From: Matteo F. <mf...@us...> - 2004-12-15 14:14:57
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Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv437/src/org/openscience/cdk/qsar Added Files: RuleOfFiveDescriptor.java Log Message: added Lipinski's rule of five prediction descriptor --- NEW FILE: RuleOfFiveDescriptor.java --- /* * $RCSfile: RuleOfFiveDescriptor.java,v $ * $Author: mfe4 $ * $Date: 2004/12/15 14:14:48 $ * $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.AtomContainer; import org.openscience.cdk.Bond; import org.openscience.cdk.Molecule; import org.openscience.cdk.CDKConstants; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.RingSet; import org.openscience.cdk.ringsearch.AllRingsFinder; import org.openscience.cdk.qsar.result.*; import java.util.Map; import java.util.Hashtable; import org.openscience.cdk.tools.HydrogenAdder; /** * This Class contains a method that returns the number failures of the Lipinski's Rule Of 5.. * See http://www.lifechemicals.com/eng/services/HTS/five/. * @author mfe4 * @cdk.created 2004-11-03 * @cdk.module qsar * @cdk.set qsar-descriptors */ public class RuleOfFiveDescriptor implements Descriptor { private boolean checkAromaticity = false; /** * Constructor for the RuleOfFiveDescriptor object */ public RuleOfFiveDescriptor() { } /** * Gets the specification attribute of the RuleOfFiveDescriptor object * *@return The specification value */ public DescriptorSpecification getSpecification() { return new DescriptorSpecification( "http://qsar.sourceforge.net/dicts/qsar-descriptors:lipinskifailures", this.getClass().getName(), "$Id: RuleOfFiveDescriptor.java,v 1.1 2004/12/15 14:14:48 mfe4 Exp $", "The Chemistry Development Kit"); } /** * Sets the parameters attribute of the RuleOfFiveDescriptor object * *@param params Parameter is only one: a boolean. *@exception CDKException Possible Exceptions */ public void setParameters(Object[] params) throws CDKException { if (params.length > 1) { throw new CDKException("RuleOfFiveDescriptor only expects one parameter"); } if (!(params[0] instanceof Boolean)) { throw new CDKException("The first parameter must be of type Boolean"); } // ok, all should be fine checkAromaticity = ((Boolean) params[0]).booleanValue(); } /** * Gets the parameters attribute of the RuleOfFiveDescriptor 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 take a boolean checkAromaticity: if the boolean is true, it means that * aromaticity has to be checked. * *@param ac atom container *@return number of aromatic bonds in the atom container *@exception CDKException Possible Exceptions */ public DescriptorResult calculate(AtomContainer mol) throws CDKException { int lipinskifailures = 0; Descriptor xlogP = new XLogPDescriptor(); Object[] xlogPparams = {new Boolean(checkAromaticity)}; xlogP.setParameters(xlogPparams); double xlogPvalue = ((DoubleResult)xlogP.calculate(mol)).doubleValue(); Descriptor acc = new HBondAcceptorCountDescriptor(); acc.setParameters(xlogPparams); int acceptors = ((IntegerResult)acc.calculate(mol)).intValue(); Descriptor don = new HBondDonorCountDescriptor(); don.setParameters(xlogPparams); int donors = ((IntegerResult)don.calculate(mol)).intValue(); Descriptor mw = new WeightDescriptor(); Object[] mwparams = {new String("")}; mw.setParameters(mwparams); double mwvalue = ((DoubleResult)mw.calculate(mol)).doubleValue(); Descriptor rotata = new RotatableBondsCountDescriptor(); rotata.setParameters(xlogPparams); int rotatablebonds = ((IntegerResult)rotata.calculate(mol)).intValue(); if(xlogPvalue > 5.0) { lipinskifailures += 1; } if(acceptors > 10) { lipinskifailures += 1; } if(donors > 5) { lipinskifailures += 1; } if(mwvalue > 500.0) { lipinskifailures += 1; } if(rotatablebonds > 10.0) { lipinskifailures += 1; } return new IntegerResult(lipinskifailures); } /** * Gets the parameterNames attribute of the RuleOfFiveDescriptor * object * *@return The parameterNames value */ public String[] getParameterNames() { String[] params = new String[1]; params[0] = "True is the aromaticity has to be checked"; return params; } /** * Gets the parameterType attribute of the RuleOfFiveDescriptor 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; } } |