether
* aromaticity has been checked (TRUE) or not (FALSE).
*
* @param params The new parameters value
* @throws CDKException if more than one parameter or a non-Boolean parameter is specified
* @see #getParameters
*/
@TestMethod("testSetParameters_arrayObject")
public void setParameters(Object[] params) throws CDKException {
if (params.length > 2) {
throw new CDKException("LargestChainDescriptor only expects two parameter");
}
if (!(params[0] instanceof Boolean) || !(params[1] instanceof Boolean)) {
throw new CDKException("Both parameters must be of type Boolean");
}
// ok, all should be fine
checkAromaticity = (Boolean) params[0];
checkRingSystem = (Boolean) params[1];
}
/**
* Gets the parameters attribute of the LargestChainDescriptor object.
*
* @return The parameters value
* @see #setParameters
*/
@TestMethod("testGetParameters")
public Object[] getParameters() {
// return the parameters as used for the descriptor calculation
Object[] params = new Object[2];
params[0] = checkAromaticity;
params[1] = checkRingSystem;
return params;
}
@TestMethod(value="testNamesConsistency")
public String[] getDescriptorNames() {
return names;
}
private DescriptorValue getDummyDescriptorValue(Exception e) {
return new DescriptorValue(getSpecification(), getParameterNames(),
getParameters(), new IntegerResult((int) Double.NaN), getDescriptorNames(), e);
}
/**
* Calculate the count of atoms of the largest chain in the supplied {@link IAtomContainer}.
* <p/>
* <p>The method require two parameters:
* <ol>
* <li>if checkAromaticity is true, the method check the aromaticity,
* <li>if false, means that the aromaticity has already been checked
* </ol>
* <p/>
* <p>Same for checkRingSystem, if true the CDKConstant.ISINRING will be set
*
* @param atomContainer The {@link AtomContainer} for which this descriptor is to be calculated
* @return the number of atoms in the largest chain of this AtomContainer
* @see #setParameters
*/
@TestMethod("testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtomContainer atomContainer) {
IAtomContainer container;
try {
container = (IAtomContainer) atomContainer.clone();
} catch (CloneNotSupportedException e) {
return getDummyDescriptorValue(e);
}
//logger.debug("LargestChainDescriptor");
boolean[] originalFlag4 = new boolean[container.getAtomCount()];
for (int i=0; i<originalFlag4.length; i++) {
originalFlag4[i] = container.getAtom(i).getFlag(4);
}
if (checkRingSystem) {
IRingSet rs;
try {
rs = new SpanningTree(container).getBasicRings();
} catch (NoSuchAtomException e) {
return getDummyDescriptorValue(e);
}
for (int i = 0; i < container.getAtomCount(); i++) {
if (rs.contains(container.getAtom(i))) {
container.getAtom(i).setFlag(CDKConstants.ISINRING, true);
}
}
}
if (checkAromaticity) {
try {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(container);
CDKHueckelAromaticityDetector.detectAromaticity(container);
} catch (CDKException e) {
return getDummyDescriptorValue(e);
}
}
// get rid of hydrogens in our local copy
container = AtomContainerManipulator.removeHydrogens(container);
int largestChainAtomsCount = 0;
//IAtom[] atoms = container.getAtoms();
ArrayList<IAtom> startSphere;
ArrayList<IAtom> path;
//Set all VisitedFlags to False
for (int i = 0; i < container.getAtomCount(); i++) {
container.getAtom(i).setFlag(CDKConstants.VISITED, false);
}
//logger.debug("Set all atoms to Visited False");
for (int i = 0; i < container.getAtomCount(); i++) {
IAtom atomi = container.getAtom(i);
// chain sp3
//logger.debug("atom:"+i+" maxBondOrder:"+container.getMaximumBondOrder(atoms[i])+" Aromatic:"+atoms[i].getFlag(CDKConstants.ISAROMATIC)+" Ring:"+atoms[i].getFlag(CDKConstants.ISINRING)+" FormalCharge:"+atoms[i].getFormalCharge()+" Charge:"+atoms[i].getCharge()+" Flag:"+atoms[i].getFlag(CDKConstants.VISITED));
if ((!atomi.getFlag(CDKConstants.ISAROMATIC) && !atomi.getFlag(CDKConstants.ISINRING)) & !atomi.getFlag(CDKConstants.VISITED))
{
//logger.debug("...... -> containercepted");
startSphere = new ArrayList<IAtom>();
path = new ArrayList<IAtom>();
startSphere.add(atomi);
try {
breadthFirstSearch(container, startSphere, path);
} catch (CDKException e) {
return getDummyDescriptorValue(e);
}
if (path.size() > largestChainAtomsCount) {
largestChainAtomsCount = path.size();
}
}
}
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new IntegerResult(largestChainAtomsCount),
getDescriptorNames());
}
/**
* Returns the specific type of the DescriptorResult object.
