org.openscience.cdk.qsar.descriptors.molecular

Class ALOGPDescriptor

java.lang.Object

org.openscience.cdk.qsar.AbstractMolecularDescriptor

org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

public class ALOGPDescriptor
extends AbstractMolecularDescriptor
implements IMolecularDescriptor

This class calculates ALOGP (Ghose-Crippen LogKow) and the Ghose-Crippen molar refractivity [Ghose, A.K. and Crippen, G.M. , Atomic physicochemical parameters for three-dimensional structure-directed quantitative structure-activity relationships. I. Partition coefficients as a measure of hydrophobicity, Journal of Computational Chemistry, 1986, 7:565-577, doi:10.1002/jcc.540070419, Ghose, A.K. and Crippen, G.M. , Atomic physicochemical parameters for three-dimensional-structure-directed quantitative structure-activity relationships. 2. Modeling dispersive and hydrophobic interactions, Journal of Chemical Information and Computer Science, 1987, 27:21-35, doi:10.1021/ci00053a005]. Note The code assumes that aromaticity has been detected before evaluating this descriptor. The code also expects that the molecule will have hydrogens explicitly set. For SD files, this is usually not a problem since hydrogens are explicit. But for the case of molecules obtained from SMILES, hydrogens must be made explicit.

TODO: what should sub return if have missing fragment? Just report sum for other fragments? Or report as -9999 and then do not use descriptor if have this value for any chemicals in cluster?

Parameters for this descriptor:

Name	Default	Description
		no parameters

Returns three values

1. ALogP - Ghose-Crippen LogKow
2. ALogP2
3. amr - molar refractivity

Author:

Todd Martin

See Also:

CDKHydrogenAdder

Source code:

master

Belongs to CDK module:

qsarmolecular

Keywords:

logP, lipophilicity, refractivity

Field Summary

Fields

Modifier and Type	Field and Description
int[]	alogpfrag

Constructor Summary

Constructors

Constructor and Description
ALOGPDescriptor()

Method Summary

Methods

Modifier and Type	Method and Description
DescriptorValue	calculate(IAtomContainer atomContainer) The AlogP descriptor.
String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
IDescriptorResult	getDescriptorResultType() Returns the specific type of the DescriptorResult object.
String[]	getParameterNames() Returns the names of the parameters for this descriptor.
Object[]	getParameters() Returns the current parameter values.
Object	getParameterType(String name) Returns a class matching that of the parameter with the given name.
DescriptorSpecification	getSpecification() Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.
void	initialise(IChemObjectBuilder builder) Default implementation of initialise allows optional override.
void	setParameters(Object[] params) Sets the parameters for this descriptor.

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

Field Detail

alogpfrag

public int[] alogpfrag

Constructor Detail

ALOGPDescriptor

public ALOGPDescriptor()
                throws CDKException

Throws:

CDKException

Method Detail

calculate

public DescriptorValue calculate(IAtomContainer atomContainer)

The AlogP descriptor. TODO Ideally we should explicit H addition should be cached

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

atomContainer - the molecule to calculate on

Returns:

the result of the calculation

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

getSpecification

public DescriptorSpecification getSpecification()

Description copied from interface: IDescriptor

Returns a IImplementationSpecification which specifies which descriptor is implemented by this class. These fields are used in the map:

• Specification-Reference: refers to an entry in a unique dictionary
• Implementation-Title: anything
• Implementation-Identifier: a unique identifier for this version of this class
• Implementation-Vendor: CDK, JOELib, or anything else

Specified by:

getSpecification in interface IDescriptor

Returns:

An object containing the descriptor specification

getParameterNames

public String[] getParameterNames()

Description copied from interface: IDescriptor

Returns the names of the parameters for this descriptor. The method returns null or a zero-length Object[] array if the descriptor does not have any parameters.

Specified by:

getParameterNames in interface IDescriptor

Returns:

An array of String containing the names of the parameters that this descriptor can accept.

getParameterType

public Object getParameterType(String name)

Description copied from interface: IDescriptor

Returns a class matching that of the parameter with the given name. May only return null for when 'name' does not match any parameters returned by the getParameters() method.

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - The name of the parameter whose type is requested

Returns:

An Object of the class corresponding to the parameter with the supplied name

setParameters

public void setParameters(Object[] params)
                   throws CDKException

Description copied from interface: IDescriptor

Sets the parameters for this descriptor. Must be done before calling calculate as the parameters influence the calculation outcome.

Specified by:

setParameters in interface IDescriptor

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

public Object[] getParameters()

Description copied from interface: IDescriptor

Returns the current parameter values. If not parameters have been set, it must return the default parameters. The method returns null or a zero-length Object[] array if the descriptor does not have any parameters.

Specified by:

getParameters in interface IDescriptor

Returns:

An array of Object containing the parameter default values

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 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..

initialise

public void initialise(IChemObjectBuilder builder)

Default implementation of initialise allows optional override.

Specified by:

initialise in interface IDescriptor

Parameters:

builder - chem object build