A variable in the expression defining the fitness. More...

Collaboration diagram for denoptim.fitness.Variable:

Public Member Functions
	Variable (String varName)
	Constructs a named variable. More...

String	getName ()
	Get the name of this variable, i.e., the string used in the fitness-defining expression. More...

String	getDescriptorName ()
	Get the short name of the descriptor implementation. More...

void	setDescriptorName (String descName)
	Set the short name of the descriptor implementation. More...

void	setSMARTS (ArrayList< String > smarts)
	Set the list of smarts used to identify atom/bond-specific values. More...

void	setDescriptorParameters (String[] params)
	Set the list of strings defining customisable parameter for the descriptor implementation. More...

String	toString ()
	Returns a human readable string. More...

Static Public Member Functions
static Variable	atomSpecific (String varName, String descName, String smartsIdentifier)
	Returns an atom specific variable, i.e., a variable the value of which needs to be obtained from the calculation of the given descriptor on a specific atom that is defined by the given SMARTS string. More...

static Variable	parametrized (String varName, String descName, String paramsStr)
	Returns an parameterized variable, i.e., a variable the value of which needs to be obtained from the calculation of the given descriptor according to the given parameters. More...

Protected Attributes
ArrayList< String >	smarts
	SMARTS strings used to select atom/bond specific values. More...

String[]	params
	Definition of custom parameters for the configuration of the descriptor implementation. More...

Private Attributes
String	varName
	The string used to represent this variable in the fitness defining expression. More...

String	descName
	The short name of the descriptor implementation. More...

Detailed Description

A variable in the expression defining the fitness.

This is typically obtained by computing a descriptor with any of the available implementations. Since

the calculation of the descriptor can be tuned by means of parameters, and
the numerical value can be chosen to be atom/bond specific,

this class collects all the information that is needed to configure a descriptor calculation, process the result (e.g. take only specific values among those produced by the descriptor implementation), and keep a relation between such value and the variable name in the fitness defining expression.

Definition at line 41 of file Variable.java.

Constructor & Destructor Documentation

◆ Variable()

denoptim.fitness.Variable.Variable ( String varName )

Constructs a named variable.

Parameters

varName

Definition at line 71 of file Variable.java.

References denoptim.fitness.Variable.varName.

Referenced by denoptim.fitness.Variable.atomSpecific(), and denoptim.fitness.Variable.parametrized().

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Member Function Documentation

◆ atomSpecific()

static Variable denoptim.fitness.Variable.atomSpecific	(	String	varName,
		String	descName,
		String	smartsIdentifier
	)

static

Returns an atom specific variable, i.e., a variable the value of which needs to be obtained from the calculation of the given descriptor on a specific atom that is defined by the given SMARTS string.

Parameters

varName	the name of the variable
descName	the name of the descriptor as defined in any implementation of `IDescriptor`.
smartsIdentifier	the SMARTS that identifies the atom/s to consider for the calculation of the descriptor and thus the value.

Returns: the variable instance.

Definition at line 91 of file Variable.java.

References denoptim.fitness.Variable.descName, denoptim.fitness.Variable.setDescriptorName(), denoptim.fitness.Variable.setSMARTS(), denoptim.fitness.Variable.smarts, denoptim.fitness.Variable.Variable(), and denoptim.fitness.Variable.varName.

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◆ getDescriptorName()

String denoptim.fitness.Variable.getDescriptorName ( )

Get the short name of the descriptor implementation.

Returns: the short name of the descriptor implementation

Definition at line 143 of file Variable.java.

References denoptim.fitness.Variable.descName.

Referenced by denoptim.fitness.FitnessExpressionParser.parse().

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◆ getName()

String denoptim.fitness.Variable.getName ( )

Get the name of this variable, i.e., the string used in the fitness-defining expression.

Returns: the string used in the fitness-defining expression.

Definition at line 132 of file Variable.java.

References denoptim.fitness.Variable.varName.

Referenced by denoptim.fitness.FitnessExpressionParser.parse().

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◆ parametrized()

static Variable denoptim.fitness.Variable.parametrized	(	String	varName,
		String	descName,
		String	paramsStr
	)

static

Returns an parameterized variable, i.e., a variable the value of which needs to be obtained from the calculation of the given descriptor according to the given parameters.

