Class SigmaElectronegativityDescriptor
- java.lang.Object
-
- org.openscience.cdk.qsar.AbstractAtomicDescriptor
-
- org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor
-
- All Implemented Interfaces:
IAtomicDescriptor
,IDescriptor
public class SigmaElectronegativityDescriptor extends AbstractAtomicDescriptor implements IAtomicDescriptor
Atomic descriptor that reflects that Gasteiger-Marsili sigma electronegativity. The used approach is given byX = a + bq + c(q*q)
where a, b, and c are the Gasteiger-Marsili parameters and q is the sigma charge. For the actual calculation it uses theElectronegativity
class.Parameters for this descriptor: Name Default Description maxIterations 0 Number of maximum iterations - Author:
- mfe4
- See Also:
Electronegativity
- Dictionary pointer(s):
- sigmaElectronegativity in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:sigmaElectronegativity]
- Source code:
- main
- Belongs to CDK module:
- qsaratomic
- Created on:
- 2004-11-03
-
-
Constructor Summary
Constructors Constructor Description SigmaElectronegativityDescriptor()
Constructor for the SigmaElectronegativityDescriptor object
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description DescriptorValue
calculate(IAtom atom, IAtomContainer ac)
The method calculates the sigma electronegativity of a given atom 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 SigmaElectronegativityDescriptor objectObject[]
getParameters()
Gets the parameters attribute of the SigmaElectronegativityDescriptor objectObject
getParameterType(String name)
Gets the parameterType attribute of the SigmaElectronegativityDescriptor objectDescriptorSpecification
getSpecification()
Gets the specification attribute of the SigmaElectronegativityDescriptor objectvoid
initialise(IChemObjectBuilder builder)
Default implementation of initialise allows optional override.void
setParameters(Object[] params)
Sets the parameters attribute of the SigmaElectronegativityDescriptor object-
Methods inherited from class org.openscience.cdk.qsar.AbstractAtomicDescriptor
cacheDescriptorValue, getCachedDescriptorValue, isCachedAtomContainer
-
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
Methods inherited from interface org.openscience.cdk.qsar.IDescriptor
initialise
-
-
-
-
Method Detail
-
getSpecification
public DescriptorSpecification getSpecification()
Gets the specification attribute of the SigmaElectronegativityDescriptor object- Specified by:
getSpecification
in interfaceIDescriptor
- Returns:
- The specification value
-
setParameters
public void setParameters(Object[] params) throws CDKException
Sets the parameters attribute of the SigmaElectronegativityDescriptor object- Specified by:
setParameters
in interfaceIDescriptor
- Parameters:
params
- 1: max iterations (optional, defaults to 20)- Throws:
CDKException
- Description of the Exception- See Also:
IDescriptor.getParameters()
-
getParameters
public Object[] getParameters()
Gets the parameters attribute of the SigmaElectronegativityDescriptor object- Specified by:
getParameters
in interfaceIDescriptor
- Returns:
- The parameters value
- See Also:
IDescriptor.setParameters(java.lang.Object[])
-
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- Specified by:
getDescriptorNames
in interfaceIDescriptor
- Returns:
- An array of descriptor names, equal in length to the number of descriptor calculated..
-
calculate
public DescriptorValue calculate(IAtom atom, IAtomContainer ac)
The method calculates the sigma electronegativity of a given atom It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.- Specified by:
calculate
in interfaceIAtomicDescriptor
- Parameters:
atom
- The IAtom for which the DescriptorValue is requestedac
- AtomContainer- Returns:
- return the sigma electronegativity
-
getParameterNames
public String[] getParameterNames()
Gets the parameterNames attribute of the SigmaElectronegativityDescriptor object- Specified by:
getParameterNames
in interfaceIDescriptor
- Returns:
- The parameterNames value
-
getParameterType
public Object getParameterType(String name)
Gets the parameterType attribute of the SigmaElectronegativityDescriptor object- Specified by:
getParameterType
in interfaceIDescriptor
- Parameters:
name
- Description of the Parameter- Returns:
- An Object of class equal to that of the parameter being requested
-
initialise
public void initialise(IChemObjectBuilder builder)
Default implementation of initialise allows optional override.- Specified by:
initialise
in interfaceIDescriptor
- Parameters:
builder
- chem object build
-
-