A B C D E F G H I J L M N O P R S T U W Y

A

abort() - Method in class org.simtk.isimsu.JarDefinedExecutableThread

accept(File) - Method in class org.simtk.file.FileNameFilter

actionPerformed(ActionEvent) - Method in class org.simtk.isimsu.BrowserLaunchListener

actionPerformed(ActionEvent) - Method in class org.simtk.isimsu.IonCountDialog

Respond to pressing the "dismiss" button

actionPerformed(ActionEvent) - Method in class org.simtk.isimsu.IonSelectionDialog

actionPerformed(ActionEvent) - Method in class org.simtk.isimsu.LogDialog

Respond to dismiss button press

actionPerformed(ActionEvent) - Method in class org.simtk.isimsu.SimulationDetailsDialog

Respond to pressing the "dismiss" button

addIonButton - Variable in class org.simtk.isimsu.IonSelectionDialog

addIonButtonPressed() - Method in class org.simtk.isimsu.IonSelectionDialog

addIonConcentration(IonConcentration) - Method in class org.simtk.isimsu.SaltCondition

addIonSelectionPanel(IonSelectionPanel) - Method in class org.simtk.isimsu.IonSelectionDialog

addIonSpecies(IonSpecies) - Method in class org.simtk.isimsu.SaltConditionRange

addPrerequisite(DependentTask) - Method in class org.simtk.isimsu.DependentTask

addRanges(URL) - Method in class org.simtk.isimsu.SaltRangeSet

addSaltCondition(SaltCondition) - Method in class org.simtk.isimsu.SaltConditionRange

addSaltSelectionListener(SaltSelectionListener) - Method in class org.simtk.isimsu.IonSelectionDialog

addSaltSelectionListener(SaltSelectionListener) - Method in interface org.simtk.isimsu.SaltSelectionObservable

addSaltSelectionListener(SaltSelectionListener) - Method in class org.simtk.isimsu.SaltSelectionObservableClass

ALWAYS_OVERWRITE - Static variable in class org.simtk.file.CopyDirectoryChooser

append(String) - Method in class org.simtk.isimsu.LogDialog

appendToLog(String) - Method in class org.simtk.isimsu.ISIMWrapper

ASK_BEFORE_OVERWRITE - Static variable in class org.simtk.file.CopyDirectoryChooser

askToSaveWork() - Method in class org.simtk.isimsu.ISIMWrapper

available() - Method in class org.simtk.file.UncompressInputStream

availableIons() - Method in class org.simtk.isimsu.IonSelectionDialog

B

BrowserLaunchListener - Class in org.simtk.isimsu

C

cancel() - Method in class org.simtk.file.CopyDirectoryChooser

cancelButton - Variable in class org.simtk.isimsu.IonSelectionDialog

cancelButtonPressed() - Method in class org.simtk.isimsu.IonSelectionDialog

compareTo(IonConcentration) - Method in class org.simtk.isimsu.IonConcentration

compareTo(IonSpecies) - Method in class org.simtk.isimsu.IonSpecies

compareTo(SaltCondition) - Method in class org.simtk.isimsu.SaltCondition

completeableRanges() - Method in class org.simtk.isimsu.IonSelectionDialog

ConstIonType - Interface in org.simtk.isimsu

copy(InputStream, OutputStream) - Static method in class org.simtk.isimsu.StreamCopy

copyDirectory(File, File) - Method in class org.simtk.file.CopyDirectoryChooser

CopyDirectoryChooser - Class in org.simtk.file

CopyDirectoryChooser(CopyDirectoryChooser.OverwritePolicy) - Constructor for class org.simtk.file.CopyDirectoryChooser

copyFile(File, File) - Method in class org.simtk.file.CopyDirectoryChooser

currentlyDisplayedIons() - Method in class org.simtk.isimsu.IonSelectionDialog

CustomTickSliderUI - Interface in org.simtk.isimsu

D

deleteIonSelectionPanel(IonSelectionPanel) - Method in class org.simtk.isimsu.IonSelectionDialog

