/*
* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* 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.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.IMolecularDescriptor;
import org.openscience.cdk.qsar.result.IDescriptorResult;
import org.openscience.cdk.qsar.result.IntegerResult;
/**
* This descriptor calculates the number of hydrogen bond donors using a slightly simplified version of the
* <a href="http://www.chemie.uni-erlangen.de/model2001/abstracts/rester.html">PHACIR atom types</a>.
* The following groups are counted as hydrogen bond donors:
* <ul>
* <li>Any-OH where the formal charge of the oxygen is non-negative (i.e. formal charge >= 0)</li>
* <li>Any-NH where the formal charge of the nitrogen is non-negative (i.e. formal charge >= 0)</li>
* </ul>
* <p>
* This descriptor uses no parameters.
* <p>
* This descriptor works properly with AtomContainers whose atoms contain either <b>implicit</b> or <b>explicit
* hydrogen</b> atoms. It does not work with atoms that contain neither implicit nor explicit hydrogens.
*
* Returns a single value named <i>nHBAcc</i>.
*
* <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 ulif
* @cdk.created 2005-22-07
* @cdk.module qsarmolecular
* @cdk.githash
* @cdk.set qsar-descriptors
* @cdk.dictref qsar-descriptors:hBondDonors
*/
@TestClass("org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptorTest")
public class HBondDonorCountDescriptor implements IMolecularDescriptor {
private static final String[] names = {"nHBDon"};
/**
* Constructor for the HBondDonorCountDescriptor object
*/
public HBondDonorCountDescriptor() { }
/**
* Gets the specification attribute of the HBondDonorCountDescriptor
* object
*
* @return The specification value
*/
@TestMethod("testGetSpecification")
public DescriptorSpecification getSpecification() {
return new DescriptorSpecification(
"http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#hBondDonors",
this.getClass().getName(),
"$Id$",
"The Chemistry Development Kit");
}
/**
* Sets the parameter of this HBondDonorCountDescriptor instance.
*
* @param params this descriptor does not have any parameters
* @exception CDKException Description of the Exception
*/
@TestMethod("testSetParameters_arrayObject")
public void setParameters(Object[] params) throws CDKException {
// this descriptor has no parameters; nothing has to be done here
}
/**
* Gets the parameters of the HBondDonorCountDescriptor instance.
*
* @return null as this descriptor does not have any parameters
*/
@TestMethod("testGetParameters")
public Object[] getParameters() {
// no parameters; thus we return null
return null;
}
@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);
}
/**
* Calculates the number of H bond donors.
*
* @param atomContainer AtomContainer
* @return number of H bond donors
*/
@TestMethod("testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtomContainer atomContainer) {
int hBondDonors = 0;
IAtomContainer ac;
try {
ac = (IAtomContainer) atomContainer.clone();
} catch (CloneNotSupportedException e) {
return getDummyDescriptorValue(e);
}
//org.openscience.cdk.interfaces.IAtom[] atoms = ac.getAtoms();
// iterate over all atoms of this AtomContainer; use label atomloop to allow for labelled continue
atomloop:
for (int atomIndex = 0; atomIndex < ac.getAtomCount(); atomIndex++) {
IAtom atom = (IAtom) ac.getAtom(atomIndex);
// checking for O and N atoms where the formal charge is >= 0
if ((atom.getSymbol().equals("O") || atom.getSymbol().equals("N")) && atom.getFormalCharge() >= 0) {
// implicit hydrogens
Integer implicitH = atom.getHydrogenCount();
if (implicitH == CDKConstants.UNSET) implicitH = 0;
if (implicitH > 0) {
hBondDonors++;
continue atomloop; // we skip the explicit hydrogens part cause we found implicit hydrogens
}
// explicit hydrogens
java.util.List neighbours = ac.getConnectedAtomsList(atom);
for (Object neighbour : neighbours) {
if (((IAtom) neighbour).getSymbol().equals("H")) {
hBondDonors++;
continue atomloop;
}
}
}
}
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new IntegerResult(hBondDonors),
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);
}
/**
* Gets the parameterNames of the HBondDonorCountDescriptor.
*
* @return null as this descriptor does not have any parameters
*/
@TestMethod("testGetParameterNames")
public String[] getParameterNames() {
// no parameters; thus we return null
return null;
}
/**
* Gets the parameterType of the HBondDonorCountDescriptor.
*
* @param name Description of the Parameter
* @return null as this descriptor does not have any parameters
*/
@TestMethod("testGetParameterType_String")
public Object getParameterType(String name) {
// no parameters; thus we return null
return null;
}
}