@TestClass(value="org.openscience.cdk.charges.GasteigerPEPEPartialChargesTest") public class GasteigerPEPEPartialCharges extends Object implements IChargeCalculator
The calculation of the Gasteiger (PEPE) partial charges is based on . This class doesn't implement the original method of the Marsili but the method based on H. Saller which is described from Petra manual version 2.6
They are calculated by generating all valence bond (resonance) structures for this system and then weighting them on the basis of pi-orbital electronegativities and formal considerations based on PEPE (Partial Equalization of pi-electronegativity).
GasteigerMarsiliPartialCharges
Constructor and Description |
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GasteigerPEPEPartialCharges()
Constructor for the GasteigerPEPEPartialCharges object
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Modifier and Type | Method and Description |
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IAtomContainer |
assignGasteigerPiPartialCharges(IAtomContainer ac,
boolean setCharge)
Main method which assigns Gasteiger partial pi charges.
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double[][] |
assignrPiMarsilliFactors(IAtomContainerSet setAc)
Method which stores and assigns the factors a,b,c and CHI+
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void |
calculateCharges(IAtomContainer container) |
int |
getMaxGasteigerIters()
Gets the maxGasteigerIters attribute of the GasteigerPEPEPartialCharges
object
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int |
getMaxResoStruc()
Gets the maximum resonance structures to be searched
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int |
getStepSize()
Get the StepSize attribute of the GasteigerMarsiliPartialCharges
object
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void |
setMaxGasteigerIters(int iters)
Sets the maxGasteigerIters attribute of the GasteigerPEPEPartialCharges
object
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void |
setMaxResoStruc(int numbReson)
Sets the maximum resonance structures to be searched
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void |
setStepSize(int step)
Set the StepSize attribute of the GasteigerMarsiliPartialCharges
object
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public GasteigerPEPEPartialCharges()
@TestMethod(value="testSetMaxGasteigerIters_Double") public void setMaxGasteigerIters(int iters)
iters
- The new maxGasteigerIters value@TestMethod(value="testSetMaxResoStruc_Int") public void setMaxResoStruc(int numbReson)
numbReson
- The number of resonance Structures to be searched@TestMethod(value="testGetMaxGasteigerIters") public int getMaxGasteigerIters()
@TestMethod(value="testGetMaxResoStruc") public int getMaxResoStruc()
@TestMethod(value="testAssignGasteigerPiPartialCharges_IAtomContainer_Boolean") public IAtomContainer assignGasteigerPiPartialCharges(IAtomContainer ac, boolean setCharge) throws Exception
ac
- AtomContainersetCharge
- currently unusedException
- Possible Exceptions@TestMethod(value="testCalculateCharges_IAtomContainer") public void calculateCharges(IAtomContainer container) throws CDKException
calculateCharges
in interface IElectronicPropertyCalculator
CDKException
@TestMethod(value="testGetStepSize") public int getStepSize()
@TestMethod(value="testSetStepSize") public void setStepSize(int step)
step
- @TestMethod(value="testAssignrPiMarsilliFactors_IAtomContainerSet") public double[][] assignrPiMarsilliFactors(IAtomContainerSet setAc)