DependentTask - Class in org.simtk.isimsu

DependentTask() - Constructor for class org.simtk.isimsu.DependentTask

disposeSplash() - Static method in class org.simtk.splashscreen.SplashWindow

E

equals(Object) - Method in class org.simtk.isimsu.IonSpecies

exception - Variable in class org.simtk.isimsu.ExternalProcessManager

ExternalProcessManager - Class in org.simtk.isimsu

ExternalProcessThread - Class in org.simtk.isimsu

ExternalProcessThread() - Constructor for class org.simtk.isimsu.ExternalProcessThread

F

FileNameFilter - Class in org.simtk.file

finishedButton - Variable in class org.simtk.isimsu.IonSelectionDialog

finishedButtonPressed() - Method in class org.simtk.isimsu.IonSelectionDialog

firstAvailableIon() - Method in class org.simtk.isimsu.IonSelectionDialog

G

getApbsParameters() - Method in class org.simtk.isimsu.ISIMWrapper

getAvailableRanges() - Method in class org.simtk.isimsu.IonSelectionDialog

getAvailableRanges(Set<IonSpecies>) - Method in class org.simtk.isimsu.IonSelectionDialog

getBasicService() - Method in class org.simtk.isimsu.MuffinWrapper

getCharge() - Method in interface org.simtk.isimsu.ConstIonType

getCharge() - Method in class org.simtk.isimsu.IonConcentration

getCharge() - Method in class org.simtk.isimsu.IonSpecies

getConcentration() - Method in class org.simtk.isimsu.IonConcentration

getDescription() - Method in class org.simtk.file.FileNameFilter

getExcessChemicalPotential() - Method in class org.simtk.isimsu.IonConcentration

getIonCount() - Method in class org.simtk.isimsu.SaltCondition

getIonId() - Method in interface org.simtk.isimsu.ConstIonType

getIonId() - Method in class org.simtk.isimsu.IonConcentration

getIonId() - Method in class org.simtk.isimsu.IonSpecies

getIonSpecies() - Method in class org.simtk.isimsu.IonConcentration

getIonSpecies() - Method in class org.simtk.isimsu.SaltConditionRange

getIonSurfaceModel() - Method in class org.simtk.isimsu.SaltConditionRange

getIsimParameters() - Method in class org.simtk.isimsu.ISIMWrapper

getMaximum() - Method in class org.simtk.isimsu.JarDefinedExecutableThread

getMinimum() - Method in class org.simtk.isimsu.JarDefinedExecutableThread

getName() - Method in class org.simtk.isimsu.SaltCondition

getOsType() - Static method in class org.simtk.isimsu.ExternalProcessManager

getParentRange() - Method in class org.simtk.isimsu.SaltCondition

getParentSaltCondition() - Method in class org.simtk.isimsu.IonConcentration

getPersistentService() - Method in class org.simtk.isimsu.MuffinWrapper

getProgress() - Method in class org.simtk.isimsu.JarDefinedExecutableThread

GetPymolLocation - Class in org.simtk.isimsu

getRadius() - Method in interface org.simtk.isimsu.ConstIonType

getRadius() - Method in class org.simtk.isimsu.IonConcentration

getRadius() - Method in class org.simtk.isimsu.IonSpecies

getSaltCondition() - Method in class org.simtk.isimsu.SaltSelectionEvent

getSolventPermittivity() - Method in class org.simtk.isimsu.SaltCondition

getSolventPermittivity() - Method in class org.simtk.isimsu.SaltConditionRange

getStatus() - Method in class org.simtk.isimsu.DependentTask

getStatusDescription() - Method in class org.simtk.isimsu.DependentTask

getSurfaceWellDepth() - Method in interface org.simtk.isimsu.ConstIonType

getSurfaceWellDepth() - Method in class org.simtk.isimsu.IonConcentration

getSurfaceWellDepth() - Method in class org.simtk.isimsu.IonSpecies

getTemperature() - Method in class org.simtk.isimsu.SaltCondition

getTemperature() - Method in class org.simtk.isimsu.SaltConditionRange

H

hashCode() - Method in class org.simtk.isimsu.IonSpecies

helpButton - Variable in class org.simtk.isimsu.IonSelectionDialog

helpButtonPressed() - Method in class org.simtk.isimsu.IonSelectionDialog

I

interfaceName - Variable in class org.simtk.isimsu.ISIMWrapper

invokeMain(String, String[]) - Static method in class org.simtk.splashscreen.SplashWindow

Uses reflection to avoid loading many classes before this routine is actually called, allowing rapid splash screen display.

