org.openscience.cdk.qsar.descriptors.molecular
Class IPMolecularLearningDescriptor

java.lang.Object
  org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

@TestClass(value="org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptorTest")
public class IPMolecularLearningDescriptor
extends java.lang.Object
implements IMolecularDescriptor

This class returns the ionization potential of a molecule. Up to now is only possible for atomContainers which contain; see IPAtomicDescriptor and IPBondDescriptor. The descriptor assumes that explicit hydrogens have been added to the molecule TODO: IP: Include the ionization for bonds

This descriptor uses these parameters:

Name	Default	Description
addlp	true	If true lone pairs are added to the molecule

Author:

Miguel Rojas

See Also:

IPAtomicHOSEDescriptor, IPBondLearningDescriptor

Belongs to the set:

qsar-descriptors

Keywords:

ionization potential

Created on:

2006-05-26

Belongs to CDK module:

qsarionpot

This class is affected by these bug(s):

1651264 1856148

Dictionary pointer(s):

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

Source code:

revision 10995

Constructor Summary

IPMolecularLearningDescriptor()
Constructor for the IPMolecularLearningDescriptor object

Method Summary

DescriptorValue	calculate(IAtomContainer atomContainer) It calculates the first ionization energy of a molecule.
DescriptorValue	calculatePlus(IAtomContainer container) It calculates the 1,2,..
java.lang.String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
IDescriptorResult	getDescriptorResultType() Returns the specific type of the DescriptorResult object.
java.lang.String[]	getParameterNames() Gets the parameterNames attribute of the IPMolecularLearningDescriptor object
java.lang.Object[]	getParameters() Gets the parameters attribute of the IPMolecularLearningDescriptor object
java.lang.Object	getParameterType(java.lang.String name) Gets the parameterType attribute of the IPMolecularLearningDescriptor object
DescriptorSpecification	getSpecification() Gets the specification attribute of the IPMolecularLearningDescriptor object
void	setParameters(java.lang.Object[] params) Sets the parameters attribute of the IPMolecularLearningDescriptor object

Methods inherited from class java.lang.Object

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

Constructor Detail

IPMolecularLearningDescriptor

public IPMolecularLearningDescriptor()

Constructor for the IPMolecularLearningDescriptor object

Method Detail

getSpecification

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

Gets the specification attribute of the IPMolecularLearningDescriptor object

Specified by:

getSpecification in interface IDescriptor

Returns:

The specification value

setParameters

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

Sets the parameters attribute of the IPMolecularLearningDescriptor object

Specified by:

setParameters in interface IDescriptor

Parameters:

params - The new parameters value

Throws:

CDKException - Description of the Exception

See Also:

IDescriptor.getParameters()

getParameters

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

Gets the parameters attribute of the IPMolecularLearningDescriptor object

Specified by:

getParameters in interface IDescriptor

Returns:

The parameters value

See Also:

IDescriptor.setParameters(java.lang.Object[])

getDescriptorNames

@TestMethod(value="testNamesConsistency")
public java.lang.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

Specified by:

getDescriptorNames in interface IDescriptor

Returns:

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

calculate

@TestMethod(value="testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtomContainer atomContainer)

It calculates the first ionization energy of a molecule.

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

atomContainer - AtomContainer

Returns:

The first ionization energy

calculatePlus

@TestMethod(value="testCalculatePlus_IAtomContainer")
public DescriptorValue calculatePlus(IAtomContainer container)
                              throws CDKException

It calculates the 1,2,.. ionization energies of a molecule.

Parameters:

container - AtomContainer

Returns:

The 1, 2, .. ionization energies

Throws:

CDKException - Possible Exceptions

getDescriptorResultType

public IDescriptorResult getDescriptorResultType()

Returns the specific type of the DescriptorResult object.

The return value from this method really indicates what type of result will be obtained from the DescriptorValue object. Note that the same result can be achieved by interrogating the DescriptorValue object; this method allows you to do the same thing, without actually calculating the descriptor.

Specified by:

getDescriptorResultType in interface IMolecularDescriptor

Returns:

an object that implements the IDescriptorResult interface indicating the actual type of values returned by the descriptor in the DescriptorValue object

getParameterNames

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

Gets the parameterNames attribute of the IPMolecularLearningDescriptor object

Specified by:

getParameterNames in interface IDescriptor

Returns:

The parameterNames value

getParameterType

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

Gets the parameterType attribute of the IPMolecularLearningDescriptor object

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - Description of the Parameter

Returns:

The parameterType value