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private double[] calculateHeteroAtomConjugatedDescriptor(IAtom atom, IAtomContainer atomContainer, IAtomContainer conjugatedSys) throws CDKException {

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double[] results = new double[4];

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results[0] = -10.0;

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results[1] = 0.0;

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results[2] = 0.0;

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results[3] = 0.0;

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/*calculation of the atomic descriptors*/

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Iterator atomIt = conjugatedSys.atoms();

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while(atomIt.hasNext()){

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IAtom atomsss = (IAtom) atomIt.next();

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if(atomContainer.getConnectedLonePairsCount(atomsss) == 0){

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PartialPiChargeDescriptor descriptor1 = new PartialPiChargeDescriptor();

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double result1;

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result1 = ((DoubleResult)descriptor1.calculate(atomsss,atomContainer).getValue()).doubleValue();

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if(result1 != 0.0)

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if(result1 > results[0])

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results[0] = result1;

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}else{

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PartialPiChargeDescriptor descriptor1 = new PartialPiChargeDescriptor();

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double result1 = ((DoubleResult)descriptor1.calculate(atomsss,atomContainer).getValue()).doubleValue();

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results[1] = result1;

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}

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SigmaElectronegativityDescriptor descriptor2 = new SigmaElectronegativityDescriptor();

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double result2 = ((DoubleResult)descriptor2.calculate(atomsss,atomContainer).getValue()).doubleValue();

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results[3] += result2;

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}

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/*calculation of the bond descriptors*/

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Iterator bondIt = conjugatedSys.bonds();

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while(bondIt.hasNext()){

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IBond bondsss = (IBond) bondIt.next();

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ResonancePositiveChargeDescriptor descriptor5 = new ResonancePositiveChargeDescriptor();

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DoubleArrayResult dar;

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dar = ((DoubleArrayResult)descriptor5.calculate(bondsss,atomContainer).getValue());

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double result1 = dar.get(0);

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double resutt2 = dar.get(1);

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double result12 = (result1+resutt2);

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double resultT = 0;

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if(result12 != 0)

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resultT = result12/2;

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results[2] += resultT;

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}

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if(results[2] != 0)

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results[2] = results[1]/conjugatedSys.getAtomCount();

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if(results[3] != 0)

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results[3] = results[2]/conjugatedSys.getAtomCount();

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return results;

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}

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/**

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* Calculate the necessary descriptors for Heteratom atoms

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* @param atomContainer The IAtomContainer

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* @return Array with the values of the descriptors.

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* @throws CDKException

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private double[] calculateHeteroAtomDescriptor(IAtom atom, IAtomContainer atomContainer) throws CDKException {

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double[] results = new double[4];

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SigmaElectronegativityDescriptor descriptor1 = new SigmaElectronegativityDescriptor();

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PartialSigmaChargeDescriptor descriptor2 = new PartialSigmaChargeDescriptor();

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EffectiveAtomPolarizabilityDescriptor descriptor3 = new EffectiveAtomPolarizabilityDescriptor();

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PiElectronegativityDescriptor descriptor4 = new PiElectronegativityDescriptor();

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results[0]= ((DoubleResult)descriptor1.calculate(atom,atomContainer).getValue()).doubleValue();

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results[1]= ((DoubleResult)descriptor2.calculate(atom,atomContainer).getValue()).doubleValue();

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results[2]= ((DoubleResult)descriptor3.calculate(atom,atomContainer).getValue()).doubleValue();

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results[3]= ((DoubleResult)descriptor4.calculate(atom,atomContainer).getValue()).doubleValue();

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return results;

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}

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/**

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* Calculate the necessary descriptors for Carbonyl group

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* @param atomContainer The IAtomContainer

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* @return Array with the values of the descriptors.

