/* * $RCSfile$ * $Author: egonw $ * $Date: 2007-02-07 23:20:44 +0100 (Wed, 07 Feb 2007) $ * $Revision: 7895 $ * * Copyright (C) 2004-2007 Miguel Rojas <miguel.rojas@uni-koeln.de> * * 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.atomic; import org.openscience.cdk.CDKConstants; import org.openscience.cdk.config.AtomTypeFactory; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IAtomType; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IAtomicDescriptor; import org.openscience.cdk.qsar.result.IntegerResult; import org.openscience.cdk.tools.LoggingTool; /** * This class returns the hybridization of an atom. * * <p>This class try to find a SIMPLE WAY the molecular geometry for following from * Valence Shell Electron Pair Repulsion or VSEPR model and at the same time its * hybridization of atoms in a molecule. * * <p>The basic premise of the model is that the electrons are paired in a molecule * and that the molecule geometry is determined only by the repulsion between the pairs. * The geomtry adopted by a molecule is then the one in which the reulsions are minimized. * * <p>It counts the number of electron pairs in the lewis dot diagram which * are attached to an atom. Then uses the following table. * <pre> * pairs on hybridization * an atom of the atom geomtry number for CDK.Constants * ****************************************************************************************** * 2 sp linear 1 * 3 sp^2 trigonal planarb 2 * 4 sp^3 tetrahedral 3 * 5 sp^3d trigonal bipyramid 4 * 6 sp^3d^2 octahedral 5 * 7 sp^3d^3 pentagonal bipyramid 6 * 8 sp^3d^4 square antiprim 7 * 9 sp^3d^5 tricapped trigonal prism 8 * </pre> * * <p>This table only works if the central atom is a p-block element * (groups IIA through VIIIA), not a transition metal. * * * <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 Miguel Rojas *@cdk.created 2005-03-24 *@cdk.module qsar *@cdk.set qsar-descriptors * @cdk.dictref qsar-descriptors:atomHybridizationVSEPR */ 00090 public class AtomHybridizationVSEPRDescriptor implements IAtomicDescriptor { org.openscience.cdk.interfaces.IAtom atom = null; private LoggingTool logger; private static AtomTypeFactory atomATF = null; /** * Constructor for the AtomHybridizationVSEPRDescriptor object */ 00099 public AtomHybridizationVSEPRDescriptor() { logger = new LoggingTool(this); } /** * Gets the specification attribute of the AtomHybridizationVSEPRDescriptor object * *@return The specification value */ 00109 public DescriptorSpecification getSpecification() { return new DescriptorSpecification( "http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#atomHybridizationVSEPR", this.getClass().getName(), "$Id: AtomHybridizationVSEPRDescriptor.java 7895 2007-02-07 22:20:44Z egonw $", "The Chemistry Development Kit"); } /** * This descriptor does have any parameter. */ 00121 public void setParameters(Object[] params) throws CDKException { } /** * Gets the parameters attribute of the AtomHybridizationVSEPRDescriptor object * * @return The parameters value * @see #setParameters */ 00131 public Object[] getParameters() { return null; } /** * This method calculates the hybridization of an atom. * *@param atom The IAtom for which the DescriptorValue is requested *@param container Parameter is the atom container. *@return The hybridization *@exception CDKException Description of the Exception */ 00145 public DescriptorValue calculate(IAtom atom, IAtomContainer container) throws CDKException { IAtomType atomType = findMatchingAtomType(container, atom); double bondOrderSum = container.getBondOrderSum(atom); int charge = atom.getFormalCharge(); int hcount = atom.getHydrogenCount(); int valency = atomType.getValency(); double nLonePair = (valency - ( hcount + bondOrderSum ) - charge) / 2; int hybridization = (int)nLonePair + ( hcount + container.getConnectedAtomsList(atom).size() ); logger.debug("ATOM : bondOrderSum " + bondOrderSum + ", charge " + charge + ", hcount " + hcount + ", valency " + valency + ", nLonePair " + nLonePair + ", hybridization " + hybridization); int hybridizationCDK = 0; switch (hybridization) { case 2: hybridizationCDK = CDKConstants.HYBRIDIZATION_SP1;break; case 3: hybridizationCDK = CDKConstants.HYBRIDIZATION_SP2;break; case 4: hybridizationCDK = CDKConstants.HYBRIDIZATION_SP3;break; case 5: hybridizationCDK = CDKConstants.HYBRIDIZATION_SP3D1;break; case 6: hybridizationCDK = CDKConstants.HYBRIDIZATION_SP3D2;break; case 7: hybridizationCDK = CDKConstants.HYBRIDIZATION_SP3D3;break; case 8: hybridizationCDK = CDKConstants.HYBRIDIZATION_SP3D4;break; case 9: hybridizationCDK = CDKConstants.HYBRIDIZATION_SP3D5;break; default: hybridizationCDK = CDKConstants.HYBRIDIZATION_UNSET;break; } return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new IntegerResult(hybridizationCDK)); } private IAtomType findMatchingAtomType(IAtomContainer container, org.openscience.cdk.interfaces.IAtom atom) throws CDKException { try { if(atomATF==null) atomATF = AtomTypeFactory.getInstance("org/openscience/cdk/config/data/valency2_atomtypes.xml", container.getBuilder()); // take atomtype for the given element... IAtomType atomType = atomATF.getAtomType(atom.getSymbol()); return atomType; } catch (Exception ex1) { logger.error(ex1.getMessage()); logger.debug(ex1); throw new CDKException("Problems with AtomTypeFactory due to " + ex1.toString(), ex1); } } /** * Gets the parameterNames attribute of the AtomHybridizationVSEPRDescriptor object * *@return The parameterNames value */ 00214 public String[] getParameterNames() { return new String[0]; } /** * Gets the parameterType attribute of the AtomHybridizationVSEPRDescriptor object * *@param name Description of the Parameter * @return An Object of class equal to that of the parameter being requested */ 00225 public Object getParameterType(String name) { String[] params = new String[1]; params[0] = "targetPosition"; return params; } }