[Cdk-commits] CVS: cdk/src/org/openscience/cdk/qsar ConnectivityOrderOneDescriptor.java,NONE,1.1 ConnectivityOrderZeroDescriptor.java,NONE,1.1 ValenceConnectivityOrderOneDescriptor.java,NONE,1.1 ValenceConnectivityOrderZeroDescriptor.java,NONE,1.1

[Matteo F. <mf...@us...>]

Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv4682/src/org/openscience/cdk/qsar

Added Files:
	ConnectivityOrderOneDescriptor.java 
	ConnectivityOrderZeroDescriptor.java 
	ValenceConnectivityOrderOneDescriptor.java 
	ValenceConnectivityOrderZeroDescriptor.java 
Log Message:
added new set of 8 Kier-Hall descriptors, with test file, and added a ZagrebIndex test file

--- NEW FILE: ConnectivityOrderOneDescriptor.java ---
/*
 *  $RCSfile: ConnectivityOrderOneDescriptor.java,v $
 *  $Author: mfe4 $
 *  $Date: 2004/12/02 12:27:27 $
 *  $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.Bond;
import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.exception.CDKException;
import java.util.Map;
import java.util.Hashtable;
import java.util.ArrayList;

/**
 *  Connectivity index (order 1):
 *  http://www.edusoft-lc.com/molconn/manuals/400/chaptwo.html
 *  http://www.chemcomp.com/Journal_of_CCG/Features/descr.htm#KH
 *  returned values are:
 *  chi1 is the Atomic connectivity index (order 1),
 *  chi1_C is the Carbon connectivity index (order 1);
 *
 *@author         mfe4
 *@cdk.created    2004-11-03
 * @cdk.module	qsar
 */
public class ConnectivityOrderOneDescriptor implements Descriptor {

	/**
	 *  Constructor for the ConnectivityOrderOneDescriptor object
	 */
	public ConnectivityOrderOneDescriptor() { }


	/**
	 *  Gets the specification attribute of the ConnectivityOrderOneDescriptor object
	 *
	 *@return    The specification value
	 */
	public Map getSpecification() {
		Hashtable specs = new Hashtable();
		specs.put("Specification-Reference", "http://qsar.sourceforge.net/dicts/qsar-descriptors:chiValuesCOO");
		specs.put("Implementation-Title", this.getClass().getName());
		specs.put("Implementation-Identifier", "$Id: ConnectivityOrderOneDescriptor.java,v 1.1 2004/12/02 12:27:27 mfe4 Exp $");
		// added by CVS
		specs.put("Implementation-Vendor", "The Chemistry Development Kit");
		return specs;
	}


	/**
	 *  Sets the parameters attribute of the ConnectivityOrderOneDescriptor object
	 *
	 *@param  params            The new parameters value
	 *@exception  CDKException  Description of the Exception
	 */
	public void setParameters(Object[] params) throws CDKException {
		// no parameters for this descriptor
	}


	/**
	 *  Gets the parameters attribute of the ConnectivityOrderOneDescriptor object
	 *
	 *@return    The parameters value
	 */
	public Object[] getParameters() {
		return (null);
		// no parameters to return
	}