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private double[] calculateCarbonylDescriptor(IAtom atom, IAtomContainer atomContainer) {

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double[] results = new double[6];

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IAtom positionX = atom;

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IAtom positionC = null;

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List listAtoms = atomContainer.getConnectedAtomsList(atom);

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for(Iterator it = listAtoms.iterator(); it.hasNext();){

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IAtom atom2 = (IAtom)it.next();

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if(((IBond)atomContainer.getBond(atom, atom2)).getOrder() > 1)

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positionC = atom2;

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}

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IBond bond = atomContainer.getBond(positionX, positionC);

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try {

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AtomContainerSet conjugatedPi = ConjugatedPiSystemsDetector.detect(atomContainer);

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if(conjugatedPi.getAtomContainerCount() == 1){

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IAtomContainer conjugatedSy = conjugatedPi.getAtomContainer(0);

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Iterator atomIt = conjugatedSy.atoms();

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while(atomIt.hasNext()){

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IAtom atomsss = (IAtom) atomIt.next();

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if(atomsss.getSymbol().equals("C")){

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PartialPiChargeDescriptor descriptor1 = new PartialPiChargeDescriptor();

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double result1 = ((DoubleResult)descriptor1.calculate(atomsss,atomContainer).getValue()).doubleValue();

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if(result1 > results[1])

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results[1] = result1;

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SigmaElectronegativityDescriptor descriptor2 = new SigmaElectronegativityDescriptor();

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double result2 = ((DoubleResult)descriptor2.calculate(atomsss,atomContainer).getValue()).doubleValue();

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results[0] += result2;

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}

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}

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if(results[0] != 0)

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results[0] = results[0]/conjugatedSy.getAtomCount();

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if(results[1] != 0)

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results[1] = results[1]/conjugatedSy.getAtomCount();

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}else{

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/* 1 */

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try{

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SigmaElectronegativityDescriptor descriptor1 = new SigmaElectronegativityDescriptor();

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results[0] = ((DoubleResult)descriptor1.calculate(positionC,(IAtomContainer) atomContainer).getValue()).doubleValue();

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}catch(Exception e){

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results[0] = 0.0;

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}

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// System.out.println("symbolC: "+atomContainer.getAtom(positionC).getSymbol());

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// System.out.println("symbolX: "+atomContainer.getAtom(positionX).getSymbol());

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/* 2 */

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try{

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PartialPiChargeDescriptor descriptor2 = new PartialPiChargeDescriptor();

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results[1] = ((DoubleResult)descriptor2.calculate(positionC,(IAtomContainer) atomContainer).getValue()).doubleValue();

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}catch(Exception e){

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results[1] = 0.0;

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}

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}

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/* 3 */

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try{

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BondPartialSigmaChargeDescriptor descriptor3 = new BondPartialSigmaChargeDescriptor();

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results[2] = ((DoubleResult)descriptor3.calculate(bond,(IAtomContainer) atomContainer).getValue()).doubleValue();

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}catch(Exception e){

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results[2] = 0.0;

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}

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/* 4 */

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try{

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SigmaElectronegativityDescriptor descriptor4 = new SigmaElectronegativityDescriptor();

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results[3] = ((DoubleResult)descriptor4.calculate(positionX,(IAtomContainer) atomContainer).getValue()).doubleValue();

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}catch(Exception e){

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results[3] = 0.0;

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}

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/* 5 */

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try{

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PartialPiChargeDescriptor descriptor5 = new PartialPiChargeDescriptor();

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results[4] = ((DoubleResult)descriptor5.calculate(positionX,(IAtomContainer) atomContainer).getValue()).doubleValue();

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}catch(Exception e){

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results[4] = 0.0;

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}

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/* 6 */

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try{

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ResonancePositiveChargeDescriptor descriptor6 = new ResonancePositiveChargeDescriptor();

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DoubleArrayResult dar = ((DoubleArrayResult)descriptor6.calculate(bond,atomContainer).getValue());

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double datT =0.0;

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if((new Double(dar.get(0))).toString().equals("Infinity")||

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(new Double(dar.get(1))).toString().equals("Infinity")){}

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else if(dar.get(0) == 0 && dar.get(1) == 0){}

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else

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datT = (dar.get(0)+dar.get(1))/2;

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results[5] = datT;

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}catch(Exception e){

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results[5] = 0.0;

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}

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} catch (CDKException e) {

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e.printStackTrace();

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}

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return results;

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}

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/**

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* Gets the parameterNames attribute of the IPAtomicDescriptor object.

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* @return The parameterNames value

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public String[] getParameterNames() {

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return new String[0];

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}

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/**

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* Gets the parameterType attribute of the IPAtomicDescriptor object.

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* @param name Description of the Parameter

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* @return An Object of class equal to that of the parameter being requested

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public Object getParameterType(String name) {

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return null;

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}

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}

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