* <p/>
* The return value from this method really indicates what type of result will
* be obtained from the {@link org.openscience.cdk.qsar.DescriptorValue} object. Note that the same result
* can be achieved by interrogating the {@link org.openscience.cdk.qsar.DescriptorValue} object; this method
* allows you to do the same thing, without actually calculating the descriptor.
*
* @return an object that implements the {@link org.openscience.cdk.qsar.result.IDescriptorResult} interface indicating
* the actual type of values returned by the descriptor in the {@link org.openscience.cdk.qsar.DescriptorValue} object
*/
@TestMethod("testGetDescriptorResultType")
public IDescriptorResult getDescriptorResultType() {
return new IntegerResult(1);
}
/**
* Performs a breadthFirstSearch in an AtomContainer starting with a
* particular sphere, which usually consists of one start atom, and searches
* for a pi system.
*
* @param container The AtomContainer to
* be searched
* @param sphere A sphere of atoms to
* start the search with
* @param path A ArrayList which stores the atoms belonging to the pi system
* @throws org.openscience.cdk.exception.CDKException
* Description of the
* Exception
*/
private void breadthFirstSearch(IAtomContainer container, List<IAtom> sphere, List<IAtom> path) throws CDKException {
IAtom atom;
IAtom nextAtom;
List<IAtom> newSphere = new ArrayList<IAtom>();
//logger.debug("Start of breadthFirstSearch");
for (int i = 0; i < sphere.size(); i++) {
atom = sphere.get(i);
//logger.debug("BreadthFirstSearch around atom " + (atomNr + 1));
List<IBond> bonds = container.getConnectedBondsList(atom);
for (IBond bond : bonds) {
nextAtom = bond.getConnectedAtom(atom);
if ((!nextAtom.getFlag(CDKConstants.ISAROMATIC) && !nextAtom.getFlag(CDKConstants.ISINRING)) & !nextAtom.getFlag(CDKConstants.VISITED)) {
//logger.debug("BDS> AtomNr:"+container.getAtomNumber(nextAtom)+" maxBondOrder:"+container.getMaximumBondOrder(nextAtom)+" Aromatic:"+nextAtom.getFlag(CDKConstants.ISAROMATIC)+" FormalCharge:"+nextAtom.getFormalCharge()+" Charge:"+nextAtom.getCharge()+" Flag:"+nextAtom.getFlag(CDKConstants.VISITED));
path.add(nextAtom);
//logger.debug("BreadthFirstSearch is meeting new atom " + (nextAtomNr + 1));
nextAtom.setFlag(CDKConstants.VISITED, true);
if (container.getConnectedBondsCount(nextAtom) > 1) {
newSphere.add(nextAtom);
}
} else {
nextAtom.setFlag(CDKConstants.VISITED, true);
}
}
}
if (newSphere.size() > 0) {
breadthFirstSearch(container, newSphere, path);
}
}
/**
* Gets the parameterNames attribute of the LargestPiSystemDescriptor object.
*
* @return The parameterNames value
*/
@TestMethod("testGetParameterNames")
public String[] getParameterNames() {
String[] params = new String[2];
params[0] = "checkAromaticity";
params[1] = "checkRingSystem";
return params;
}
/**
* Gets the parameterType attribute of the LargestChainDescriptor object.
*
* @param name Description of the Parameter
* @return An Object of class equal to that of the parameter being requested
*/
@TestMethod("testGetParameterType_String")
public Object getParameterType(String name) {
return true;
}
}