Package org.openscience.cdk.qsar.descriptors.atomic

Class RDFProtonDescriptor_G3R

java.lang.Object

org.openscience.cdk.qsar.AbstractAtomicDescriptor

org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R

All Implemented Interfaces:

IAtomicDescriptor, IDescriptor

public class RDFProtonDescriptor_G3R
extends AbstractAtomicDescriptor
implements IAtomicDescriptor

This class calculates G3R proton descriptors used in neural networks for H1 NMR shift [Aires-de-Sousa, J. et. al.. J. Chem. Inf. Mod.. 2002. 74]. It only applies to (explicit) hydrogen atoms, requires aromaticity to be perceived (possibly done via a parameter), and needs 3D coordinates for all atoms. This method only calculates values for protons bonded to specific types of rings or via non-rotatable bonds. From the original manuscript: "To account for axial and equatorial positions of protons bonded to cyclohexane-like rings, g3(r) was used"

Parameters for this descriptor:

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

Author:

Federico

This class is affected by these bug(s):

1632419

Dictionary pointer(s):

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

Source code:

main

Belongs to CDK module:

qsaratomic

Created on:

2006-12-11

Constructor Summary

Constructors

Constructor	Description
RDFProtonDescriptor_G3R()	Constructor for the RDFProtonDescriptor object

Method Summary

Modifier and Type	Method	Description
DescriptorValue	calculate(IAtom atom, IAtomContainer varAtomContainerSet)	Calculates the descriptor value for the given IAtom.
DescriptorValue	calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)
String[]	getDescriptorNames()	Returns an array of names for each descriptor value calculated.
String[]	getParameterNames()	Gets the parameterNames attribute of the RDFProtonDescriptor object
Object[]	getParameters()	Gets the parameters attribute of the RDFProtonDescriptor object
Object	getParameterType(String name)	Gets the parameterType attribute of the RDFProtonDescriptor object
DescriptorSpecification	getSpecification()	Gets the specification attribute of the RDFProtonDescriptor_G3R object
void	initialise(IChemObjectBuilder builder)	Default implementation of initialise allows optional override.
void	setParameters(Object[] params)	Sets the parameters attribute of the RDFProtonDescriptor 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

RDFProtonDescriptor_G3R

public RDFProtonDescriptor_G3R()

Constructor for the RDFProtonDescriptor object

Method Detail

getSpecification

public DescriptorSpecification getSpecification()

Gets the specification attribute of the RDFProtonDescriptor_G3R 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 RDFProtonDescriptor object

Specified by:

setParameters in interface IDescriptor

Parameters:

params - Parameters are the proton position and a boolean (true if you need to detect aromaticity)

Throws:

CDKException - Possible Exceptions

See Also:

IDescriptor.getParameters()

getParameters

public Object[] getParameters()

Gets the parameters attribute of the RDFProtonDescriptor 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 varAtomContainerSet)

Description copied from interface: IAtomicDescriptor

Calculates the descriptor value for the given IAtom.

Specified by:

calculate in interface IAtomicDescriptor

Parameters:

atom - An IAtom for which this descriptor should be calculated

varAtomContainerSet - TODO

Returns:

An object of DescriptorValue that contain the calculated value as well as specification details

calculate

public DescriptorValue calculate(IAtom atom,
                                 IAtomContainer atomContainer,
                                 IRingSet precalculatedringset)

getParameterNames

public String[] getParameterNames()

Gets the parameterNames attribute of the RDFProtonDescriptor object

Specified by:

getParameterNames in interface IDescriptor

Returns:

The parameterNames value

getParameterType

public Object getParameterType(String name)

Gets the parameterType attribute of the RDFProtonDescriptor 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