IonConcentration - Class in org.simtk.isimsu

IonConcentration(IonSpecies, SaltCondition) - Constructor for class org.simtk.isimsu.IonConcentration

ionConditionSet - Variable in class org.simtk.isimsu.IonSelectionDialog

IonCountDialog - Class in org.simtk.isimsu

ionDialog - Variable in class org.simtk.isimsu.ISIMWrapper

ionPanelList - Variable in class org.simtk.isimsu.IonSelectionDialog

ionRangeMap - Variable in class org.simtk.isimsu.IonSelectionDialog

IonSelectionDialog - Class in org.simtk.isimsu

ionsPanel - Variable in class org.simtk.isimsu.IonSelectionDialog

IonSpecies - Class in org.simtk.isimsu

IonSpecies() - Constructor for class org.simtk.isimsu.IonSpecies

isFailed() - Method in class org.simtk.isimsu.JarDefinedExecutableThread

isimIcon - Variable in class org.simtk.isimsu.ISIMWrapper

isimParameterDialog - Variable in class org.simtk.isimsu.ISIMWrapper

ISIMSplasher - Class in org.simtk.splashscreen

ISIMSplasher() - Constructor for class org.simtk.splashscreen.ISIMSplasher

ISIMStepParameters - Class in org.simtk.isimsu

ISIMTask - Class in org.simtk.isimsu

ISIMTask() - Constructor for class org.simtk.isimsu.ISIMTask

ISIMWrapper - Class in org.simtk.isimsu

isRunning() - Method in class org.simtk.isimsu.DependentTask

isSuccessful() - Method in class org.simtk.isimsu.JarDefinedExecutableThread

isTestRun() - Method in class org.simtk.isimsu.ISIMWrapper

Iterable - Interface in org.simtk.isimsu

Because there is no standard Iterable interface before Java 1.5

iterator() - Method in interface org.simtk.isimsu.Iterable

J

JarDefinedExecutableThread - Class in org.simtk.isimsu

JarDefinedExecutableThread() - Constructor for class org.simtk.isimsu.JarDefinedExecutableThread

L

loadAllIonCounts() - Method in class org.simtk.isimsu.IonCountDialog

loadIonConditions(URL) - Static method in class org.simtk.isimsu.SaltRangeSet

loadMoleculeCharge() - Method in class org.simtk.isimsu.IonCountDialog

LogDialog - Class in org.simtk.isimsu

M

main(String[]) - Static method in class org.simtk.file.CopyDirectoryChooser

main(String[]) - Static method in class org.simtk.file.UncompressInputStream

main(String[]) - Static method in class org.simtk.isimsu.ISIMWrapper

main(String[]) - Static method in class org.simtk.isimsu.TestExe

main(String[]) - Static method in class org.simtk.splashscreen.ISIMSplasher

moleculeChargeLabel - Variable in class org.simtk.isimsu.IonCountDialog

mouseDragged(MouseEvent) - Method in class org.simtk.isimsu.IonCountDialog

mouseMoved(MouseEvent) - Method in class org.simtk.isimsu.IonCountDialog

MuffinWrapper - Class in org.simtk.isimsu

N

netCharge() - Method in class org.simtk.isimsu.IonSelectionDialog

netChargeLabel - Variable in class org.simtk.isimsu.IonSelectionDialog

NEVER_OVERWRITE - Static variable in class org.simtk.file.CopyDirectoryChooser

O

org.simtk.file - package org.simtk.file

org.simtk.isimsu - package org.simtk.isimsu

org.simtk.splashscreen - package org.simtk.splashscreen

outputMessage(String) - Method in class org.simtk.isimsu.ExternalProcessManager

P

paint(Graphics) - Method in class org.simtk.splashscreen.SplashWindow

PDB - Class in org.simtk.isimsu

PDB() - Constructor for class org.simtk.isimsu.PDB

PDBToPQRThread - Class in org.simtk.isimsu

programName - Variable in class org.simtk.isimsu.IonSelectionDialog

programName - Variable in class org.simtk.isimsu.ISIMWrapper

R

rangeIonMap - Variable in class org.simtk.isimsu.IonSelectionDialog

read() - Method in class org.simtk.file.UncompressInputStream

read(byte[], int, int) - Method in class org.simtk.file.UncompressInputStream

removeSaltSelectionListener(SaltSelectionListener) - Method in class org.simtk.isimsu.IonSelectionDialog

