From: Matteo F. <mf...@us...> - 2004-11-29 13:29:20
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Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv11084/src/org/openscience/cdk/qsar Added Files: HBondDonorCountDescriptor.java Log Message: adding new descriptor class and its test class: H bond donors count --- NEW FILE: HBondDonorCountDescriptor.java --- /* * $RCSfile: HBondDonorCountDescriptor.java,v $ * $Author: mfe4 $ * $Date: 2004/11/29 13:29:08 $ * $Revision: 1.1 $ * * Copyright (C) 2004 The Chemistry Development Kit (CDK) project * * Contact: cdk...@li... * * 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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package org.openscience.cdk.qsar; import org.openscience.cdk.Atom; import org.openscience.cdk.Element; import org.openscience.cdk.AtomContainer; import org.openscience.cdk.Molecule; import org.openscience.cdk.CDKConstants; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.aromaticity.HueckelAromaticityDetector; import java.util.Map; import java.util.Hashtable; /** * The number of hydrogen bond donors is defined by Daylight: * (http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html) * [!H0;#7,#8,#9]. * *@author mfe4 *@cdk.created 2004-11-03 * @cdk.module qsar */ public class HBondDonorCountDescriptor implements Descriptor { private boolean checkAromaticity = false; /** * Constructor for the HBondDonorCountDescriptor object */ public HBondDonorCountDescriptor() { } /** * Gets the specification attribute of the HBondDonorCountDescriptor * object * *@return The specification value */ public Map getSpecification() { Hashtable specs = new Hashtable(); specs.put("Specification-Reference", "http://qsar.sourceforge.net/dicts/qsar-descriptors:hBondDonors"); specs.put("Implementation-Title", this.getClass().getName()); specs.put("Implementation-Identifier", "$Id: HBondDonorCountDescriptor.java,v 1.1 2004/11/29 13:29:08 mfe4 Exp $"); // added by CVS specs.put("Implementation-Vendor", "The Chemistry Development Kit"); return specs; } /** * Sets the parameters attribute of the HBondDonorCountDescriptor object * *@param params a boolean true means that aromaticity has to be checked *@exception CDKException Description of the Exception */ public void setParameters(Object[] params) throws CDKException { if (params.length > 1) { throw new CDKException("HBondDonorCountDescriptor only expects less than two parameters"); } if (!(params[0] instanceof Boolean)) { throw new CDKException("The parameter must be of type Boolean"); } // ok, all should be fine checkAromaticity = ((Boolean) params[0]).booleanValue(); } /** * Gets the parameters attribute of the HBondDonorCountDescriptor object * *@return The parameters value */ public Object[] getParameters() { // return the parameters as used for the descriptor calculation Object[] params = new Object[1]; params[0] = new Boolean(checkAromaticity); return params; } /** * The method calculates the number of H bond donors. * *@param ac AtomContainer *@return number of H bond donors *@exception CDKException Possible Exceptions */ public Object calculate(AtomContainer ac) throws CDKException { Molecule mol = new Molecule(ac); if (checkAromaticity) { HueckelAromaticityDetector.detectAromaticity(mol); } int hBondDonors = 0; int hcounter = 0; int atomicNumber = 0; String symbol = null; Atom[] atoms = mol.getAtoms(); Atom[] neighboors = null; for (int i = 0; i < atoms.length; i++) { hcounter = 0; symbol = new String(atoms[i].getSymbol()); atomicNumber = atoms[i].getAtomicNumber(); neighboors = mol.getConnectedAtoms(atoms[i]); for (int n = 0; n < neighboors.length; n++) { if (neighboors[n].getSymbol().equals("H")) { hcounter += 1; } else if (atoms[i].getHydrogenCount() > 0) { hcounter += 1; } else { hcounter += 0; } } if(hcounter > 0) { if(symbol.equals("O")) { hBondDonors += 1; } else if(symbol.equals("N")){ hBondDonors += 1; } else if(symbol.equals("F")){ hBondDonors += 1; } else { hBondDonors += 0; } } else { hBondDonors += 0; } } return new Integer(hBondDonors); } /** * Gets the parameterNames attribute of the HBondDonorCountDescriptor * object * *@return The parameterNames value */ public String[] getParameterNames() { String[] params = new String[1]; params[0] = "If true: aromaticity has to be checked"; return params; } /** * Gets the parameterType attribute of the HBondDonorCountDescriptor * object * *@param name Description of the Parameter *@return The parameterType value */ public Object getParameterType(String name) { Object[] paramTypes = new Object[1]; paramTypes[0] = new Boolean(true); return paramTypes; } } |