Package org.openscience.cdk.qsar.descriptors.molecular

Class RotatableBondsCountDescriptor

java.lang.Object

org.openscience.cdk.qsar.AbstractMolecularDescriptor

org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

public class RotatableBondsCountDescriptor
extends AbstractMolecularDescriptor
implements IMolecularDescriptor

The number of rotatable bonds is given by the SMARTS specified by Daylight on SMARTS tutorial

Parameters for this descriptor:

Name	Default	Description
includeTerminals	false	True if terminal bonds are included
excludeAmides	false	True if amide C-N bonds should be excluded

Returns a single value named nRotB

Author:

mfe4

Dictionary pointer(s):

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

Source code:

main

Belongs to CDK module:

qsarmolecular

Keywords:

bond count, rotatable, descriptor

Created on:

2004-11-03

Constructor Summary

Constructors

Constructor	Description
RotatableBondsCountDescriptor()	Constructor for the RotatableBondsCountDescriptor object

Method Summary

Modifier and Type	Method	Description
DescriptorValue	calculate(IAtomContainer ac)	The method calculates the number of rotatable bonds of an atom container.
String[]	getDescriptorNames()	Returns an array of names for each descriptor value calculated.
IDescriptorResult	getDescriptorResultType()	Returns the specific type of the DescriptorResult object.
String[]	getParameterNames()	Gets the parameterNames attribute of the RotatableBondsCountDescriptor object
Object[]	getParameters()	Gets the parameters attribute of the RotatableBondsCountDescriptor object
Object	getParameterType(String name)	Gets the parameterType attribute of the RotatableBondsCountDescriptor object
DescriptorSpecification	getSpecification()	Gets the specification attribute of the RotatableBondsCountDescriptor object
void	initialise(IChemObjectBuilder builder)	Default implementation of initialise allows optional override.
void	setParameters(Object[] params)	Sets the parameters attribute of the RotatableBondsCountDescriptor object

Methods inherited from class org.openscience.cdk.qsar.AbstractMolecularDescriptor

clone

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

RotatableBondsCountDescriptor

public RotatableBondsCountDescriptor()

Constructor for the RotatableBondsCountDescriptor object

Method Detail

getSpecification

public DescriptorSpecification getSpecification()

Gets the specification attribute of the RotatableBondsCountDescriptor object

Specified by:

getSpecification in interface IDescriptor

Returns:

The specification value

setParameters

public void setParameters(Object[] params)
                   throws CDKException

Sets the parameters attribute of the RotatableBondsCountDescriptor object

Specified by:

setParameters in interface IDescriptor

Parameters:

params - a boolean true means that terminal atoms must be included in the count

Throws:

CDKException - Description of the Exception

See Also:

IDescriptor.getParameters()

getParameters

public Object[] getParameters()

Gets the parameters attribute of the RotatableBondsCountDescriptor object

Specified by:

getParameters in interface IDescriptor

Returns:

The parameters value

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..

calculate

public DescriptorValue calculate(IAtomContainer ac)

The method calculates the number of rotatable bonds of an atom container. If the boolean parameter is set to true, terminal bonds are included.

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

ac - AtomContainer

Returns:

number of rotatable bonds

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 String[] getParameterNames()

Gets the parameterNames attribute of the RotatableBondsCountDescriptor object

Specified by:

getParameterNames in interface IDescriptor

Returns:

The parameterNames value

getParameterType

public Object getParameterType(String name)

Gets the parameterType attribute of the RotatableBondsCountDescriptor object

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - Description of the Parameter

Returns:

The parameterType value

initialise

public void initialise(IChemObjectBuilder builder)

Default implementation of initialise allows optional override.

Specified by:

initialise in interface IDescriptor

Parameters:

builder - chem object build