Package org.openscience.cdk.charges
Class GasteigerMarsiliPartialCharges
- java.lang.Object
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- org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
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- All Implemented Interfaces:
IChargeCalculator
,IElectronicPropertyCalculator
public class GasteigerMarsiliPartialCharges extends Object implements IChargeCalculator
The calculation of the Gasteiger Marsili (PEOE) partial charges is based on [Gasteiger, J. and Marsili, M.. Tetrahedron. 1980. 36]. This class only implements the original method which only applies to σ-bond systems.
- Author:
- chhoppe, rojas
- Source code:
- main
- Belongs to CDK module:
- charges
- Keywords:
- partial atomic charges, charge distribution, electronegativities, partial equalization of orbital, PEOE
- Created on:
- 2004-11-03
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Constructor Summary
Constructors Constructor Description GasteigerMarsiliPartialCharges()
Constructor for the GasteigerMarsiliPartialCharges object.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description IAtomContainer
assignGasteigerMarsiliSigmaPartialCharges(IAtomContainer ac, boolean setCharge)
Main method which assigns Gasteiger Marisili partial sigma charges.double[]
assignGasteigerSigmaMarsiliFactors(IAtomContainer ac)
Method which stores and assigns the factors a,b,c and CHI+.void
calculateCharges(IAtomContainer container)
double
getChiCatHydrogen()
Gets chi_cat value for hydrogen, because H poses a special problem due to lack of possible second ionisation.double
getMaxGasteigerDamp()
Gets the maxGasteigerDamp attribute of the GasteigerMarsiliPartialCharges object.double
getMaxGasteigerIters()
Gets the maxGasteigerIters attribute of the GasteigerMarsiliPartialCharges object.int
getStepSize()
Get the StepSize attribute of the GasteigerMarsiliPartialCharges object.void
setChiCatHydrogen(double chiCat)
Sets chi_cat value for hydrogen, because H poses a special problem due to lack of possible second ionisation.void
setMaxGasteigerDamp(double damp)
Sets the maxGasteigerDamp attribute of the GasteigerMarsiliPartialCharges object.void
setMaxGasteigerIters(double iters)
Sets the maxGasteigerIters attribute of the GasteigerMarsiliPartialCharges object.void
setStepSize(int step)
Set the StepSize attribute of the GasteigerMarsiliPartialCharges object.
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Method Detail
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setChiCatHydrogen
public void setChiCatHydrogen(double chiCat)
Sets chi_cat value for hydrogen, because H poses a special problem due to lack of possible second ionisation.- Parameters:
chiCat
- The new DEOC_HYDROGEN value
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setMaxGasteigerDamp
public void setMaxGasteigerDamp(double damp)
Sets the maxGasteigerDamp attribute of the GasteigerMarsiliPartialCharges object.- Parameters:
damp
- The new maxGasteigerDamp value
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setMaxGasteigerIters
public void setMaxGasteigerIters(double iters)
Sets the maxGasteigerIters attribute of the GasteigerMarsiliPartialCharges object.- Parameters:
iters
- The new maxGasteigerIters value
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getChiCatHydrogen
public double getChiCatHydrogen()
Gets chi_cat value for hydrogen, because H poses a special problem due to lack of possible second ionisation.- Returns:
- The new DEOC_HYDROGEN value
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getMaxGasteigerDamp
public double getMaxGasteigerDamp()
Gets the maxGasteigerDamp attribute of the GasteigerMarsiliPartialCharges object.- Returns:
- The new maxGasteigerDamp value
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getMaxGasteigerIters
public double getMaxGasteigerIters()
Gets the maxGasteigerIters attribute of the GasteigerMarsiliPartialCharges object.- Returns:
- The new maxGasteigerIters value
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assignGasteigerMarsiliSigmaPartialCharges
public IAtomContainer assignGasteigerMarsiliSigmaPartialCharges(IAtomContainer ac, boolean setCharge) throws Exception
Main method which assigns Gasteiger Marisili partial sigma charges.- Parameters:
ac
- AtomContainersetCharge
- The Charge- Returns:
- AtomContainer with partial charges
- Throws:
Exception
- Possible Exceptions
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calculateCharges
public void calculateCharges(IAtomContainer container) throws CDKException
- Specified by:
calculateCharges
in interfaceIElectronicPropertyCalculator
- Throws:
CDKException
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getStepSize
public int getStepSize()
Get the StepSize attribute of the GasteigerMarsiliPartialCharges object.- Returns:
- STEP_SIZE
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setStepSize
public void setStepSize(int step)
Set the StepSize attribute of the GasteigerMarsiliPartialCharges object.- Parameters:
step
- size of the step
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assignGasteigerSigmaMarsiliFactors
public double[] assignGasteigerSigmaMarsiliFactors(IAtomContainer ac) throws CDKException
Method which stores and assigns the factors a,b,c and CHI+.- Parameters:
ac
- AtomContainer- Returns:
- Array of doubles [a1,b1,c1,denom1,chi1,q1...an,bn,cn...] 1:Atom 1-n in AtomContainer
- Throws:
CDKException
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