Calculates the molecular similarity against a target compound the fingerprint of which is given as parameter. More...

Inheritance diagram for denoptim.fitness.descriptors.TanimotoMolSimilarity:

Collaboration diagram for denoptim.fitness.descriptors.TanimotoMolSimilarity:

Public Member Functions
	TanimotoMolSimilarity ()
	Constructor for a TanimotoMolSimilarity object. More...

DescriptorSpecification	getSpecification ()
	Get the specification attribute of Tanimoto molecular similarity. More...

String[]	getParameterNames ()
	Gets the parameterNames attribute of the TanimotoMolSimilarity object. More...

Object	getParameterType (String name)

void	setParameters (Object[] params) throws CDKException
	Set the parameters attribute of TanimotoMolSimilarity object. More...

Object[]	getParameters ()

String[]	getDescriptorNames ()

DescriptorValue	calculate (IAtomContainer mol)

IDescriptorResult	getDescriptorResultType ()

String	getDictionaryTitle ()
	Gets the title of this descriptor as it should be in the dictionary. Returns the title More...

String	getDictionaryDefinition ()
	Get a string that describes the descriptor in detail.Might contain mathematical formulation. See also `DescriptorEngine` Returns the description of this descriptor, possibly containing equations that clarify how it is calculated. More...

String[]	getDictionaryClass ()
	Get the classification of this descriptor.A descriptor can belong to one or more classes simultaneously. Returns More...

String	getDictionaryTitle ()
	Gets the title of this descriptor as it should be in the dictionary. More...

String	getDictionaryDefinition ()
	Get a string that describes the descriptor in detail. More...

String[]	getDictionaryClass ()
	Get the classification of this descriptor. More...

Static Public Member Functions
static IFingerprinter	makeIFingerprinter (String classShortName) throws CDKException

Private Attributes
IBitFingerprint	referenceFingerprint

IFingerprinter	fingerprinter

String	fingerprinterName = "none"

Static Private Attributes
static final String[]	PARAMNAMES

static final String[]	NAMES = {"TanimotoSimilarity"}

static IChemObjectBuilder	cdkBuilder
	Utility for constructing CDK objects. More...

Detailed Description

Calculates the molecular similarity against a target compound the fingerprint of which is given as parameter.

Definition at line 48 of file TanimotoMolSimilarity.java.

Constructor & Destructor Documentation

◆ TanimotoMolSimilarity()

denoptim.fitness.descriptors.TanimotoMolSimilarity.TanimotoMolSimilarity ( )

Constructor for a TanimotoMolSimilarity object.

Definition at line 72 of file TanimotoMolSimilarity.java.

Member Function Documentation

◆ calculate()

DescriptorValue denoptim.fitness.descriptors.TanimotoMolSimilarity.calculate ( IAtomContainer mol )

Definition at line 221 of file TanimotoMolSimilarity.java.

References denoptim.fitness.descriptors.TanimotoMolSimilarity.fingerprinter, denoptim.fitness.descriptors.TanimotoMolSimilarity.getDescriptorNames(), denoptim.fitness.descriptors.TanimotoMolSimilarity.getParameterNames(), denoptim.fitness.descriptors.TanimotoMolSimilarity.getParameters(), denoptim.fitness.descriptors.TanimotoMolSimilarity.getSpecification(), and denoptim.fitness.descriptors.TanimotoMolSimilarity.referenceFingerprint.

Referenced by denoptim.fitness.descriptors.TanimotoMolSimilarityTest.testTanimotoMolSimilarity().

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◆ getDescriptorNames()

String[] denoptim.fitness.descriptors.TanimotoMolSimilarity.getDescriptorNames ( )

Definition at line 212 of file TanimotoMolSimilarity.java.

References denoptim.fitness.descriptors.TanimotoMolSimilarity.NAMES.

Referenced by denoptim.fitness.descriptors.TanimotoMolSimilarity.calculate().

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◆ getDescriptorResultType()

IDescriptorResult denoptim.fitness.descriptors.TanimotoMolSimilarity.getDescriptorResultType ( )

Definition at line 273 of file TanimotoMolSimilarity.java.

