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

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

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

public class LengthOverBreadthDescriptor
extends java.lang.Object
implements IMolecularDescriptor

Evaluates length over breadth descriptors.

The current implementation reproduces the results obtained from the LOVERB descriptor routine in ADAPT. As a result ti does not perform any orientation and only considers the X & Y extents for a series of rotations about the Z axis (in 10 degree increments).

The class gives two descriptors

• LOBMAX - The maximum L/B ratio
• LOBMIN - The L/B ratio for the rotation that results in the minimum area (defined by the product of the X & Y extents for that orientation)

Note: The descriptor assumes that the atoms have been configured.

Author:

Rajarshi Guha

Belongs to the set:

qsar-descriptors

Created on:

2006-09-26

Belongs to CDK module:

qsarmolecular

This class is affected by these bug(s):

1862142

Dictionary pointer(s):

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

Source code:

revision 11709

Constructor Summary

LengthOverBreadthDescriptor()
Constructor for the LengthOverBreadthDescriptor object.

Method Summary

DescriptorValue	calculate(IAtomContainer atomContainer) Evaluate the descriptor for the molecule.
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 PetitjeanNumberDescriptor object
java.lang.Object[]	getParameters() Gets the parameters attribute of the PetitjeanNumberDescriptor object
java.lang.Object	getParameterType(java.lang.String name) Gets the parameterType attribute of the PetitjeanNumberDescriptor object
DescriptorSpecification	getSpecification() Gets the specification attribute of the PetitjeanNumberDescriptor object
void	setParameters(java.lang.Object[] params) Sets the parameters attribute of the PetitjeanNumberDescriptor object

Methods inherited from class java.lang.Object

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

Constructor Detail

LengthOverBreadthDescriptor

public LengthOverBreadthDescriptor()

Constructor for the LengthOverBreadthDescriptor object.

Method Detail

getSpecification

public DescriptorSpecification getSpecification()

Gets the specification attribute of the PetitjeanNumberDescriptor object

Specified by:

getSpecification in interface IDescriptor

Returns:

The specification value

setParameters

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

Sets the parameters attribute of the PetitjeanNumberDescriptor object

Specified by:

setParameters in interface IDescriptor

Parameters:

params - The new parameters value

Throws:

CDKException - Description of the Exception

See Also:

IDescriptor.getParameters()

getParameters

public java.lang.Object[] getParameters()

Gets the parameters attribute of the PetitjeanNumberDescriptor 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

public DescriptorValue calculate(IAtomContainer atomContainer)

Evaluate the descriptor for the molecule.

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

atomContainer - AtomContainer

Returns:

A DoubleArrayResult containing LOBMAX and LOBMIN in that order

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 PetitjeanNumberDescriptor 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 PetitjeanNumberDescriptor object

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - Description of the Parameter

Returns:

The parameterType value