Index

C D F G H I M N P S
All Classes and Interfaces|All Packages|Serialized Form

C

count(String, CountFingerprint) - Method in class de.unijena.cheminf.fragment.fingerprint.FragmentFingerprinter

Method to return the count/occurrences/frequency of a given SMILES String in a given CountFingerprint instance.

CountFingerprint - Class in de.unijena.cheminf.fragment.fingerprint

The CountFingerprint class implements the CDK interface ICountFingerprint.

CountFingerprint(int, Map<Integer, Integer>) - Constructor for class de.unijena.cheminf.fragment.fingerprint.CountFingerprint

Initialization of default CountFingerprint.

CountFingerprint(int, Map<Integer, Integer>, boolean) - Constructor for class de.unijena.cheminf.fragment.fingerprint.CountFingerprint

Initialization of CountFingerprint with a given behavior statement.

D

de.unijena.cheminf.fragment.fingerprint - package de.unijena.cheminf.fragment.fingerprint

de.unijena.cheminf.fragment.fingerprint.performanceTest - package de.unijena.cheminf.fragment.fingerprint.performanceTest

F

FragmentFingerprinter - Class in de.unijena.cheminf.fragment.fingerprint

Class to generate fragment fingerprints.

FragmentFingerprinter(List<String>) - Constructor for class de.unijena.cheminf.fragment.fingerprint.FragmentFingerprinter

Initialization of the fragment fingerprinter by using a user-defined set of fragments in the form of unique SMILES.

G

getBitArray(List<String>) - Method in class de.unijena.cheminf.fragment.fingerprint.FragmentFingerprinter

Returns bit array for specified list.

getBitArray(Map<String, Integer>) - Method in class de.unijena.cheminf.fragment.fingerprint.FragmentFingerprinter

Returns bit array for the specified map.

getBitDefinition(int) - Method in class de.unijena.cheminf.fragment.fingerprint.FragmentFingerprinter

Returns the bit definitions i.e.

getBitFingerprint(List<String>) - Method in class de.unijena.cheminf.fragment.fingerprint.FragmentFingerprinter

Method to generate the bit fingerprint.

getBitFingerprint(List<String>) - Method in interface de.unijena.cheminf.fragment.fingerprint.IFragmentFingerprinter

Method for calculating a bit fingerprint.

getBitFingerprint(IAtomContainer) - Method in class de.unijena.cheminf.fragment.fingerprint.FragmentFingerprinter

getBitSet(List<String>) - Method in class de.unijena.cheminf.fragment.fingerprint.FragmentFingerprinter

Method directly returning the BitSet of the fingerprint generated from the given list of SMILES.

getBitSet(Map<String, Integer>) - Method in class de.unijena.cheminf.fragment.fingerprint.FragmentFingerprinter

Method directly returning the BitSet of the fingerprint generated from the given frequency map.

getCount(int) - Method in class de.unijena.cheminf.fragment.fingerprint.CountFingerprint

For an index specified within the fingerprint size, the corresponding frequency is returned.

getCountArray(List<String>) - Method in class de.unijena.cheminf.fragment.fingerprint.FragmentFingerprinter

Returns the count array for the specified list.

getCountArray(Map<String, Integer>) - Method in class de.unijena.cheminf.fragment.fingerprint.FragmentFingerprinter

Returns a CountArray, which is created based on the given parameter.

getCountFingerprint(List<String>) - Method in class de.unijena.cheminf.fragment.fingerprint.FragmentFingerprinter

Generates a count fingerprint for a molecule based on its fragments, represented by unique SMILES in the list given as parameters.

getCountFingerprint(List<String>) - Method in interface de.unijena.cheminf.fragment.fingerprint.IFragmentFingerprinter

Method for calculating a count fingerprint.

getCountFingerprint(Map<String, Integer>) - Method in class de.unijena.cheminf.fragment.fingerprint.FragmentFingerprinter

Generates count fingerprint for a molecule based on its fragments represented by unique SMILES strings in the key set and their frequencies in the value set of the given map.

getCountFingerprint(Map<String, Integer>) - Method in interface de.unijena.cheminf.fragment.fingerprint.IFragmentFingerprinter

Method for calculating a count fingerprint.

