A B C D E F G H I L M N O P Q R S T U V

A

addAllVertices(Graph) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Graph

addBothNeighbours(Vertex) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

addColumn(String, String, String) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Database

Adds a new column to a given table of a database.

addConnections(Graph, List<PolymerNotation>, List<ConnectionNotation>) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.MoleculeGraphUtils

Adds the connections between polymers of the molecule.

addNeighbour(Vertex) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

addVertex(MonomerNotation) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Graph

AlertBox - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout

AlertBox class implements alert dialogs to update the user about errors, information and help.

AlertBox() - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout.AlertBox

alertDialog - Static variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout.AlertBox

analogsCheckBox - Static variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Options

B

buildChemPart(PolymerNotation, int) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.MoleculeGraphUtils

Builds the CHEM part of the molecule.

buildDatabaseButton - Variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Input

buildMoleculeGraph(List<PolymerNotation>, List<ConnectionNotation>) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.MoleculeGraphUtils

* Method builds a moleculeGraph from a list of PolymerNotations and a * list of Connections.

buildPeptidePart(PolymerNotation, int) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.MoleculeGraphUtils

Builds the PEPTIDE part of the molecule.

buildRNAPart(PolymerNotation, int) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.MoleculeGraphUtils

Builds the RNA part of the molecule.

button - Static variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Options

C

calculateFingerprint(HELM2Notation) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.Fingerprinter

Calculates the fingerprint for a given HELM notation by enumerating all of the monomer paths and representing each path as one bit in the fingerprint of size 1024.

calculateFingerprintNaturalAnalogs(HELM2Notation) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.Fingerprinter

Calculates a combined fingerprint for a given HELM notation by enumerating all of the original monomer paths and all of the monomer paths converted into natural analogs and representing each path as one bit in the fingerprint of size 1024.

calculateSimilarity(HELM2Notation, HELM2Notation) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.Similarity

Method calculates the similarity (tanimoto coefficient) of two HELM notations

calculateSimilarity(BitSet, BitSet) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.Similarity

Method calculates the similarity (tanimoto coefficient) of two bitset fingerprints.

calculateSimilarityNatAnalogs(HELM2Notation, HELM2Notation) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.Similarity

Method calculates the similarity (tanimoto coefficient) of two HELM notations and takes the natural analogs of modified monomers into account.

call() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.CreateDatabaseTask

call() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.ExportTask

call() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.SimilaritySearchTask

changeInfoText(String) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Results

checkAndStorePath(String, List<String>, String, List<String>) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.PathGenerator

Checks if path already exists as palindrome, stores valide paths depending on lexicographical order.

checkHelmRelationship(HELM2Notation, HELM2Notation) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.Subset

Method checks if the parentNotation is completely enclosed in the childNotation.

checkHelmRelationship(BitSet, BitSet) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.Subset

Method checks if parentFprint is a subset of childFprint and returns true in that case.

clear() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Graph

clearPaths() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.PathGenerator

CreateDatabaseTask - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app

CreateDatabaseTask extends javafx.concurrent.Task class in order to run the generation of a database from a helm textfile in a new thread.

CreateDatabaseTask(Database) - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.CreateDatabaseTask

createTable(String, String, String, String) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Database

Method creates a table with two columns (int, text) for ID and HELM in a database.

D

Database - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app

This database singleton class implements methods to work with a SQLite database while doing similarity search.

databaseNameDisplay - Static variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Input

databaseText - Variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Input

deleteContentFromDB(String) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Database

Method deletes content from a database in order to be able to overwrite it with new content.

doQuery(HELM2Notation, double) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.SimilaritySearchTask

Method calls the corresponding methods to build moleculeGraphs, find paths, generate fingerprints, calculate tanimoto values, check for subset, store the values in a database and select the desired notations with a specified minimum similarity or subset notations.

doResults(List<Map<String, Object>>) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Results

Method processes the results to be stores in the TableView.

E

equals(Graph) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Graph

equals(Vertex) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

ErrorBox(String, String) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout.AlertBox

exportButton - Static variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Results

exportInfoText - Static variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.ExportTask

ExportTask - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app

ExportTask class extends javafx.concurrent.Task and runs the task to export results in a new thread.

ExportTask() - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.ExportTask

F

FileToDatabase - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app

FromFileToDatabase class takes a text file with helm notations and stores the notations in a SQLite database.

FileToDatabase() - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.FileToDatabase

fillHELMTable(String, String, CreateDatabaseTask) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Database

Fills the table with CID and HELM from an inputfile.

fillHELMTanimotoTable(String, String, List<Integer>, List<Double>) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Database

Method fills table with tanimoto value at the corresponding ID.

findPaths(Graph) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.PathGenerator

Calls depthFirstSearch for every monomer (vertex).

Fingerprinter - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary

Fingerprinter class creates a hashed fingerprint from a set of paths using SHA-2 as the kryptographical hash function.

