org.openscience.cdk.qsar.descriptors.atomic
Class ProtonAffinityHOSEDescriptor

java.lang.Object
  org.openscience.cdk.qsar.AbstractAtomicDescriptor
      org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor

All Implemented Interfaces:

IAtomicDescriptor, IDescriptor

@TestClass(value="org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptorTest")
public class ProtonAffinityHOSEDescriptor
extends AbstractAtomicDescriptor

This class returns the proton affinity of an atom containing.

This descriptor uses these parameters:

Name	Default	Description
		no parameters

Author:

Miguel Rojas

Belongs to the set:

qsar-descriptors

Created on:

2006-05-26

Belongs to CDK module:

qsaratomic

Dictionary pointer(s):

protonaffinity in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:protonaffinity]

Source code:

cdk-1.4.x

Constructor Summary

ProtonAffinityHOSEDescriptor()
Constructor for the ProtonAffinityDescriptor object.

Method Summary

DescriptorValue	calculate(IAtom atom, IAtomContainer container) This method calculates the protonation affinity of an atom.
String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
String[]	getParameterNames() Gets the parameterNames attribute of the ProtonAffinityDescriptor object.
Object[]	getParameters() Gets the parameters attribute of the ProtonAffinityDescriptor object.
Object	getParameterType(String name) Gets the parameterType attribute of the ProtonAffinityDescriptor object.
DescriptorSpecification	getSpecification() Gets the specification attribute of the ProtonAffinityDescriptor object
void	setParameters(Object[] params) This descriptor does have any parameter.

Methods inherited from class org.openscience.cdk.qsar.AbstractAtomicDescriptor

cacheDescriptorValue, getCachedDescriptorValue, isCachedAtomContainer

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ProtonAffinityHOSEDescriptor

public ProtonAffinityHOSEDescriptor()

Constructor for the ProtonAffinityDescriptor object.

Method Detail

getSpecification

@TestMethod(value="testGetSpecification")
public DescriptorSpecification getSpecification()

Gets the specification attribute of the ProtonAffinityDescriptor object

Returns:

The specification value

setParameters

@TestMethod(value="testSetParameters_arrayObject")
public void setParameters(Object[] params)
                   throws CDKException

This descriptor does have any parameter.

Parameters:

params - An array of Object containing the parameters for this descriptor

Throws:

CDKException - if invalid number of type of parameters are passed to it

See Also:

IDescriptor.getParameters()

getParameters

@TestMethod(value="testGetParameters")
public Object[] getParameters()

Gets the parameters attribute of the ProtonAffinityDescriptor object.

Returns:

The parameters value

See Also:

setParameters(java.lang.Object[])

getDescriptorNames

@TestMethod(value="testNamesConsistency")
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 decsriptor (e.g., the CPSA descriptor).

Note that by default if a descriptor returns a single value (such as ALOGPDescriptor the return array will have a single element

Returns:

An array of descriptor names, equal in length to the number of descriptor calculated..

calculate

@TestMethod(value="testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtom atom,
                                                 IAtomContainer container)

This method calculates the protonation affinity of an atom.

Parameters:

atom - The IAtom to protonate

container - Parameter is the IAtomContainer.

Returns:

The protonation affinity. Not possible the ionization.

getParameterNames

@TestMethod(value="testGetParameterNames")
public String[] getParameterNames()

Gets the parameterNames attribute of the ProtonAffinityDescriptor object.

Returns:

The parameterNames value

getParameterType

@TestMethod(value="testGetParameterType_String")
public Object getParameterType(String name)

Gets the parameterType attribute of the ProtonAffinityDescriptor object.

Parameters:

name - Description of the Parameter

Returns:

An Object of class equal to that of the parameter being requested