removeSaltSelectionListener(SaltSelectionListener) - Method in interface org.simtk.isimsu.SaltSelectionObservable

removeSaltSelectionListener(SaltSelectionListener) - Method in class org.simtk.isimsu.SaltSelectionObservableClass

run() - Method in class org.simtk.isimsu.ExternalProcessManager

run() - Method in class org.simtk.isimsu.PDBToPQRThread

run() - Method in class org.simtk.isimsu.RunAPBSThread

run() - Method in class org.simtk.isimsu.RunISIMThread

run() - Method in class org.simtk.isimsu.RunPsizeThread

run() - Method in class org.simtk.isimsu.RunPymolThread

run() - Method in class org.simtk.isimsu.SimulateIonsThread

RunAPBSThread - Class in org.simtk.isimsu

RunISIMThread - Class in org.simtk.isimsu

RunPsizeThread - Class in org.simtk.isimsu

RunPsizeThread(ISIMStepParameters, APBSParameters, File, ISIMWrapper) - Constructor for class org.simtk.isimsu.RunPsizeThread

RunPymolThread - Class in org.simtk.isimsu

S

SaltCondition - Class in org.simtk.isimsu

SaltCondition(SaltConditionRange) - Constructor for class org.simtk.isimsu.SaltCondition

saltCondition - Variable in class org.simtk.isimsu.SaltSelectionEvent

SaltConditionRange - Class in org.simtk.isimsu

SaltConditionRange() - Constructor for class org.simtk.isimsu.SaltConditionRange

SaltRangeSet - Class in org.simtk.isimsu

SaltRangeSet() - Constructor for class org.simtk.isimsu.SaltRangeSet

saltSelected(SaltSelectionEvent) - Method in class org.simtk.isimsu.ISIMWrapper

saltSelected(SaltSelectionEvent) - Method in interface org.simtk.isimsu.SaltSelectionListener

SaltSelectionEvent - Class in org.simtk.isimsu

SaltSelectionEvent(Object, SaltCondition) - Constructor for class org.simtk.isimsu.SaltSelectionEvent

SaltSelectionListener - Interface in org.simtk.isimsu

saltSelectionObservable - Variable in class org.simtk.isimsu.IonSelectionDialog

SaltSelectionObservable - Interface in org.simtk.isimsu

SaltSelectionObservableClass - Class in org.simtk.isimsu

SaltSelectionObservableClass() - Constructor for class org.simtk.isimsu.SaltSelectionObservableClass

saveWork() - Method in class org.simtk.isimsu.ISIMWrapper

selectSalt(SaltSelectionObservable, SaltCondition) - Method in class org.simtk.isimsu.IonSelectionDialog

selectSalt(SaltSelectionObservable, SaltCondition) - Method in interface org.simtk.isimsu.SaltSelectionObservable

selectSalt(SaltSelectionObservable, SaltCondition) - Method in class org.simtk.isimsu.SaltSelectionObservableClass

serialVersionUID - Static variable in class org.simtk.isimsu.LogDialog

setCharge(float) - Method in class org.simtk.isimsu.IonSpecies

setConcentration(float) - Method in class org.simtk.isimsu.IonConcentration

setExcessChemicalPotential(float) - Method in class org.simtk.isimsu.IonConcentration

setFailed() - Method in class org.simtk.isimsu.JarDefinedExecutableThread

setFailed(String) - Method in class org.simtk.isimsu.PDBToPQRThread

setFailed(String) - Method in class org.simtk.isimsu.RunPsizeThread

setIonId(String) - Method in class org.simtk.isimsu.IonSpecies

setIonSpecies(Set<IonSpecies>) - Method in class org.simtk.isimsu.SaltConditionRange