	/**
	 *  Description of the Method
	 *
	 *@param  ac                AtomContainer
	 *@return                   chiValuesCOO is an arrayList that contains chi1 and chi1_C
	 *@exception  CDKException  Possible Exceptions
	 */
	public Object calculate(AtomContainer ac) throws CDKException {
		ArrayList chiValuesCOO = new ArrayList(2);
		ArrayList degrees = new ArrayList(2);
		double chi1 = 0;
		double chi1_C = 0;
		double val0 = 0;
		double val1 = 0;
		int atomDegree = 0;
		Bond[] bonds = ac.getBonds();
		Atom[] atoms = null;
		for (int b = 0; b < bonds.length; b++) {
			atoms = bonds[b].getAtoms();
			if ((!atoms[0].getSymbol().equals("H")) || (!atoms[1].getSymbol().equals("H"))) {
				degrees.clear();
				for (int a = 0; a < atoms.length; a++) {
					atomDegree = 0;
					Atom[] neighboors = ac.getConnectedAtoms(atoms[a]);
					for (int n = 0; n < neighboors.length; n++) {
						if (!neighboors[n].getSymbol().equals("H")) {
							atomDegree += 1;
						}
					}
					if(atomDegree > 0) {
						degrees.add(new Double(atomDegree));
					}
				}
				val0 = ( (Double)degrees.get(0) ).doubleValue();
				val1 = ( (Double)degrees.get(1) ).doubleValue();
				if((atoms[0].getSymbol().equals("C")) && (atoms[1].getSymbol().equals("C"))) {
					chi1_C += 1/(Math.sqrt(val0 * val1));
				}
				chi1 += 1/(Math.sqrt(val0 * val1));
			}
		}
		chiValuesCOO.add(new Double(chi1));
		chiValuesCOO.add(new Double(chi1_C));		
		return new ArrayList(chiValuesCOO);
	}


	/**
	 *  Gets the parameterNames attribute of the ConnectivityOrderOneDescriptor object
	 *
	 *@return    The parameterNames value
	 */
	public String[] getParameterNames() {
		// no param names to return
		return (null);
	}



	/**
	 *  Gets the parameterType attribute of the ConnectivityOrderOneDescriptor object
	 *
	 *@param  name  Description of the Parameter
	 *@return       The parameterType value
	 */
	public Object getParameterType(String name) {
		return (null);
	}
}


--- NEW FILE: ConnectivityOrderZeroDescriptor.java ---
/*
 *  $RCSfile: ConnectivityOrderZeroDescriptor.java,v $
 *  $Author: mfe4 $
 *  $Date: 2004/12/02 12:27:27 $
 *  $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.AtomContainer;
import org.openscience.cdk.exception.CDKException;
import java.util.Map;
import java.util.Hashtable;
import java.util.ArrayList;

/**
 *  Connectivity index (order 0):
 *  http://www.edusoft-lc.com/molconn/manuals/400/chaptwo.html
 *  http://www.chemcomp.com/Journal_of_CCG/Features/descr.htm#KH
 *  returned values are:
 *  chi0 is the Atomic connectivity index (order 0),
 *  chi0_C is the Carbon connectivity index (order 0);
 *
 *@author         mfe4
 *@cdk.created    2004-11-03
 * @cdk.module	qsar
 */
public class ConnectivityOrderZeroDescriptor implements Descriptor {

	/**
	 *  Constructor for the ConnectivityOrderZeroDescriptor object
	 */
	public ConnectivityOrderZeroDescriptor() { }


	/**
	 *  Gets the specification attribute of the ConnectivityOrderZeroDescriptor object
	 *
	 *@return    The specification value
	 */
	public Map getSpecification() {
		Hashtable specs = new Hashtable();
		specs.put("Specification-Reference", "http://qsar.sourceforge.net/dicts/qsar-descriptors:chiValuesCOZ");
		specs.put("Implementation-Title", this.getClass().getName());
		specs.put("Implementation-Identifier", "$Id: ConnectivityOrderZeroDescriptor.java,v 1.1 2004/12/02 12:27:27 mfe4 Exp $");
		// added by CVS
		specs.put("Implementation-Vendor", "The Chemistry Development Kit");
		return specs;
	}


	/**
	 *  Sets the parameters attribute of the ConnectivityOrderZeroDescriptor object
	 *
	 *@param  params            The new parameters value
	 *@exception  CDKException  Description of the Exception
	 */
	public void setParameters(Object[] params) throws CDKException {
		// no parameters for this descriptor
	}


	/**
	 *  Gets the parameters attribute of the ConnectivityOrderZeroDescriptor object
	 *
	 *@return    The parameters value
	 */
	public Object[] getParameters() {
		return (null);
		// no parameters to return
	}


