/*
* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* 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.molecular;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
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.BondManipulator;
import java.util.List;
/**
* The number of rotatable bonds is given by the SMARTS specified by Daylight on
* <a href="http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html#EXMPL">SMARTS tutorial</a><p>
*
* <p>This descriptor uses these parameters:
* <table border="1">
* <tr>
* <td>Name</td>
* <td>Default</td>
* <td>Description</td>
* </tr>
* <tr>
* <td>includeTerminals</td>
* <td>false</td>
* <td>True if terminal bonds are included</td>
* </tr>
* </table>
*
* Returns a single value named <i>nRotB</i>
*
* @author mfe4
* @cdk.created 2004-11-03
* @cdk.module qsarmolecular
* @cdk.githash
* @cdk.set qsar-descriptors
* @cdk.dictref qsar-descriptors:rotatableBondsCount
*
* @cdk.keyword bond count, rotatable
* @cdk.keyword descriptor
*/
@TestClass("org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptorTest")
public class RotatableBondsCountDescriptor implements IMolecularDescriptor {
private boolean includeTerminals = false;
/**
* Constructor for the RotatableBondsCountDescriptor object
*/
public RotatableBondsCountDescriptor() { }
/**
* Gets the specification attribute of the RotatableBondsCountDescriptor
* object
*
*@return The specification value
*/
@TestMethod("testGetSpecification")
public DescriptorSpecification getSpecification() {
return new DescriptorSpecification(
"http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#rotatableBondsCount",
this.getClass().getName(),
"$Id$",
"The Chemistry Development Kit");
}
/**
* Sets the parameters attribute of the RotatableBondsCountDescriptor object
*
*@param params a boolean true means that terminal atoms must be included in the count
*@exception CDKException Description of the Exception
*/
@TestMethod("testSetParameters_arrayObject")
public void setParameters(Object[] params) throws CDKException {
if (params.length != 1) {
throw new CDKException("RotatableBondsCount expects one parameter");
}
if (!(params[0] instanceof Boolean)) {
throw new CDKException("The parameter must be of type Boolean");
}
// ok, all should be fine
includeTerminals = (Boolean) params[0];
}
/**
* Gets the parameters attribute of the RotatableBondsCountDescriptor object
*
*@return The parameters value
*/
@TestMethod("testGetParameters")
public Object[] getParameters() {
// return the parameters as used for the descriptor calculation
Object[] params = new Object[1];
params[0] = includeTerminals;
return params;
}
@TestMethod(value="testNamesConsistency")
public String[] getDescriptorNames() {
return new String[] { includeTerminals ? "nRotBt" : "nRotB"};
}
/**
* The method calculates the number of rotatable bonds of an atom container.
* If the boolean parameter is set to true, terminal bonds are included.
*
*@param ac AtomContainer
*@return number of rotatable bonds
*/
@TestMethod("testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtomContainer ac) {
int rotatableBondsCount = 0;
int degree0;
int degree1;
IRingSet ringSet;
try {
ringSet = new SpanningTree(ac).getBasicRings();
} catch (NoSuchAtomException e) {
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new IntegerResult((int) Double.NaN), getDescriptorNames(), e);
}
for (IBond bond : ac.bonds()) {
if (ringSet.getRings(bond).getAtomContainerCount() > 0) {
bond.setFlag(CDKConstants.ISINRING, true);
}
}
for (IBond bond : ac.bonds()) {
IAtom atom0 = bond.getAtom(0);
IAtom atom1 = bond.getAtom(1);
if (atom0.getSymbol().equals("H") || atom1.getSymbol().equals("H")) continue;
if (bond.getOrder() == CDKConstants.BONDORDER_SINGLE) {
if ((BondManipulator.isLowerOrder(ac.getMaximumBondOrder(atom0), IBond.Order.TRIPLE)) &&
(BondManipulator.isLowerOrder(ac.getMaximumBondOrder(atom1), IBond.Order.TRIPLE))) {
if (!bond.getFlag(CDKConstants.ISINRING)) {
// if there are explicit H's we should ignore those bonds
degree0 = ac.getConnectedBondsCount(atom0) - getConnectedHCount(ac, atom0);
degree1 = ac.getConnectedBondsCount(atom1) - getConnectedHCount(ac, atom1);
if ((degree0 == 1) || (degree1 == 1)) {
if (includeTerminals) {
rotatableBondsCount += 1;
}
} else {
rotatableBondsCount += 1;
}
}
}
}
}
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new IntegerResult(rotatableBondsCount), getDescriptorNames());
}
private int getConnectedHCount(IAtomContainer atomContainer, IAtom atom) {
List<IAtom> connectedAtoms = atomContainer.getConnectedAtomsList(atom);
int n = 0;
for (IAtom anAtom : connectedAtoms) if (anAtom.getSymbol().equals("H")) n++;
return n;
}
/**
* 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);
}
/**
* Gets the parameterNames attribute of the RotatableBondsCountDescriptor
* object
*
*@return The parameterNames value
*/
@TestMethod("testGetParameterNames")
public String[] getParameterNames() {
String[] params = new String[1];
params[0] = "includeTerminals";
return params;
}
/**
* Gets the parameterType attribute of the RotatableBondsCountDescriptor
* object
*
*@param name Description of the Parameter
*@return The parameterType value
*/
@TestMethod("testGetParameterType_String")
public Object getParameterType(String name) {
return true;
}
}