/* $Revision$ $Author$ $Date$
*
* Copyright (C) 2007 Rajarshi Guha <rajarshi@users.sourceforge.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 java.util.List;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
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.IntegerArrayResult;
import org.openscience.cdk.qsar.result.IntegerArrayResultType;
import org.openscience.cdk.tools.manipulator.BondManipulator;
/**
* Topological descriptor characterizing the carbon connectivity.
* <p/>
* The class calculates 9 descriptors in the following order
* <ul>
* <li>C1SP1 triply hound carbon bound to one other carbon
* <li>C2SP1 triply bound carbon bound to two other carbons
* <li>C1SP2 doubly hound carbon bound to one other carbon
* <li>C2SP2 doubly bound carbon bound to two other carbons
* <li>C3SP2 doubly bound carbon bound to three other carbons
* <li>C1SP3 singly bound carbon bound to one other carbon
* <li>C2SP3 singly bound carbon bound to two other carbons
* <li>C3SP3 singly bound carbon bound to three other carbons
* <li>C4SP3 singly bound carbon bound to four other carbons
* </ul>
* <p>This descriptor uses these parameters:
* <table border="1">
* <tr>
* <td>Name</td>
* <td>Default</td>
* <td>Description</td>
* </tr>
* <tr>
* <td></td>
* <td></td>
* <td>no parameters</td>
* </tr>
* </table>
*
* @author Rajarshi Guha
* @cdk.created 2007-09-28
* @cdk.module qsarmolecular
* @cdk.githash
* @cdk.set qsar-descriptors
* @cdk.dictref qsar-descriptors:carbonTypes
* @cdk.keyword topological bond order ctypes
* @cdk.keyword descriptor
*/
@TestClass("org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptorTest")
public class CarbonTypesDescriptor implements IMolecularDescriptor {
private final static String[] names = {
"C1SP1", "C2SP1",
"C1SP2", "C2SP2", "C3SP2",
"C1SP3", "C2SP3", "C3SP3", "C4SP3"
};
public CarbonTypesDescriptor() {
}
@TestMethod("testGetSpecification")
public DescriptorSpecification getSpecification() {
return new DescriptorSpecification(
"http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#carbonTypes",
this.getClass().getName(),
"$Id$",
"The Chemistry Development Kit");
}
/**
* Sets the parameters attribute of the GravitationalIndexDescriptor object.
*
* @param params The new parameters value
* @throws org.openscience.cdk.exception.CDKException
* Description of the Exception
* @see #getParameters
*/
@TestMethod("testSetParameters_arrayObject")
public void setParameters(Object[] params) throws CDKException {
// no parameters for this descriptor
}
/**
* Gets the parameters attribute of the GravitationalIndexDescriptor object.
*
* @return The parameters value
* @see #setParameters
*/
@TestMethod("testGetParameters")
public Object[] getParameters() {
// no parameters to return
return (null);
}
@TestMethod(value="testNamesConsistency")
public String[] getDescriptorNames() {
return names;
}
/**
* Gets the parameterNames attribute of the GravitationalIndexDescriptor object.
*
* @return The parameterNames value
*/
@TestMethod("testGetParameterNames")
public String[] getParameterNames() {
// no param names to return
return (null);
}
/**
* Gets the parameterType attribute of the GravitationalIndexDescriptor object.
*
* @param name Description of the Parameter
* @return The parameterType value
*/
@TestMethod("testGetParameterType_String")
public Object getParameterType(String name) {
return (null);
}
/**
* Calculates the 9 carbon types descriptors
*
* @param container Parameter is the atom container.
* @return An ArrayList containing 9 elements in the order described above
*/
@TestMethod("testCalculate_IAtomContainer,testButane,testComplex1,testComplex2")
public DescriptorValue calculate(IAtomContainer container) {
int c1sp1 = 0;
int c2sp1 = 0;
int c1sp2 = 0;
int c2sp2 = 0;
int c3sp2 = 0;
int c1sp3 = 0;
int c2sp3 = 0;
int c3sp3 = 0;
int c4sp3 = 0;
for (IAtom atom : container.atoms()) {
if (!atom.getSymbol().equals("C") && !atom.getSymbol().equals("c")) continue;
List<IAtom> connectedAtoms = container.getConnectedAtomsList(atom);
int cc = 0;
for (IAtom connectedAtom : connectedAtoms) {
if (connectedAtom.getSymbol().equals("C") || connectedAtom.getSymbol().equals("c")) cc++;
}
IBond.Order maxBondOrder = getHighestBondOrder(container, atom);
if (maxBondOrder == IBond.Order.TRIPLE && cc == 1) c1sp1++;
else if (maxBondOrder == IBond.Order.TRIPLE && cc == 2) c2sp1++;
else if (maxBondOrder == IBond.Order.DOUBLE && cc == 1) c1sp2++;
else if (maxBondOrder == IBond.Order.DOUBLE && cc == 2) c2sp2++;
else if (maxBondOrder == IBond.Order.DOUBLE && cc == 3) c3sp2++;
else if (maxBondOrder == IBond.Order.SINGLE && cc == 1) c1sp3++;
else if (maxBondOrder == IBond.Order.SINGLE && cc == 2) c2sp3++;
else if (maxBondOrder == IBond.Order.SINGLE && cc == 3) c3sp3++;
else if (maxBondOrder == IBond.Order.SINGLE && cc == 4) c4sp3++;
}
IntegerArrayResult retval = new IntegerArrayResult(9);
retval.add(c1sp1);
retval.add(c2sp1);
retval.add(c1sp2);
retval.add(c2sp2);
retval.add(c3sp2);
retval.add(c1sp3);
retval.add(c2sp3);
retval.add(c3sp3);
retval.add(c4sp3);
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
retval, getDescriptorNames());
}
private IBond.Order getHighestBondOrder(IAtomContainer container, IAtom atom) {
List<IBond> bonds = container.getConnectedBondsList(atom);
IBond.Order maxOrder = IBond.Order.SINGLE;
for (IBond bond : bonds) {
if (BondManipulator.isHigherOrder(bond.getOrder(), maxOrder))
maxOrder = bond.getOrder();
}
return maxOrder;
}
/**
* 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 IntegerArrayResultType(9);
}
}