	/**
	 *  Description of the Method
	 *
	 *@param  ac                AtomContainer
	 *@return                   chiValuesCOZ is an arrayList that contains chi0 and chi0_C
	 *@exception  CDKException  Possible Exceptions
	 */
	public Object calculate(AtomContainer ac) throws CDKException {
		ArrayList chiValuesCOZ = new ArrayList(2);
		double chi0 = 0;
		double chi0_C = 0;
		Atom[] atoms = ac.getAtoms();
		for (int i = 0; i < atoms.length; i++) {
			int atomDegree = 0;
			Atom[] neighboors = ac.getConnectedAtoms(atoms[i]);
			for (int a = 0; a < neighboors.length; a++) {
				if (!neighboors[a].getSymbol().equals("H")) {
					atomDegree += 1;
				}
			}
			if(atomDegree > 0) {
				if(atoms[i].getSymbol().equals("C")) {
					chi0_C += 1/(Math.sqrt(atomDegree));
				}
				chi0 += 1/(Math.sqrt(atomDegree));
			}
		}
		chiValuesCOZ.add(new Double(chi0));
		chiValuesCOZ.add(new Double(chi0_C));		
		return new ArrayList(chiValuesCOZ);
	}


	/**
	 *  Gets the parameterNames attribute of the ConnectivityOrderZeroDescriptor object
	 *
	 *@return    The parameterNames value
	 */
	public String[] getParameterNames() {
		// no param names to return
		return (null);
	}



	/**
	 *  Gets the parameterType attribute of the ConnectivityOrderZeroDescriptor object
	 *
	 *@param  name  Description of the Parameter
	 *@return       The parameterType value
	 */
	public Object getParameterType(String name) {
		return (null);
	}
}


--- NEW FILE: ValenceConnectivityOrderOneDescriptor.java ---
/*
 *  $RCSfile: ValenceConnectivityOrderOneDescriptor.java,v $
 *  $Author: mfe4 $
 *  $Date: 2004/12/02 12:27:27 $
 *  $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.Bond;
import org.openscience.cdk.Element;
import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.tools.*;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.config.IsotopeFactory;
import junit.framework.AssertionFailedError;
import java.util.Map;
import java.util.Hashtable;
import java.util.ArrayList;


/**
 *  Atomic valence connectivity index (order 1):
 *  http://www.edusoft-lc.com/molconn/manuals/400/chaptwo.html
 *  http://www.chemcomp.com/Journal_of_CCG/Features/descr.htm#KH
 *  returned values are:
 *  chi1v is the Atomic valence connectivity index (order 1),
 *  chi1_C is the Carbon valence connectivity index (order 1);
 *  valence is the number of s and p valence electrons of atom.
 *
 *@author         mfe4
 *@cdk.created    2004-11-03
 * @cdk.module	qsar
 */
public class ValenceConnectivityOrderOneDescriptor implements Descriptor {

	/**
	 *  Constructor for the ValenceConnectivityOrderOneDescriptor object
	 */
	public ValenceConnectivityOrderOneDescriptor() { }


	/**
	 *  Gets the specification attribute of the
	 *  ValenceConnectivityOrderOneDescriptor object
	 *
	 *@return    The specification value
	 */
	public Map getSpecification() {
		Hashtable specs = new Hashtable();
		specs.put("Specification-Reference", "http://qsar.sourceforge.net/dicts/qsar-descriptors:chiValuesVCOO");
		specs.put("Implementation-Title", this.getClass().getName());
		specs.put("Implementation-Identifier", "$Id: ValenceConnectivityOrderOneDescriptor.java,v 1.1 2004/12/02 12:27:27 mfe4 Exp $");
		// added by CVS
		specs.put("Implementation-Vendor", "The Chemistry Development Kit");
		return specs;
	}


	/**
	 *  Sets the parameters attribute of the
	 *  ValenceConnectivityOrderOneDescriptor object
	 *
	 *@param  params            The new parameters value
	 *@exception  CDKException  Description of the Exception
	 */
	public void setParameters(Object[] params) throws CDKException {
		// no parameters for this descriptor
	}


	/**
	 *  Gets the parameters attribute of the
	 *  ValenceConnectivityOrderOneDescriptor object
	 *
	 *@return    The parameters value
	 */
	public Object[] getParameters() {
		// no parameters to return
		return (null);
	}