Parameters

varName	the name of the variable
descName	the name of the descriptor as defined in any implementation of `IDescriptor`.
paramsStr	string defining all the parameters for the calculation of the descriptor.

Returns: the variable instance.

Definition at line 116 of file Variable.java.

References denoptim.fitness.Variable.descName, denoptim.fitness.Variable.setDescriptorName(), denoptim.fitness.Variable.setDescriptorParameters(), denoptim.fitness.Variable.Variable(), and denoptim.fitness.Variable.varName.

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◆ setDescriptorName()

void denoptim.fitness.Variable.setDescriptorName ( String descName )

Set the short name of the descriptor implementation.

Parameters

descName the short name of the descriptor implementation.

Definition at line 154 of file Variable.java.

References denoptim.fitness.Variable.descName.

Referenced by denoptim.fitness.Variable.atomSpecific(), and denoptim.fitness.Variable.parametrized().

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◆ setDescriptorParameters()

void denoptim.fitness.Variable.setDescriptorParameters ( String[] params )

Set the list of strings defining customisable parameter for the descriptor implementation.

The order is expected to be that of the parameters as given by IDescriptor#getParameterNames().

Parameters

params the list of strings

Definition at line 178 of file Variable.java.

References denoptim.fitness.Variable.params.

Referenced by denoptim.fitness.Variable.parametrized().

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◆ setSMARTS()

void denoptim.fitness.Variable.setSMARTS ( ArrayList< String > smarts )

Set the list of smarts used to identify atom/bond-specific values.

Parameters

smarts the list of SMARTS string

Definition at line 165 of file Variable.java.

References denoptim.fitness.Variable.smarts.

Referenced by denoptim.fitness.Variable.atomSpecific().

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◆ toString()

String denoptim.fitness.Variable.toString ( )

Returns a human readable string.

Definition at line 188 of file Variable.java.

References denoptim.fitness.Variable.descName, denoptim.fitness.Variable.params, denoptim.fitness.Variable.smarts, and denoptim.fitness.Variable.varName.

Member Data Documentation

◆ descName

String denoptim.fitness.Variable.descName

private

The short name of the descriptor implementation.

Definition at line 52 of file Variable.java.

Referenced by denoptim.fitness.Variable.atomSpecific(), denoptim.fitness.Variable.getDescriptorName(), denoptim.fitness.Variable.parametrized(), denoptim.fitness.Variable.setDescriptorName(), and denoptim.fitness.Variable.toString().

◆ params

String [] denoptim.fitness.Variable.params

protected

Definition of custom parameters for the configuration of the descriptor implementation.

Definition at line 63 of file Variable.java.

Referenced by denoptim.fitness.FitnessExpressionParser.parse(), denoptim.fitness.Variable.setDescriptorParameters(), and denoptim.fitness.Variable.toString().

◆ smarts

ArrayList<String> denoptim.fitness.Variable.smarts

protected

SMARTS strings used to select atom/bond specific values.

Definition at line 57 of file Variable.java.

Referenced by denoptim.fitness.Variable.atomSpecific(), denoptim.fitness.Variable.setSMARTS(), and denoptim.fitness.Variable.toString().

◆ varName

String denoptim.fitness.Variable.varName

private

The string used to represent this variable in the fitness defining expression.

Definition at line 47 of file Variable.java.

Referenced by denoptim.fitness.Variable.atomSpecific(), denoptim.fitness.Variable.getName(), denoptim.fitness.Variable.parametrized(), denoptim.fitness.Variable.toString(), and denoptim.fitness.Variable.Variable().

The documentation for this class was generated from the following file:

/github/workspace/src/main/java/denoptim/fitness/Variable.java

Public Member Functions

Static Public Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Variable()

Member Function Documentation

◆ atomSpecific()

◆ getDescriptorName()

◆ getName()

◆ parametrized()

◆ setDescriptorName()

◆ setDescriptorParameters()

◆ setSMARTS()

◆ toString()

Member Data Documentation

◆ descName

◆ params

◆ smarts

◆ varName