Class PartialPiChargeDescriptor
- java.lang.Object
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- org.openscience.cdk.qsar.AbstractAtomicDescriptor
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- org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor
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- All Implemented Interfaces:
IAtomicDescriptor
,IDescriptor
public class PartialPiChargeDescriptor extends AbstractAtomicDescriptor
The calculation of pi partial charges in pi-bonded systems of an heavy atom was made by Saller-Gasteiger. It is based on the qualitative concept of resonance and implemented with the Partial Equalization of Pi-Electronegativity (PEPE).
Parameters for this descriptor: Name Default Description maxIterations 0 Number of maximum iterations - Author:
- Miguel Rojas
- See Also:
GasteigerPEPEPartialCharges
- Dictionary pointer(s):
- partialPiCharge in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:partialPiCharge]
- Source code:
- main
- Belongs to CDK module:
- qsaratomic
- Created on:
- 2006-04-15
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Constructor Summary
Constructors Constructor Description PartialPiChargeDescriptor()
Constructor for the PartialPiChargeDescriptor object
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description DescriptorValue
calculate(IAtom atom, IAtomContainer ac)
The method returns apha partial charges assigned to an heavy atom through Gasteiger Marsili It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.String[]
getDescriptorNames()
Returns an array of names for each descriptor value calculated.String[]
getParameterNames()
Gets the parameterNames attribute of the PartialPiChargeDescriptor objectObject[]
getParameters()
Gets the parameters attribute of the PartialPiChargeDescriptor objectObject
getParameterType(String name)
Gets the parameterType attribute of the PartialPiChargeDescriptor objectDescriptorSpecification
getSpecification()
Gets the specification attribute of the PartialPiChargeDescriptor objectvoid
initialise(IChemObjectBuilder builder)
Default implementation of initialise allows optional override.void
setParameters(Object[] params)
Sets the parameters attribute of the PartialPiChargeDescriptor object-
Methods inherited from class org.openscience.cdk.qsar.AbstractAtomicDescriptor
cacheDescriptorValue, getCachedDescriptorValue, isCachedAtomContainer
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.openscience.cdk.qsar.IDescriptor
initialise
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Method Detail
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getSpecification
public DescriptorSpecification getSpecification()
Gets the specification attribute of the PartialPiChargeDescriptor object- Returns:
- The specification value
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setParameters
public void setParameters(Object[] params) throws CDKException
Sets the parameters attribute of the PartialPiChargeDescriptor object- Parameters:
params
- 1:Number of maximum iterations, 2: checking lone pair electrons, 3: number of maximum resonance structures to be searched.- Throws:
CDKException
- Description of the Exception- See Also:
IDescriptor.getParameters()
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getParameters
public Object[] getParameters()
Gets the parameters attribute of the PartialPiChargeDescriptor object- Returns:
- The parameters value
- See Also:
IDescriptor.setParameters(java.lang.Object[])
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getDescriptorNames
public String[] getDescriptorNames()
Description copied from interface:IDescriptor
Returns an array of names for each descriptor value calculated. Many descriptors return multiple values. In general it is useful for the descriptor to indicate the names for each value. In many cases, these names can be as simple as X1, X2, ..., XN where X is a prefix and 1, 2, ..., N are the indices. On the other hand it is also possible to return other arbitrary names, which should be documented in the Javadocs for the descriptor (e.g., the CPSA descriptor). Note that by default if a descriptor returns a single value (such asALOGPDescriptor
the return array will have a single element- Returns:
- An array of descriptor names, equal in length to the number of descriptor calculated..
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calculate
public DescriptorValue calculate(IAtom atom, IAtomContainer ac)
The method returns apha partial charges assigned to an heavy atom through Gasteiger Marsili It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder. For this method will be only possible if the heavy atom has single bond.- Parameters:
atom
- The IAtom for which the DescriptorValue is requestedac
- AtomContainer- Returns:
- Value of the alpha partial charge
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getParameterNames
public String[] getParameterNames()
Gets the parameterNames attribute of the PartialPiChargeDescriptor object- Returns:
- The parameterNames value
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getParameterType
public Object getParameterType(String name)
Gets the parameterType attribute of the PartialPiChargeDescriptor object- Parameters:
name
- Description of the Parameter- Returns:
- The parameterType value
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initialise
public void initialise(IChemObjectBuilder builder)
Default implementation of initialise allows optional override.- Specified by:
initialise
in interfaceIDescriptor
- Parameters:
builder
- chem object build
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