Calculates the molecular similarity against a target compound the fingerprint of which is given as parameter, and using a given list of substructures. More...

Inheritance diagram for denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure:

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Collaboration diagram for denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure:

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Public Member Functions
	TanimotoMolSimilarityBySubstructure ()
	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 TanimotoMolSimilarityBySubstructure object. More...

Object	getParameterType (String name)

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

Private Attributes
IBitFingerprint	referenceFingerprint

IFingerprinter	fingerprinter

String[]	substructuressmarts

Static Private Attributes
static final String[]	PARAMNAMES

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

Detailed Description

Calculates the molecular similarity against a target compound the fingerprint of which is given as parameter, and using a given list of substructures.

Definition at line 44 of file TanimotoMolSimilarityBySubstructure.java.

Constructor & Destructor Documentation

◆ TanimotoMolSimilarityBySubstructure()

denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure.TanimotoMolSimilarityBySubstructure ( )

Constructor for a TanimotoMolSimilarity object.

Definition at line 62 of file TanimotoMolSimilarityBySubstructure.java.

Member Function Documentation

◆ calculate()

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

Definition at line 177 of file TanimotoMolSimilarityBySubstructure.java.

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

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◆ getDescriptorNames()

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

Definition at line 168 of file TanimotoMolSimilarityBySubstructure.java.

References denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure.NAMES.

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

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◆ getDescriptorResultType()

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

Definition at line 216 of file TanimotoMolSimilarityBySubstructure.java.

◆ getDictionaryClass()

String[] denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure.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 253 of file TanimotoMolSimilarityBySubstructure.java.

◆ getDictionaryDefinition()

String denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure.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 234 of file TanimotoMolSimilarityBySubstructure.java.

References denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure.PARAMNAMES.

◆ getDictionaryTitle()

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

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

Returns: the title

Implements denoptim.fitness.IDenoptimDescriptor.

Definition at line 225 of file TanimotoMolSimilarityBySubstructure.java.

◆ getParameterNames()

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

Gets the parameterNames attribute of the TanimotoMolSimilarityBySubstructure object.

Returns: the parameterNames value

Definition at line 97 of file TanimotoMolSimilarityBySubstructure.java.

References denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure.PARAMNAMES.

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

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◆ getParameters()

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

Definition at line 156 of file TanimotoMolSimilarityBySubstructure.java.

References denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure.referenceFingerprint, and denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure.substructuressmarts.

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

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◆ getParameterType()

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

Definition at line 105 of file TanimotoMolSimilarityBySubstructure.java.

References denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure.PARAMNAMES.

◆ getSpecification()

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

Get the specification attribute of Tanimoto molecular similarity.

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

Returns: the specification of this descriptor.

Definition at line 77 of file TanimotoMolSimilarityBySubstructure.java.

References denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure.fingerprinter, denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure.referenceFingerprint, and denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure.substructuressmarts.

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

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◆ setParameters()

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

Set the parameters attribute of TanimotoMolSimilarityBySubstructure object.

The descriptor takes two parameters: the array of substructures defining the fingerprint bits, and the fingerprint against which we want to calculate similarity.

Parameters

params the array of parameters

Definition at line 128 of file TanimotoMolSimilarityBySubstructure.java.

References denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure.fingerprinter, denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure.referenceFingerprint, and denoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure.substructuressmarts.