org.openscience.cdk.qsar.descriptors.atomic

Class DistanceToAtomDescriptor

java.lang.Object

org.openscience.cdk.qsar.AbstractAtomicDescriptor

org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor

All Implemented Interfaces:

IAtomicDescriptor, IDescriptor

public class DistanceToAtomDescriptor
extends AbstractAtomicDescriptor
implements IAtomicDescriptor

This class returns the 3D distance between two atoms. Only works with 3D coordinates, which must be calculated beforehand.

Parameters for this descriptor:

Name	Default	Description
focusPosition	0	The position of the second atom

Author:

mfe4

Dictionary pointer(s):

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

Source code:

master

Belongs to CDK module:

qsaratomic

Created on:

2004-11-13

Constructor Summary

Constructors

Constructor and Description
DistanceToAtomDescriptor() Constructor for the DistanceToAtomDescriptor object

Method Summary

Modifier and Type	Method and Description
DescriptorValue	calculate(IAtom atom, IAtomContainer container) This method calculate the 3D distance between two atoms.
String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
String[]	getParameterNames() Gets the parameterNames attribute of the DistanceToAtomDescriptor object
Object[]	getParameters() Gets the parameters attribute of the DistanceToAtomDescriptor object
Object	getParameterType(String name) Gets the parameterType attribute of the DistanceToAtomDescriptor object
DescriptorSpecification	getSpecification() Gets the specification attribute of the DistanceToAtomDescriptor object
void	initialise(IChemObjectBuilder builder) Default implementation of initialise allows optional override.
void	setParameters(Object[] params) Sets the parameters attribute of the DistanceToAtomDescriptor object

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

cacheDescriptorValue, getCachedDescriptorValue, isCachedAtomContainer

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

DistanceToAtomDescriptor

public DistanceToAtomDescriptor()

Constructor for the DistanceToAtomDescriptor object

Method Detail

getSpecification

public DescriptorSpecification getSpecification()

Gets the specification attribute of the DistanceToAtomDescriptor 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 DistanceToAtomDescriptor object

Specified by:

setParameters in interface IDescriptor

Parameters:

params - The parameter is the position to focus

Throws:

CDKException - Description of the Exception

See Also:

IDescriptor.getParameters()

getParameters

public Object[] getParameters()

Gets the parameters attribute of the DistanceToAtomDescriptor 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(IAtom atom,
                                 IAtomContainer container)

This method calculate the 3D distance between two atoms.

Specified by:

calculate in interface IAtomicDescriptor

Parameters:

atom - The IAtom for which the DescriptorValue is requested

container - Parameter is the atom container.

Returns:

The number of bonds on the shortest path between two atoms

getParameterNames

public String[] getParameterNames()

Gets the parameterNames attribute of the DistanceToAtomDescriptor object

Specified by:

getParameterNames in interface IDescriptor

Returns:

The parameterNames value

getParameterType

public Object getParameterType(String name)

Gets the parameterType attribute of the DistanceToAtomDescriptor 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