org.openscience.cdk.qsar.descriptors.molecular

Class MannholdLogPDescriptor

java.lang.Object

org.openscience.cdk.qsar.AbstractMolecularDescriptor

org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

public class MannholdLogPDescriptor
extends AbstractMolecularDescriptor
implements IMolecularDescriptor

Prediction of logP based on the number of carbon and hetero atoms. The implemented equation was proposed in [Mannhold, R. and Poda, G.I. and Ostermann, C. and Tetko, I.V., Calculation of molecular lipophilicity: State-of-the-art and comparison of log P methods on more than 96,000 compounds, J.Pharm.Sci., 2009, 98:861--893].

Dictionary pointer(s):

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

Source code:

master

Belongs to CDK module:

qsarmolecular

Keywords:

LogP, descriptor

Constructor Summary

Constructors

Constructor and Description
MannholdLogPDescriptor()

Method Summary

Methods

Modifier and Type	Method and Description
DescriptorValue	calculate(IAtomContainer atomContainer) Calculates the Mannhold LogP for an atom container.
String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
IDescriptorResult	getDescriptorResultType() Returns a type of return value calculated by this descriptor.
String[]	getParameterNames() Gets the parameterNames attribute for this descriptor.
Object[]	getParameters() Gets the parameters attribute of the MannholdLogPDescriptor object.
Object	getParameterType(String name) Gets the parameterType attribute for a given parameter name.
DescriptorSpecification	getSpecification() Gets the specification attribute of the MannholdLogPDescriptor object.
void	initialise(IChemObjectBuilder builder) Default implementation of initialise allows optional override.
void	setParameters(Object[] params) This IDescriptor does not have any parameters.

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

Constructor Detail

MannholdLogPDescriptor

public MannholdLogPDescriptor()

Method Detail

getSpecification

public DescriptorSpecification getSpecification()

Gets the specification attribute of the MannholdLogPDescriptor object.

Specified by:

getSpecification in interface IDescriptor

Returns:

The specification value

setParameters

public void setParameters(Object[] params)
                   throws CDKException

This IDescriptor does not have any parameters. If it had, this would have been the method to set them.

Specified by:

setParameters in interface IDescriptor

Parameters:

params - The new parameter value

Throws:

CDKException - Exception throw when invalid parameter values are passed

See Also:

getParameters()

getParameters

public Object[] getParameters()

Gets the parameters attribute of the MannholdLogPDescriptor object.

Specified by:

getParameters in interface IDescriptor

Returns:

A zero-length Object array.

See Also:

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 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

public DescriptorValue calculate(IAtomContainer atomContainer)

Calculates the Mannhold LogP for an atom container.

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

atomContainer - IAtomContainer to calculate the descriptor value for.

Returns:

A descriptor value wrapping a DoubleResult.

getDescriptorResultType

public IDescriptorResult getDescriptorResultType()

Returns a type of return value calculated by this descriptor.

Specified by:

getDescriptorResultType in interface IMolecularDescriptor

Returns:

returns a DoubleResult.

getParameterNames

public String[] getParameterNames()

Gets the parameterNames attribute for this descriptor.

Specified by:

getParameterNames in interface IDescriptor

Returns:

A zero-length String array.

getParameterType

public Object getParameterType(String name)

Gets the parameterType attribute for a given parameter name. It always returns null, as this descriptor does not have any parameters.

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - Name of the parameter for which the type is requested.

Returns:

The parameterType of the given parameter.

initialise

public void initialise(IChemObjectBuilder builder)

Default implementation of initialise allows optional override.

Specified by:

initialise in interface IDescriptor

Parameters:

builder - chem object build