getCountFingerprint(IAtomContainer) - Method in class de.unijena.cheminf.fragment.fingerprint.FragmentFingerprinter

getCountForHash(int) - Method in class de.unijena.cheminf.fragment.fingerprint.CountFingerprint

Since the fragment fingerprint is a key-based fingerprint and the hash value therefore indicates the position of the respective bin in the fingerprint, each hash value occurs only once in the fingerprint.

getDefinedFingerprintSize() - Method in class de.unijena.cheminf.fragment.fingerprint.CountFingerprint

Public getter for internally used size of given pre-defined fingerprint.

getFingerprint(IAtomContainer) - Method in class de.unijena.cheminf.fragment.fingerprint.FragmentFingerprinter

getFloatFingerprint(Map<String, Integer>, float[], boolean) - Method in class de.unijena.cheminf.fragment.fingerprint.FragmentFingerprinter

Method to generate the float fingerprint of a given molecule's fragments (i.e.

getFragmentsComponentsFloatMatrix(Map<String, Integer>[], float[][], boolean) - Method in class de.unijena.cheminf.fragment.fingerprint.FragmentFingerprinter

Public method to get a float[][] matrix containing the fingerprints for the given maps list (fragment sets of distinct molecules) in regard to the pre-defined fragment fingerprint.

getHash(int) - Method in class de.unijena.cheminf.fragment.fingerprint.CountFingerprint

getRawFingerprint(IAtomContainer) - Method in class de.unijena.cheminf.fragment.fingerprint.FragmentFingerprinter

UnsupportedOperationException.

getSize() - Method in class de.unijena.cheminf.fragment.fingerprint.FragmentFingerprinter

Since the FragmentFingerprinter is a key-based fingerprint, the size of the fingerprint is equal to the number of predefined fragments (unique SMILES) if the list of key fragments passed during initialization does not contain duplicates, otherwise the size of the fingerprint may be smaller than the number of fragments passed since duplicates are removed.

getSmilesPositionToFrequencyMap() - Method in class de.unijena.cheminf.fragment.fingerprint.CountFingerprint

Public getter for internal map of smiles fingerprint position to corresponding frequency.

getVersionDescription() - Method in class de.unijena.cheminf.fragment.fingerprint.FragmentFingerprinter

H

hasHash(int) - Method in class de.unijena.cheminf.fragment.fingerprint.CountFingerprint

I

IFragmentFingerprinter - Interface in de.unijena.cheminf.fragment.fingerprint

Interface for implementing fragment fingerprinters.

M

main(String[]) - Static method in class de.unijena.cheminf.fragment.fingerprint.performanceTest.Main

Starts the application.

Main - Class in de.unijena.cheminf.fragment.fingerprint.performanceTest

Main class for starting the PerformanceTest application.

Main() - Constructor for class de.unijena.cheminf.fragment.fingerprint.performanceTest.Main

merge(ICountFingerprint) - Method in class de.unijena.cheminf.fragment.fingerprint.CountFingerprint

UnsupportedOperationException.

mergeCountFingerprint(CountFingerprint, CountFingerprint) - Static method in class de.unijena.cheminf.fragment.fingerprint.CountFingerprint

Static method to merge two specified CountFingerprint instances into a NEW CountFingerprint instance created from their combined frequency maps.

N

numOfPopulatedbins() - Method in class de.unijena.cheminf.fragment.fingerprint.CountFingerprint

Fragment fingerprints are key-based fingerprints, therefore the number of populated bins corresponds to the number of predefined fragments (unique SMILES).

P

PerformanceTest - Class in de.unijena.cheminf.fragment.fingerprint.performanceTest

A class for testing the performance of the fragment fingerprinter.

PerformanceTest(String[]) - Constructor for class de.unijena.cheminf.fragment.fingerprint.performanceTest.PerformanceTest

Constructor.

S

setBehaveAsBitFingerprint(boolean) - Method in class de.unijena.cheminf.fragment.fingerprint.CountFingerprint

size() - Method in class de.unijena.cheminf.fragment.fingerprint.CountFingerprint

Since fragment fingerprints are key-based, the number of bits in the fingerprint is equal to the number of predefined fragments (unique SMILES) if the list of key fragments passed during initialization does not contain duplicates, otherwise the size of the fingerprint may be smaller than the number of fragments passed since duplicates are removed/ignored.

C D F G H I M N P S
All Classes and Interfaces|All Packages|Serialized Form