setIonSurfaceModel(IonSpecies.IonSurfaceModel) - Method in class org.simtk.isimsu.SaltConditionRange

setIsTestRun(int, String, String) - Method in class org.simtk.isimsu.ISIMWrapper

setLogDialog(LogDialog) - Method in class org.simtk.isimsu.ExternalProcessManager

setMajorTickPositions(Set<Integer>) - Method in interface org.simtk.isimsu.CustomTickSliderUI

setMinorTickPositions(Set<Integer>) - Method in interface org.simtk.isimsu.CustomTickSliderUI

setName(String) - Method in class org.simtk.isimsu.SaltCondition

setPqrFile(File) - Method in class org.simtk.isimsu.ISIMWrapper

setPqrFile(File) - Method in class org.simtk.isimsu.PDBToPQRThread

setPrintToOutFile(boolean) - Method in class org.simtk.isimsu.LogDialog

setRadius(float) - Method in class org.simtk.isimsu.IonSpecies

setSolventPermittivity(float) - Method in class org.simtk.isimsu.SaltConditionRange

setStatus(TaskStatus, String) - Method in class org.simtk.isimsu.DependentTask

setStatusForce(TaskStatus, String) - Method in class org.simtk.isimsu.DependentTask

setSuccessful() - Method in class org.simtk.isimsu.JarDefinedExecutableThread

setSurfaceWellDepth(float) - Method in class org.simtk.isimsu.IonSpecies

setTemperature(float) - Method in class org.simtk.isimsu.SaltConditionRange

setWaitForCompletion(int) - Method in class org.simtk.isimsu.ExternalProcessManager

showAndCopy(Frame, File) - Method in class org.simtk.file.CopyDirectoryChooser

Routine used by client program to manage the copy

showLicenseDialog() - Method in class org.simtk.isimsu.ISIMWrapper

showServices() - Method in class org.simtk.isimsu.MuffinWrapper

SimulateIonsThread - Class in org.simtk.isimsu

SimulationDetailsDialog - Class in org.simtk.isimsu

skip(long) - Method in class org.simtk.file.UncompressInputStream

splash(URL) - Static method in class org.simtk.splashscreen.SplashWindow

splash(Image) - Static method in class org.simtk.splashscreen.SplashWindow

SplashWindow - Class in org.simtk.splashscreen

StreamCopy - Class in org.simtk.isimsu

StreamCopy() - Constructor for class org.simtk.isimsu.StreamCopy

T

tableColumnToolTips - Variable in class org.simtk.isimsu.IonCountDialog

TestExe - Class in org.simtk.isimsu

TestExe() - Constructor for class org.simtk.isimsu.TestExe

toInputText() - Method in class org.simtk.isimsu.SaltCondition

Display set of ions in format suitable for ISIM input file IONS section e.g.

toString() - Method in class org.simtk.isimsu.SaltCondition

totalChargeLabel - Variable in class org.simtk.isimsu.IonCountDialog

U

UncompressInputStream - Class in org.simtk.file

This class decompresses an input stream containing data compressed with the unix "compress" utility (LZC, a LZW variant).

UncompressInputStream(InputStream) - Constructor for class org.simtk.file.UncompressInputStream

update(Observable, Object) - Method in class org.simtk.isimsu.DependentTask

update(Graphics) - Method in class org.simtk.splashscreen.SplashWindow

updateButtons() - Method in class org.simtk.isimsu.IonSelectionDialog

updateConcentrationRanges(Set<SaltConditionRange>) - Method in class org.simtk.isimsu.IonSelectionDialog

updateIonChoices() - Method in class org.simtk.isimsu.IonSelectionDialog

Ensure that each ion panel has an appropriate choice of other ions to change to.

updateNetCharge() - Method in class org.simtk.isimsu.IonSelectionDialog

W

workIsSaved - Variable in class org.simtk.isimsu.ISIMWrapper

Y

yourMoleculeLabel - Variable in class org.simtk.isimsu.IonCountDialog

A B C D E F G H I J L M N O P R S T U W Y