◆ getDictionaryClass()

String[] denoptim.fitness.descriptors.TanimotoMolSimilarity.getDictionaryClass ( )

Get the classification of this descriptor.A descriptor can belong to one or more classes simultaneously.

Returns

Implements denoptim.fitness.IDenoptimDescriptor.

Definition at line 308 of file TanimotoMolSimilarity.java.

◆ getDictionaryDefinition()

String denoptim.fitness.descriptors.TanimotoMolSimilarity.getDictionaryDefinition ( )

Get a string that describes the descriptor in detail.Might contain mathematical formulation.

See also: DescriptorEngine

Returns: the description of this descriptor, possibly containing equations that clarify how it is calculated.

Implements denoptim.fitness.IDenoptimDescriptor.

Definition at line 291 of file TanimotoMolSimilarity.java.

References denoptim.fitness.descriptors.TanimotoMolSimilarity.PARAMNAMES.

◆ getDictionaryTitle()

String denoptim.fitness.descriptors.TanimotoMolSimilarity.getDictionaryTitle ( )

Gets the title of this descriptor as it should be in the dictionary.

Returns: the title

Implements denoptim.fitness.IDenoptimDescriptor.

Definition at line 282 of file TanimotoMolSimilarity.java.

◆ getParameterNames()

String[] denoptim.fitness.descriptors.TanimotoMolSimilarity.getParameterNames ( )

Gets the parameterNames attribute of the TanimotoMolSimilarity object.

Returns: the parameterNames value

Definition at line 104 of file TanimotoMolSimilarity.java.

References denoptim.fitness.descriptors.TanimotoMolSimilarity.PARAMNAMES.

Referenced by denoptim.fitness.descriptors.TanimotoMolSimilarity.calculate().

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◆ getParameters()

Object[] denoptim.fitness.descriptors.TanimotoMolSimilarity.getParameters ( )

Definition at line 200 of file TanimotoMolSimilarity.java.

References denoptim.fitness.descriptors.TanimotoMolSimilarity.fingerprinterName, and denoptim.fitness.descriptors.TanimotoMolSimilarity.referenceFingerprint.

Referenced by denoptim.fitness.descriptors.TanimotoMolSimilarity.calculate().

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◆ getParameterType()

Object denoptim.fitness.descriptors.TanimotoMolSimilarity.getParameterType ( String name )

Definition at line 112 of file TanimotoMolSimilarity.java.

References denoptim.fitness.descriptors.TanimotoMolSimilarity.PARAMNAMES.

◆ getSpecification()

DescriptorSpecification denoptim.fitness.descriptors.TanimotoMolSimilarity.getSpecification ( )

Get the specification attribute of Tanimoto molecular similarity.

Given the dependency on the fingerpringer and reference fingerprint, the implementation identifier is made dependent on those two parameters. Consequently resetting the parameter with two new instances of the fingerpringer and reference fingerprint (even is effectively equal) will result in two different DescriptorSpecification objects.

Returns: the specification of this descriptor.

Definition at line 86 of file TanimotoMolSimilarity.java.

References denoptim.fitness.descriptors.TanimotoMolSimilarity.fingerprinter, denoptim.fitness.descriptors.TanimotoMolSimilarity.fingerprinterName, and denoptim.fitness.descriptors.TanimotoMolSimilarity.referenceFingerprint.

Referenced by denoptim.fitness.descriptors.TanimotoMolSimilarity.calculate().

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◆ makeIFingerprinter()

static IFingerprinter denoptim.fitness.descriptors.TanimotoMolSimilarity.makeIFingerprinter ( String classShortName ) throws CDKException

static

Definition at line 162 of file TanimotoMolSimilarity.java.

References denoptim.fitness.descriptors.TanimotoMolSimilarity.cdkBuilder.

Referenced by denoptim.fitness.FitnessExpressionParser.makeIFingerprinter(), and denoptim.fitness.descriptors.TanimotoMolSimilarity.setParameters().

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◆ setParameters()

void denoptim.fitness.descriptors.TanimotoMolSimilarity.setParameters ( Object[] params ) throws CDKException

Set the parameters attribute of TanimotoMolSimilarity object.

The descriptor takes two parameters: the class name of the fingerprinter used to generate the fingerprints (e.g., org.openscience.cdk.fingerprint.PubchemFingerprinter), and the fingerprint against which we want to calculate similarity.

