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

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

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

public class RuleOfFiveDescriptor
extends java.lang.Object
implements IMolecularDescriptor

This Class contains a method that returns the number failures of the Lipinski's Rule Of 5. See http://www.lifechemicals.com/eng/services/HTS/five/.

This descriptor uses these parameters:

Name	Default	Description
checkAromaticity	false	True is the aromaticity has to be checked

Returns a single value named LipinskiFailures.

Author:

mfe4

Belongs to the set:

qsar-descriptors

Keywords:

Lipinski, rule-of-five, descriptor

Created on:

2004-11-03

Belongs to CDK module:

qsarmolecular

Dictionary pointer(s):

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

Source code:

revision 11707

Constructor Summary

RuleOfFiveDescriptor()
Constructor for the RuleOfFiveDescriptor object.

Method Summary

DescriptorValue	calculate(IAtomContainer mol) the method take a boolean checkAromaticity: if the boolean is true, it means that aromaticity has to be checked.
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 RuleOfFiveDescriptor object.
java.lang.Object[]	getParameters() Gets the parameters attribute of the RuleOfFiveDescriptor object.
java.lang.Object	getParameterType(java.lang.String name) Gets the parameterType attribute of the RuleOfFiveDescriptor object.
DescriptorSpecification	getSpecification() Returns a Map which specifies which descriptor is implemented by this class.
void	setParameters(java.lang.Object[] params) Sets the parameters attribute of the RuleOfFiveDescriptor object.

Methods inherited from class java.lang.Object

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

Constructor Detail

RuleOfFiveDescriptor

public RuleOfFiveDescriptor()

Constructor for the RuleOfFiveDescriptor object.

Method Detail

getSpecification

public DescriptorSpecification getSpecification()

Returns a Map 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

setParameters

public void setParameters(java.lang.Object[] params)
                   throws CDKException

Sets the parameters attribute of the RuleOfFiveDescriptor object. There is only one parameter, which should be a Boolean indicating whether aromaticity should be checked or has already been checked. The name of the paramete is checkAromaticity.

Specified by:

setParameters in interface IDescriptor

Parameters:

params - Parameter is only one: a boolean.

Throws:

CDKException - if more than 1 parameter or a non-Boolean parameter is specified

See Also:

getParameters()

getParameters

public java.lang.Object[] getParameters()

Gets the parameters attribute of the RuleOfFiveDescriptor object.

Specified by:

getParameters in interface IDescriptor

Returns:

The parameters value

See Also:

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

public DescriptorValue calculate(IAtomContainer mol)

the method take a boolean checkAromaticity: if the boolean is true, it means that aromaticity has to be checked.

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

mol - AtomContainer for which this descriptor is to be calculated

Returns:

The number of failures of the Lipinski rule

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

public java.lang.String[] getParameterNames()

Gets the parameterNames attribute of the RuleOfFiveDescriptor object.

Specified by:

getParameterNames in interface IDescriptor

Returns:

The parameterNames value

getParameterType

public java.lang.Object getParameterType(java.lang.String name)

Gets the parameterType attribute of the RuleOfFiveDescriptor object.

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - The name of the parameter. In this case it is 'checkAromaticity'.

Returns:

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