	/**
	 *  calculates the chi1v and chi1v_C descriptors for an atom container
	 *
	 *@param  ac                AtomContainer
	 *@return                   chi1v and chi1_C returned as arrayList
	 *@exception  CDKException  Possible Exceptions
	 */
	public Object calculate(AtomContainer ac) throws CDKException {
		Hashtable valences = new Hashtable();
		valences.put("Li", new Integer(1));
		valences.put("Be", new Integer(2));
		valences.put("B", new Integer(3));
		valences.put("C", new Integer(4));
		valences.put("N", new Integer(5));
		valences.put("O", new Integer(6));
		valences.put("F", new Integer(7));
		valences.put("Na", new Integer(1));
		valences.put("Mg", new Integer(2));
		valences.put("Al", new Integer(3));
		valences.put("Si", new Integer(4));
		valences.put("P", new Integer(5));
		valences.put("S", new Integer(6));
		valences.put("Cl", new Integer(7));
		valences.put("K", new Integer(1));
		valences.put("Ca", new Integer(2));
		valences.put("Ga", new Integer(3));
		valences.put("Ge", new Integer(4));
		valences.put("As", new Integer(5));
		valences.put("Se", new Integer(6));
		valences.put("Br", new Integer(7));
		valences.put("Rb", new Integer(1));
		valences.put("Sr", new Integer(2));
		valences.put("In", new Integer(3));
		valences.put("Sn", new Integer(4));
		valences.put("Sb", new Integer(5));
		valences.put("Te", new Integer(6));
		valences.put("I", new Integer(7));
		valences.put("Cs", new Integer(1));
		valences.put("Ba", new Integer(2));
		valences.put("Tl", new Integer(3));
		valences.put("Pb", new Integer(4));
		valences.put("Bi", new Integer(5));
		valences.put("Po", new Integer(6));
		valences.put("At", new Integer(7));
		valences.put("Fr", new Integer(1));
		valences.put("Ra", new Integer(2));
		
		int valence = 0;
		int atomicNumber = 0;
		int hcount = 0;
		int atomValue = 0;
		double val0 = 0;
		double val1 = 0;
		ArrayList chiValuesVCOO = new ArrayList(2);
		ArrayList chiAtom = new ArrayList(2);
		ArrayList chiCarbon = new ArrayList(2);
		double chi1v = 0;
		double chi1v_C = 0;
		Atom[] atoms = null;
		Atom[] neighatoms = null;
		Element element = null;
		IsotopeFactory elfac = null;
		String symbol = null;
		Bond[] bonds = ac.getBonds();
		for (int b = 0; b < bonds.length; b++) {
			atoms = bonds[b].getAtoms();
			if ((!atoms[0].getSymbol().equals("H")) || (!atoms[1].getSymbol().equals("H"))) {
				val0 = 0;
				val1 = 0;
				chiAtom.clear();
				chiCarbon.clear();
				for (int a = 0; a < atoms.length; a++) {
					symbol = atoms[a].getSymbol();
					try {
						elfac = IsotopeFactory.getInstance();
					} catch (Exception exc) {
						throw new AssertionFailedError("Problem instantiating IsotopeFactory: " + exc.toString());
					}
					try {
						element = elfac.getElement(symbol);
					} catch (Exception exc) {
						throw new AssertionFailedError("Problem getting isotope " + symbol + " from ElementFactory: " + exc.toString());
					}
					atomicNumber = element.getAtomicNumber();
					valence = ((Integer)valences.get(symbol)).intValue();
					hcount = 0;
					atomValue = 0;
					neighatoms = ac.getConnectedAtoms(atoms[a]);
					for (int n = 0; n < neighatoms.length; n++) {
						if (neighatoms[n].getSymbol().equals("H")) {
							hcount += 1;
						}
					}
					hcount += atoms[a].getHydrogenCount();
					atomValue = (valence - hcount) / (atomicNumber - valence - 1);
					if(atomValue > 0) {
						chiAtom.add(new Double(atomValue));
						System.out.println(symbol+"= atomvalue: "+atomValue+",val: "+valence+",h:"+hcount);
					}
				}
				val0 = ( (Double)chiAtom.get(0) ).doubleValue();
				val1 = ( (Double)chiAtom.get(1) ).doubleValue();
				if((atoms[0].getSymbol().equals("C")) && (atoms[1].getSymbol().equals("C"))) {
					chi1v_C += 1/(Math.sqrt(val0 * val1));
				}
				chi1v += 1/(Math.sqrt(val0 * val1));
			}
		}
		chiValuesVCOO.add(new Double(chi1v));
		chiValuesVCOO.add(new Double(chi1v_C));		
		return new ArrayList(chiValuesVCOO);
	}


