magpie.attributes.generators.composition

Class IonicityAttributeGenerator

java.lang.Object

magpie.attributes.generators.BaseAttributeGenerator

magpie.attributes.generators.composition.IonicityAttributeGenerator

All Implemented Interfaces:

java.io.Serializable, Citable, Commandable, Options

public class IonicityAttributeGenerator
extends BaseAttributeGenerator
implements Citable

Generate attributes based on the "ioncity" of a compound.

Creates attributes based on whether it is possible to form a charge-neutral ionic compound, and two measures based a simple measure of "bond ionicity" (see W.D. Callister's text):

$I(x,y)\; =\; 1\; -\; exp(-0.25\; *\; ({\rm X}(x)\; -\; {\rm X}(y))2)$

1. Maximum ionic character: Max I(x,y) between any two constituents
2. Mean ionic character: sum(x_i * x_j * I(i,j)) where x_i is the fraction of element i.

Usage: *No options*

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
IonicityAttributeGenerator()

Method Summary

Modifier and Type	Method and Description
void	addAttributes(Dataset data) Generate new attributes for a dataset.
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	setOptions(java.util.List<java.lang.Object> Options) Set any options for this object.

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

Constructor Detail

IonicityAttributeGenerator

public IonicityAttributeGenerator()

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

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]