Fingerprinter() - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.Fingerprinter

G

getBiggestTanimoto(String) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Database

Returns the maximum similarity value that is found of a notation to the query.

getDatabaseDirPath() - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Input

getDatabaseName() - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Input

getDatabasePath() - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Input

getHashedFingerprint(Set<String>) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.Fingerprinter

getHelmNotation() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.ResultUnit

getId() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.ResultUnit

getIndex() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

getInstance() - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Database

This is the static instance method.

getMonomer() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

getMostSimilarNotations(String, String, String) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Database

Method selects ten notations with the highest similarity to the query.

getNaturalPaths() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.PathGenerator

getNaturalPeptide(String) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.PathGenerator

Gets the natural analog of a peptide monomer.

getNaturalRNA(String) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.PathGenerator

Gets the natural analog of a RNA monomer.

getNeighbourList() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

getNotationsWithSpecificTanimoto(String, String, String, double) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Database

Selects the helm notations with a tanimoto bigger than or equal to the desired similarity.

getNotationsWithSubset(String, String, String) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Database

Selects the helm notations that the query notation is a subset of.

getParent() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

getPaths() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.PathGenerator

getQueryNotation() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Options

getResultNotations() - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Results

getSimilarity() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Options

getTanimotoValue() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.ResultUnit

getTextfileName() - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Input

getTextfilePath() - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Input

getVertices() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Graph

Graph - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary.utils

Graph class is a data model for a moleculeGraph with vertices.

Graph() - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Graph

Graph(List<Vertex>) - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Graph

H

handle(ActionEvent) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Input

Method handles the helpButtons action and displays an AlertBox for user support.

handle(ActionEvent) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Main

hasUniqueUnit() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

HELM2Object - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary

HELM2Object class to generate HELM2Notation object from HELM string

HELM2Object() - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.HELM2Object

helmList - Static variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.SimilaritySearchTask

helmText - Variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Options

HelpBox(String) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout.AlertBox

helpButton - Variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Input

I

idList - Static variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.SimilaritySearchTask

InfoBox(String) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout.AlertBox

infoText - Static variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.FileToDatabase

infoText - Static variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Results

init() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Main

Method performs initialization of layouts prior to actual starting of the application.

Input - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app

Input class handles the input section of the user interface.

Input(Stage) - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Input

This constructor instantiates all of the controls of the interfaces input section and calls several methods to set the controls properties and event handling.

inputTitle - Variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Input

insertFingerprints(String, List<BitSet>, List<BitSet>, List<Integer>, String) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Database

Fill table with HELM fingerprint at the corresponding ID.

isChem() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

isNonNatural() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

isPeptide() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

isRNA() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

isVisited() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

L

loadDriver(String) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Database

Method loads the database's driver dynamically once for entire application's lifetime.

M

Main - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app

Main class to set the layout of the user interface and its node positions within the stage.

Main() - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Main

main(String[]) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Main

makeHELM2NotationObject(String) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.HELM2Object

Generates HELM2Notation object from HELM string

MAX_PROGRESS - Static variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.SimilaritySearchTask

MoleculeGraphUtils - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary.utils

MoleculeGraphUtils class implements a moleculeGraph of type Graph with a list of vertices and edges between vertices that are represented by neighbors for each vertex.

MoleculeGraphUtils() - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.MoleculeGraphUtils

monomerType - Variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

MyBitSet - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary.utils

MyBitSet class extends java.util.BitSet to create a list from a string of integers that represent the bits that are set and create a java.util.BitSet from the list of set bits.

MyBitSet(int) - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.MyBitSet

MyBitSet(String) - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.MyBitSet

MyButton - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout

MyButton class extends Button class and specifies the text and font of the button.

MyButton(String) - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout.MyButton

MyButton(String, boolean) - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout.MyButton

MyCheckBox - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout

MyCheckBox class extends CheckBox and specifies the text and font of the checkbox.

MyCheckBox(String) - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout.MyCheckBox

MyLabel - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout

MyLabel class extends Label class and specifies the text and font of the label.

MyLabel(String) - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout.MyLabel

MyProgressBar - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout

MyProgressBar class extends ProgressBar class and specifies the width of the bar.

MyProgressBar() - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout.MyProgressBar

MyRadioButton - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout

MyRadioButton class extends RadioButton class and specifies the text and font of the label.

MyRadioButton(String, double, ToggleGroup) - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout.MyRadioButton

MyTableColumn<T,E> - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout

MyTableColumn class extends TableColumn with several specified properties.

MyTableColumn(String, double, String) - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout.MyTableColumn

MyText - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout

MyText class extends Text class and specifies the text and font of the Text.

MyText(String) - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout.MyText

MyText(boolean) - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout.MyText

MyTextField - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout

MyTextField class extends TextField with several specified properties.

