/* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2007 Miguel Rojasch <miguelrojasch@users.sf.net>
*
* 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.formula.rules;
import java.io.IOException;
import java.util.Iterator;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.formula.MolecularFormulaRange;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IElement;
import org.openscience.cdk.interfaces.IIsotope;
import org.openscience.cdk.interfaces.IMolecularFormula;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator;
/**
* This class validate if the occurrence of the IElements in the IMolecularFormula
* are into a limits. As default defines all elements of the periodic table with
* a occurrence of zero to 100.
*
*
* <p>This rule uses these parameters:
* <table border="1">
* <tr>
* <td>Name</td>
* <td>Default</td>
* <td>Description</td>
* </tr>
* <tr>
* <td>elements</td>
* <td>C,H,N,O</td>
* <td>The IELements to be analyzed</td>
* </tr>
* </table>
*
* @cdk.module formula
* @author miguelrojasch
* @cdk.created 2007-11-20
*/
public class ElementRule implements IRule{
private static ILoggingTool logger =
LoggingToolFactory.createLoggingTool(ElementRule.class);
private MolecularFormulaRange mfRange;
/**
* Constructor for the ElementRule object.
*
* @throws IOException If an error occurs when reading atom type information
* @throws ClassNotFoundException If an error occurs during tom typing
*/
public ElementRule(){
}
/**
* Sets the parameters attribute of the ElementRule object.
*
* @param params The new parameters value
* @throws CDKException Description of the Exception
*
* @see #getParameters
*/
public void setParameters(Object[] params) throws CDKException {
if (params.length != 1)
throw new CDKException("ElementRule expects one parameters");
if(!(params[0] instanceof MolecularFormulaRange))
throw new CDKException("The parameter must be of type MolecularFormulaExpand");
mfRange = (MolecularFormulaRange)params[0];
}
/**
* Gets the parameters attribute of the ElementRule object.
*
* @return The parameters value
* @see #setParameters
*/
public Object[] getParameters() {
// return the parameters as used for the rule validation
Object[] params = new Object[1];
params[0] = mfRange;
return params;
}
/**
* Validate the occurrence of this IMolecularFormula.
*
* @param formula Parameter is the IMolecularFormula
* @return An ArrayList containing 9 elements in the order described above
*/
public double validate(IMolecularFormula formula) throws CDKException {
logger.info("Start validation of ",formula);
ensureDefaultOccurElements(formula.getBuilder());
double isValid = 1.0;
Iterator<IElement> itElem = MolecularFormulaManipulator.elements(formula).iterator();
while(itElem.hasNext()){
IElement element = itElem.next();
int occur = MolecularFormulaManipulator.getElementCount(formula, element);
IIsotope elemIsotope = formula.getBuilder().newIsotope(element.getSymbol());
if((occur < mfRange.getIsotopeCountMin(elemIsotope))
|| ( occur > mfRange.getIsotopeCountMax(elemIsotope)))
{
isValid = 0.0;
break;
}
}
return isValid;
}
/**
* Initiate the MolecularFormulaExpand with the maximum and minimum occurrence of the Elements.
* In this case all elements of the periodic table are loaded.
*/
private void ensureDefaultOccurElements(IChemObjectBuilder builder){
if (mfRange == null) {
String[] elements = new String[]{
"C", "H", "O", "N", "Si", "P", "S", "F", "Cl",
"Br", "I", "Sn", "B", "Pb", "Tl", "Ba", "In", "Pd",
"Pt", "Os", "Ag", "Zr", "Se", "Zn", "Cu", "Ni", "Co",
"Fe", "Cr", "Ti", "Ca", "K", "Al", "Mg", "Na", "Ce",
"Hg", "Au", "Ir", "Re", "W", "Ta", "Hf", "Lu", "Yb",
"Tm", "Er", "Ho", "Dy", "Tb", "Gd", "Eu", "Sm", "Pm",
"Nd", "Pr", "La", "Cs", "Xe", "Te", "Sb", "Cd", "Rh",
"Ru", "Tc", "Mo", "Nb", "Y", "Sr", "Rb", "Kr", "As",
"Ge", "Ga", "Mn", "V", "Sc", "Ar", "Ne", "Be", "Li",
"Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac",
"Th", "Pa", "U", "Np", "Pu"};
mfRange = new MolecularFormulaRange();
for(int i = 0; i < elements.length ; i++)
mfRange.addIsotope( builder.newIsotope(elements[i]), 0, 50);
}
}
}