	/**
	 *  Gets the parameterNames attribute of the
	 *  ValenceConnectivityOrderOneDescriptor object
	 *
	 *@return    The parameterNames value
	 */
	public String[] getParameterNames() {
		// no param names to return
		return (null);
	}



	/**
	 *  Gets the parameterType attribute of the
	 *  ValenceConnectivityOrderOneDescriptor object
	 *
	 *@param  name  Description of the Parameter
	 *@return       The parameterType value
	 */
	public Object getParameterType(String name) {
		return (null);
	}
}


--- NEW FILE: ValenceConnectivityOrderZeroDescriptor.java ---
/*
 *  $RCSfile: ValenceConnectivityOrderZeroDescriptor.java,v $
 *  $Author: mfe4 $
 *  $Date: 2004/12/02 12:27:27 $
 *  $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.tools.*;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.config.IsotopeFactory;
import junit.framework.AssertionFailedError;
import java.util.Map;
import java.util.Hashtable;
import java.util.ArrayList;


/**
 *  Atomic valence connectivity index (order 0):
 *  http://www.edusoft-lc.com/molconn/manuals/400/chaptwo.html
 *  http://www.chemcomp.com/Journal_of_CCG/Features/descr.htm#KH
 *  returned values are:
 *  chi0v is the Atomic valence connectivity index (order 0),
 *  chi0_C is the Carbon valence connectivity index (order 0);
 *  valence is the number of s and p valence electrons of atom.
 *
 *@author         mfe4
 *@cdk.created    2004-11-03
 * @cdk.module	qsar
 */
public class ValenceConnectivityOrderZeroDescriptor implements Descriptor {

	/**
	 *  Constructor for the ValenceConnectivityOrderZeroDescriptor object
	 */
	public ValenceConnectivityOrderZeroDescriptor() { }


	/**
	 *  Gets the specification attribute of the
	 *  ValenceConnectivityOrderZeroDescriptor object
	 *
	 *@return    The specification value
	 */
	public Map getSpecification() {
		Hashtable specs = new Hashtable();
		specs.put("Specification-Reference", "http://qsar.sourceforge.net/dicts/qsar-descriptors:chiValuesVCOZ");
		specs.put("Implementation-Title", this.getClass().getName());
		specs.put("Implementation-Identifier", "$Id: ValenceConnectivityOrderZeroDescriptor.java,v 1.1 2004/12/02 12:27:27 mfe4 Exp $");
		// added by CVS
		specs.put("Implementation-Vendor", "The Chemistry Development Kit");
		return specs;
	}


	/**
	 *  Sets the parameters attribute of the
	 *  ValenceConnectivityOrderZeroDescriptor object
	 *
	 *@param  params            The new parameters value
	 *@exception  CDKException  Description of the Exception
	 */
	public void setParameters(Object[] params) throws CDKException {
		// no parameters for this descriptor
	}


	/**
	 *  Gets the parameters attribute of the
	 *  ValenceConnectivityOrderZeroDescriptor object
	 *
	 *@return    The parameters value
	 */
	public Object[] getParameters() {
		// no parameters to return
		return (null);
	}