MyTextField(String, double, double) - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout.MyTextField

N

NaturalAnalogException - Exception in org.pistoiaalliance.helm.HELMSimilarityLibrary.exception

NaturalAnalogException

NaturalAnalogException(String) - Constructor for exception org.pistoiaalliance.helm.HELMSimilarityLibrary.exception.NaturalAnalogException

O

Options - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app

Options class handles the options section of the user interface.

Options() - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Options

Options constructor instantiates all of the controls of the interfaces option section and calls several methods to set the controls properties and event handling.

org.pistoiaalliance.helm.HELMSimilarityLibrary - package org.pistoiaalliance.helm.HELMSimilarityLibrary

org.pistoiaalliance.helm.HELMSimilarityLibrary.exception - package org.pistoiaalliance.helm.HELMSimilarityLibrary.exception

org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app - package org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app

org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout - package org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.layout

org.pistoiaalliance.helm.HELMSimilarityLibrary.utils - package org.pistoiaalliance.helm.HELMSimilarityLibrary.utils

P

PathGenerator - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary

PathGenerator class takes a moleculeGraph and finds all path from each monomer (vertex) up to a maximal length (searchDepth).

PathGenerator() - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.PathGenerator

processTextFile(String) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.FileToDatabase

progress - Static variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.FileToDatabase

progressbar - Static variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.SimilaritySearchTask

Q

queryHelmTextField - Variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Options

R

radioSimSearch - Static variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Options

radioSubset - Static variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Options

readIDandHELMRecords(String, String) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Database

Method reads ID and HELM from table.

resultNotations - Static variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.SimilaritySearchTask

Results - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app

Results class handles the result section of the user interface.

Results() - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Results

Results constructor instantiates all of the controls of the interfaces results section and calls several methods to set the controls properties and event handling.

ResultUnit - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app

ResultUnit class specifies the three parts of one Result Unit: id, notation, tanimoto.

ResultUnit(Integer, String, Double) - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.ResultUnit

The ResultUnit constructor specifies the display of the similarity value with four decimal places.

S

scrollBar - Variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Options

scrollCheckBox - Variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Options

setDatabaseDirPath(String) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Input

setDatabaseName(String) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Input

setDatabasePath(String) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Input

setHasUniqueUnit(boolean) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

setHelmNotation(String) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.ResultUnit

setId(Integer) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.ResultUnit

setIndex(int) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

setMonomer(MonomerNotation) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

setNeighbourList(List<Vertex>) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

setNonNatural() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

setParent(Vertex) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

setSubset(String, BitSet, List<Integer>, List<BitSet>) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Database

Method checks for a list of fingerprints if the query notation is a subset of it and stores true or false in the database for the corresponding fingerprint.

setTanimotoValue(Double) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.ResultUnit

setTextfileName(String) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Input

setTextfilePath(String) - Static method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Input

setVisited(boolean) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

Similarity - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary

Similarity class calculates the Tanimoto value of two hashed bitstring fingerprints.

Similarity() - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.Similarity

SimilaritySearch - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app

SimilaritySearch class is to start a new thread of SimilaritySearchTask.

SimilaritySearch(HELM2Notation, double) - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.SimilaritySearch

SimilaritySearchTask - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app

SimilaritySearch class to perform the algorithm of calculating the similarity of a query helm notation and a database of more helm notations in the following steps 1.

SimilaritySearchTask(HELM2Notation, double) - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.SimilaritySearchTask

start(Stage) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Main

stop() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Main

Subset - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary

Subset class calculates the substructure relationship of two HELM notations.

Subset() - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.Subset

T

tanimotoList - Static variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.SimilaritySearchTask

tanimotoTextField - Variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Options

tanimotoUnit - Variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Options

tenSimilarCheckBox - Static variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Options

textfileButton - Variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Input

textfileNameDisplay - Variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Input

textfileText - Variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Input

title - Variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Options

title - Variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.Results

toString() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

totalNaturalPaths - Static variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.PathGenerator

totalPaths - Static variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.PathGenerator

U

updateProgress(double, double) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.CreateDatabaseTask

updateProgress(double, double) - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.SimilaritySearchTask

V

valueOf(String) - Static method in enum org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex.Type

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex.Type

Returns an array containing the constants of this enum type, in the order they are declared.

Vertex - Class in org.pistoiaalliance.helm.HELMSimilarityLibrary.utils

Vertex class is a data model for a vertex in a Graph.

Vertex() - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

Vertex(Vertex) - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

Vertex(Vertex, Vertex.Type) - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

Vertex(MonomerNotation) - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

Vertex(MonomerNotation, Vertex.Type, boolean, boolean, int) - Constructor for class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Vertex

Vertex.Type - Enum in org.pistoiaalliance.helm.HELMSimilarityLibrary.utils

vertexCount() - Method in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Graph

vertices - Variable in class org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.Graph

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