Parameters

params the array of parameters

Definition at line 134 of file TanimotoMolSimilarity.java.

References denoptim.fitness.descriptors.TanimotoMolSimilarity.fingerprinter, denoptim.fitness.descriptors.TanimotoMolSimilarity.fingerprinterName, denoptim.fitness.descriptors.TanimotoMolSimilarity.makeIFingerprinter(), and denoptim.fitness.descriptors.TanimotoMolSimilarity.referenceFingerprint.

Referenced by denoptim.fitness.descriptors.TanimotoMolSimilarityTest.testTanimotoMolSimilarity().

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Member Data Documentation

◆ cdkBuilder

IChemObjectBuilder denoptim.fitness.descriptors.TanimotoMolSimilarity.cdkBuilder

staticprivate

Initial value:

=

DefaultChemObjectBuilder.getInstance()

Utility for constructing CDK objects.

Definition at line 64 of file TanimotoMolSimilarity.java.

Referenced by denoptim.fitness.descriptors.TanimotoMolSimilarity.makeIFingerprinter().

◆ fingerprinter

IFingerprinter denoptim.fitness.descriptors.TanimotoMolSimilarity.fingerprinter

private

Definition at line 54 of file TanimotoMolSimilarity.java.

Referenced by denoptim.fitness.descriptors.TanimotoMolSimilarity.calculate(), denoptim.fitness.descriptors.TanimotoMolSimilarity.getSpecification(), and denoptim.fitness.descriptors.TanimotoMolSimilarity.setParameters().

◆ fingerprinterName

String denoptim.fitness.descriptors.TanimotoMolSimilarity.fingerprinterName = "none"

private

Definition at line 55 of file TanimotoMolSimilarity.java.

Referenced by denoptim.fitness.descriptors.TanimotoMolSimilarity.getParameters(), denoptim.fitness.descriptors.TanimotoMolSimilarity.getSpecification(), and denoptim.fitness.descriptors.TanimotoMolSimilarity.setParameters().

◆ NAMES

final String [] denoptim.fitness.descriptors.TanimotoMolSimilarity.NAMES = {"TanimotoSimilarity"}

staticprivate

Definition at line 59 of file TanimotoMolSimilarity.java.

Referenced by denoptim.fitness.descriptors.TanimotoMolSimilarity.getDescriptorNames().

◆ PARAMNAMES

final String [] denoptim.fitness.descriptors.TanimotoMolSimilarity.PARAMNAMES

staticprivate

Initial value:

= new String[] {

"fingerprinterImplementation","referenceFingerprint"}

Definition at line 56 of file TanimotoMolSimilarity.java.

Referenced by denoptim.fitness.descriptors.TanimotoMolSimilarity.getDictionaryDefinition(), denoptim.fitness.descriptors.TanimotoMolSimilarity.getParameterNames(), and denoptim.fitness.descriptors.TanimotoMolSimilarity.getParameterType().

◆ referenceFingerprint

IBitFingerprint denoptim.fitness.descriptors.TanimotoMolSimilarity.referenceFingerprint

private

Definition at line 53 of file TanimotoMolSimilarity.java.

Referenced by denoptim.fitness.descriptors.TanimotoMolSimilarity.calculate(), denoptim.fitness.descriptors.TanimotoMolSimilarity.getParameters(), denoptim.fitness.descriptors.TanimotoMolSimilarity.getSpecification(), and denoptim.fitness.descriptors.TanimotoMolSimilarity.setParameters().

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

/github/workspace/src/main/java/denoptim/fitness/descriptors/TanimotoMolSimilarity.java

Public Member Functions

Static Public Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ TanimotoMolSimilarity()

Member Function Documentation

◆ calculate()

◆ getDescriptorNames()

◆ getDescriptorResultType()

◆ getDictionaryClass()

◆ getDictionaryDefinition()

◆ getDictionaryTitle()

◆ getParameterNames()

◆ getParameters()

◆ getParameterType()

◆ getSpecification()

◆ makeIFingerprinter()

◆ setParameters()

Member Data Documentation

◆ cdkBuilder

◆ fingerprinter

◆ fingerprinterName

◆ NAMES

◆ PARAMNAMES

◆ referenceFingerprint