	/**
	 *  calculates the chiOv and chiOv_C descriptors for an atom container
	 *
	 *@param  ac                AtomContainer
	 *@return                   chi0v and chi0_C returned as arrayList
	 *@exception  CDKException  Possible Exceptions
	 */
	public Object calculate(AtomContainer ac) throws CDKException {
		Hashtable valences = new Hashtable();
		valences.put("Li", new Integer(1));
		valences.put("Be", new Integer(2));
		valences.put("B", new Integer(3));
		valences.put("C", new Integer(4));
		valences.put("N", new Integer(5));
		valences.put("O", new Integer(6));
		valences.put("F", new Integer(7));
		valences.put("Na", new Integer(1));
		valences.put("Mg", new Integer(2));
		valences.put("Al", new Integer(3));
		valences.put("Si", new Integer(4));
		valences.put("P", new Integer(5));
		valences.put("S", new Integer(6));
		valences.put("Cl", new Integer(7));
		valences.put("K", new Integer(1));
		valences.put("Ca", new Integer(2));
		valences.put("Ga", new Integer(3));
		valences.put("Ge", new Integer(4));
		valences.put("As", new Integer(5));
		valences.put("Se", new Integer(6));
		valences.put("Br", new Integer(7));
		valences.put("Rb", new Integer(1));
		valences.put("Sr", new Integer(2));
		valences.put("In", new Integer(3));
		valences.put("Sn", new Integer(4));
		valences.put("Sb", new Integer(5));
		valences.put("Te", new Integer(6));
		valences.put("I", new Integer(7));
		valences.put("Cs", new Integer(1));
		valences.put("Ba", new Integer(2));
		valences.put("Tl", new Integer(3));
		valences.put("Pb", new Integer(4));
		valences.put("Bi", new Integer(5));
		valences.put("Po", new Integer(6));
		valences.put("At", new Integer(7));
		valences.put("Fr", new Integer(1));
		valences.put("Ra", new Integer(2));
		
		int valence = 0;
		int atomicNumber = 0;
		int hcount = 0;
		int atomValue = 0;
		ArrayList chiValuesVCOZ = new ArrayList(2);
		double chi0v = 0;
		double chi0v_C = 0;
		Atom[] atoms = ac.getAtoms();
		Atom[] neighatoms = null;
		Element element = null;
		IsotopeFactory elfac = null;
		String symbol = null;
		for (int i = 0; i < atoms.length; i++) {
			symbol = atoms[i].getSymbol();
			try {
				elfac = IsotopeFactory.getInstance();
			} catch (Exception exc) {
				throw new AssertionFailedError("Problem instantiating IsotopeFactory: " + exc.toString());
			}
			try {
				element = elfac.getElement(symbol);
			} catch (Exception exc) {
				throw new AssertionFailedError("Problem getting isotope " + symbol + " from ElementFactory: " + exc.toString());
			}
			atomicNumber = element.getAtomicNumber();
			valence = ((Integer)valences.get(symbol)).intValue();
			hcount = 0;
			atomValue = 0;
			neighatoms = ac.getConnectedAtoms(atoms[i]);
			for (int a = 0; a < neighatoms.length; a++) {
				if (neighatoms[a].getSymbol().equals("H")) {
					hcount += 1;
				}
			}
			hcount += ac.getAtomAt(i).getHydrogenCount();
			atomValue = (valence - hcount) / (atomicNumber - valence - 1);
			if (atomValue > 0) {
				if(symbol.equals("C")) {
					chi0v_C  += (1/(Math.sqrt(atomValue))); // chi0v_C
				}
				chi0v += (1/(Math.sqrt(atomValue))); // chi0v
			}
		}
		chiValuesVCOZ.add(new Double(chi0v));
		chiValuesVCOZ.add(new Double(chi0v_C));		
		return new ArrayList(chiValuesVCOZ);
	}


	/**
	 *  Gets the parameterNames attribute of the
	 *  ValenceConnectivityOrderZeroDescriptor object
	 *
	 *@return    The parameterNames value
	 */
	public String[] getParameterNames() {
		// no param names to return
		return (null);
	}



	/**
	 *  Gets the parameterType attribute of the
	 *  ValenceConnectivityOrderZeroDescriptor object
	 *
	 *@param  name  Description of the Parameter
	 *@return       The parameterType value
	 */
	public Object getParameterType(String name) {
		return (null);
	}
}