magpie.attributes.generators.crystal

Class APRDFAttributeGenerator

java.lang.Object

magpie.attributes.generators.BaseAttributeGenerator

magpie.attributes.generators.crystal.APRDFAttributeGenerator

All Implemented Interfaces:

java.io.Serializable, Citable, Commandable, Options

public class APRDFAttributeGenerator
extends BaseAttributeGenerator
implements Citable

Attributes based on the Atomic Property Weighted Radial Distribution Function (AP-RDF) approach of Fernandez et al..

User can specify the cutoff distance for the AP-RDF, the number of points to evaluate it, the smoothing factors for the RDF peaks, and the properties used for weighting. The recommended values of these parameters have yet to be determined, please contact Logan Ward or the authors of this paper if you have questions or ideas for these parameters.

Usage: <cutoff> <# points> <smoothing> <properties>
cutoff: Cutoff distance for the AP-RDF
# points: Number of unique distances to evaluate
smoothing: Parameter used to smooth function
properties: Properties used to weight the RDF

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected double	CutoffDistance Cutoff distance for RDF
protected java.util.Set<java.lang.String>	ElementalProperties List of elemental properties to use for weighting
protected int	NumPoints Number of points to evaluate
protected double	SmoothParameter Smoothing parameter for AP-RDF

Constructor Summary

Constructors

Constructor and Description
APRDFAttributeGenerator()

Method Summary

Modifier and Type	Method and Description
void	addAttributes(Dataset data) Generate new attributes for a dataset.
void	addElementalProperty(java.lang.String propertyName) Add elemental property to set of those used for generating attributes
void	clearElementalProperties() Clear list of elemental properties.
java.util.List<org.apache.commons.lang3.tuple.Pair<java.lang.String,Citation>>	getCitations() Return a list of citations for this object and any underlying objects.
java.lang.String	printDescription(boolean htmlFormat) Print out description of attributes.
java.lang.String	printUsage() Print out required format for options.
void	setCutoffDistance(double cutoff) Define cutoff distance for AP-RDF.
void	setNumPoints(int numPoints) Set number of distances to evaluated for AP-RDF
void	setOptions(java.util.List<java.lang.Object> Options) Set any options for this object.
void	setSmoothParameter(double SmoothParameter) Set smoothing parameter for RDF.

Methods inherited from class magpie.attributes.generators.BaseAttributeGenerator

runCommand

Methods inherited from class java.lang.Object

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

Field Detail

CutoffDistance

protected double CutoffDistance

Cutoff distance for RDF

NumPoints

protected int NumPoints

Number of points to evaluate

SmoothParameter

protected double SmoothParameter

Smoothing parameter for AP-RDF

ElementalProperties

protected java.util.Set<java.lang.String> ElementalProperties

List of elemental properties to use for weighting

Constructor Detail

APRDFAttributeGenerator

public APRDFAttributeGenerator()

Method Detail

setOptions

public void setOptions(java.util.List<java.lang.Object> Options)
                throws java.lang.Exception

Description copied from interface: Options

Set any options for this object. If parsing the options fails, return an Exception with the usage as its message.

Specified by:

setOptions in interface Options

Parameters:

Options - Array of options as Objects - can be null

Throws:

java.lang.Exception - if problem with inputs

printUsage

public java.lang.String printUsage()

Description copied from interface: Options

Print out required format for options. For consistency, should start with "Usage: ".

Specified by:

printUsage in interface Options

Returns:

Usage for this function

setCutoffDistance

public void setCutoffDistance(double cutoff)

Define cutoff distance for AP-RDF.

Parameters:

cutoff - Desired cutoff

setNumPoints

public void setNumPoints(int numPoints)

Set number of distances to evaluated for AP-RDF

Parameters:

numPoints - Desired number of points

setSmoothParameter

public void setSmoothParameter(double SmoothParameter)

Set smoothing parameter for RDF. Controls how s

Parameters:

SmoothParameter -

clearElementalProperties

public void clearElementalProperties()

Clear list of elemental properties.

addElementalProperty

public void addElementalProperty(java.lang.String propertyName)

Add elemental property to set of those used for generating attributes

Parameters:

propertyName - Property name

addAttributes

public void addAttributes(Dataset data)
                   throws java.lang.Exception

Description copied from class: BaseAttributeGenerator

Generate new attributes for a dataset. This operation must both add the new attribute names to the dataset and new values to each entry.

Specified by:

addAttributes in class BaseAttributeGenerator

Parameters:

data - Dataset to be added to

Throws:

java.lang.Exception

See Also:

Dataset.addAttribute(java.lang.String, double[])

printDescription

public java.lang.String printDescription(boolean htmlFormat)

Description copied from class: BaseAttributeGenerator

Print out description of attributes.

Implementation Notes

Format should look like

[Full Name of generator]: (Number of attributes) Text description of what these attributes are

For HTML format, omit the ":".

Specified by:

printDescription in class BaseAttributeGenerator

Parameters:

htmlFormat - Whether to print in HTML format

Returns:

Description of the attributes

getCitations

public java.util.List<org.apache.commons.lang3.tuple.Pair<java.lang.String,Citation>> getCitations()

Description copied from interface: Citable

Return a list of citations for this object and any underlying objects.

Specified by:

getCitations in interface Citable

Returns:

List of pairs: [Reason for Citation], [Citation]