Class parsing fitness expression by means of Expression Language. More...

Collaboration diagram for denoptim.fitness.FitnessExpressionParser:

Classes
class	CustomVariableDefiningContext
	In this context we only need to know that "Variable" is mapped to the class `Variable`. More...

class	VariableDefiningContext
	This is the context on which we read a fitness expression, and parse it to identify all variables in the expression. More...

Public Member Functions
	FitnessExpressionParser ()
	Creates a new parser. More...

void	parse (String fitnessExpression, List< String > customVarDescExpressions) throws DENOPTIMException
	Parses the given expressions. More...

List< Variable >	getVariables ()
	Returns the list of variables in the expression of the fitness. More...

List< DescriptorForFitness >	getDescriptors ()
	Returns the list of descriptors needed to compute the numerical values of the variables in the expression of the fitness. More...

Private Member Functions
String[]	makeStringArray (String line) throws DENOPTIMException

IBitFingerprint	makeIBitFingerprintBySubstructure (String line, String[] smarts) throws DENOPTIMException
	For now we only accept a filename from which we read in a molecule. More...

IBitFingerprint	makeIBitFingerprint (String line, IFingerprinter fingerprinter) throws DENOPTIMException
	For now we only accept a filename from which we read in a molecule. More...

IFingerprinter	makeIFingerprinter (String classShortName) throws DENOPTIMException

Private Attributes
List< Variable >	variables = new ArrayList<Variable>()
	List of variables used in the calculation of the fitness. More...

List< DescriptorForFitness >	descriptors
	The list of descriptors needed to calculate the variables that are used to calculate the fitness with the internal fitness provider. More...

Detailed Description

Class parsing fitness expression by means of Expression Language.

Definition at line 54 of file FitnessExpressionParser.java.

Constructor & Destructor Documentation

◆ FitnessExpressionParser()

denoptim.fitness.FitnessExpressionParser.FitnessExpressionParser ( )

Creates a new parser.

Definition at line 75 of file FitnessExpressionParser.java.

Member Function Documentation

◆ getDescriptors()

List< DescriptorForFitness > denoptim.fitness.FitnessExpressionParser.getDescriptors ( )

Returns the list of descriptors needed to compute the numerical values of the variables in the expression of the fitness.

Returns: the list of descriptors needed to calculate the numerical values of the variables in the expression of the fitness.

Definition at line 624 of file FitnessExpressionParser.java.

References denoptim.fitness.FitnessExpressionParser.descriptors.

Referenced by denoptim.fitness.FitnessParameters.processParameters().

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◆ getVariables()

List< Variable > denoptim.fitness.FitnessExpressionParser.getVariables ( )

Returns the list of variables in the expression of the fitness.

Returns: the list of variables in the expression of the fitness.

Definition at line 611 of file FitnessExpressionParser.java.

References denoptim.fitness.FitnessExpressionParser.variables.

◆ makeIBitFingerprint()

IBitFingerprint denoptim.fitness.FitnessExpressionParser.makeIBitFingerprint	(	String	line,
		IFingerprinter	fingerprinter
	)		throws DENOPTIMException

private

For now we only accept a filename from which we read in a molecule.

Exceptions

DENOPTIMException

Definition at line 540 of file FitnessExpressionParser.java.

References denoptim.io.DenoptimIO.readAllAtomContainers().

Referenced by denoptim.fitness.FitnessExpressionParser.makeIBitFingerprintBySubstructure(), and denoptim.fitness.FitnessExpressionParser.parse().

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◆ makeIBitFingerprintBySubstructure()

IBitFingerprint denoptim.fitness.FitnessExpressionParser.makeIBitFingerprintBySubstructure	(	String	line,
		String[]	smarts
	)		throws DENOPTIMException

private

For now we only accept a filename from which we read in a molecule.

Exceptions

DENOPTIMException

Definition at line 527 of file FitnessExpressionParser.java.

References denoptim.fitness.FitnessExpressionParser.makeIBitFingerprint().

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

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◆ makeIFingerprinter()

IFingerprinter denoptim.fitness.FitnessExpressionParser.makeIFingerprinter ( String classShortName ) throws DENOPTIMException

private

Definition at line 590 of file FitnessExpressionParser.java.

References denoptim.fitness.descriptors.TanimotoMolSimilarity.makeIFingerprinter().

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

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◆ makeStringArray()

String[] denoptim.fitness.FitnessExpressionParser.makeStringArray ( String line ) throws DENOPTIMException

private

Definition at line 501 of file FitnessExpressionParser.java.

References denoptim.io.DenoptimIO.readList().

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

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◆ parse()

void denoptim.fitness.FitnessExpressionParser.parse	(	String	fitnessExpression,
		List< String >	customVarDescExpressions
	)		throws DENOPTIMException

Parses the given expressions.

Since the value obtained from the calculation of each single descriptor can be used for multiple purposes (i.e., as a proper descriptor and as a component used to calculate the value of more than one variable) we collect the descriptors and record the relation between each descriptor and any variables that depend on it.

Parameters

fitnessExpression the expression defining how to calculate the fitness from named variables.

customVarDescExpressions the collection of functions defining how to calculate the numerical value of the variables. Any variable that is not defined in this list is assumes to correspond to the value that is calculated by a descriptor implementation reachable in the classpath and offering a descriptor value named after the variable name. E.g., if the fitness expression contains Zagreb, we assume that the descriptor Zagreb can be calculated by a IDescriptor implementation visible in the class path.

Exceptions

DENOPTIMException

Definition at line 100 of file FitnessExpressionParser.java.

Referenced by denoptim.fitness.FitnessParameters.processParameters().

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Member Data Documentation

◆ descriptors

List<DescriptorForFitness> denoptim.fitness.FitnessExpressionParser.descriptors

private

Initial value:

=

new ArrayList<DescriptorForFitness>()

The list of descriptors needed to calculate the variables that are used to calculate the fitness with the internal fitness provider.

Definition at line 67 of file FitnessExpressionParser.java.

Referenced by denoptim.fitness.FitnessExpressionParser.getDescriptors(), and denoptim.fitness.FitnessExpressionParser.parse().

◆ variables

List<Variable> denoptim.fitness.FitnessExpressionParser.variables = new ArrayList<Variable>()

private

List of variables used in the calculation of the fitness.

For instance, atom/bond specific descriptors, and custom parameterized descriptors.

Definition at line 61 of file FitnessExpressionParser.java.

Referenced by denoptim.fitness.FitnessExpressionParser.getVariables(), and denoptim.fitness.FitnessExpressionParser.parse().

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

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

Classes

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ FitnessExpressionParser()

Member Function Documentation

◆ getDescriptors()

◆ getVariables()

◆ makeIBitFingerprint()

◆ makeIBitFingerprintBySubstructure()

◆ makeIFingerprinter()

◆ makeStringArray()

◆ parse()

Member Data Documentation

◆ descriptors

◆ variables