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

I

identifyBasePairs() - Method in class org.simtk.molecularstructure.nucleicacid.NucleicAcid

identifyHairpins() - Method in class org.simtk.molecularstructure.nucleicacid.NucleicAcid

identity(int, int) - Static method in class Jama.Matrix

Generate identity matrix

identity - Static variable in class org.simtk.geometry3d.Matrix3DClass

importSecondaryStructures() - Method in class org.simtk.rnaml.RnamlDocument

inactivate() - Method in class org.simtk.pdb.MoleculeAcquisitionMethodDialog

increment() - Method in class org.simtk.gui.Throbber

Change image to the next one in the animation sequence

indexChemicals - Variable in class org.simtk.moleculargraphics.cartoon.ToonColors

INDIAN_RED - Static variable in class org.simtk.util.ColorName

INDIAN_RED1 - Static variable in class org.simtk.util.ColorName

INDIAN_RED2 - Static variable in class org.simtk.util.ColorName

INDIAN_RED3 - Static variable in class org.simtk.util.ColorName

INDIAN_RED4 - Static variable in class org.simtk.util.ColorName

INDIGO - Static variable in class org.simtk.util.ColorName

InertialRotationThread - Class in org.simtk.moleculargraphics

InertialRotationThread(Tornado) - Constructor for class org.simtk.moleculargraphics.InertialRotationThread

initialBackgroundColor - Variable in class org.simtk.moleculargraphics.Tornado

initialize(Vector2D) - Method in class org.simtk.geometry3d.Vector2DClass

initialize(Vector3D) - Method in class org.simtk.geometry3d.Vector3DClass

initialize() - Method in class org.simtk.moleculargraphics.InertialRotationThread

initialLoadStructurePanel - Variable in class org.simtk.moleculargraphics.Tornado

initialTableSize - Variable in class org.simtk.moleculargraphics.cartoon.ToonColors

Inositate - Class in org.simtk.molecularstructure.nucleicacid

Inositate() - Constructor for class org.simtk.molecularstructure.nucleicacid.Inositate

InsufficientAtomsException - Exception in org.simtk.molecularstructure

InsufficientAtomsException() - Constructor for exception org.simtk.molecularstructure.InsufficientAtomsException

InsufficientAtomsException(String) - Constructor for exception org.simtk.molecularstructure.InsufficientAtomsException

InsufficientAtomsException(String, Throwable) - Constructor for exception org.simtk.molecularstructure.InsufficientAtomsException

InsufficientAtomsException(Throwable) - Constructor for exception org.simtk.molecularstructure.InsufficientAtomsException

InsufficientPointsException - Exception in org.simtk.geometry3d

InsufficientPointsException() - Constructor for exception org.simtk.geometry3d.InsufficientPointsException

InsufficientPointsException(String) - Constructor for exception org.simtk.geometry3d.InsufficientPointsException

InsufficientPointsException(String, Throwable) - Constructor for exception org.simtk.geometry3d.InsufficientPointsException

InsufficientPointsException(Throwable) - Constructor for exception org.simtk.geometry3d.InsufficientPointsException

InteractionMode - Variable in class org.simtk.moleculargraphics.vtkSwingPanel

InteractionModeRotate() - Method in class org.simtk.moleculargraphics.vtkSwingPanel

InteractionModeTranslate() - Method in class org.simtk.moleculargraphics.vtkSwingPanel

InteractionModeZoom() - Method in class org.simtk.moleculargraphics.vtkSwingPanel

intValue() - Method in class org.simtk.geometry3d.Angle

inverse() - Method in class Jama.Matrix

Matrix inverse or pseudoinverse

invisibleColorScheme - Variable in class org.simtk.moleculargraphics.cartoon.ActorCartoonClass

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.

IODINE - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass

IRON - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass

isAlive() - Method in interface org.simtk.gui.MonitoredProcess

isAlphaHelix() - Method in interface org.simtk.molecularstructure.Residue

isAlphaHelix() - Method in class org.simtk.molecularstructure.ResidueClass

isBetween(Residue, Residue) - Method in class org.simtk.molecularstructure.nucleicacid.BasePair

isCancelled() - Method in interface org.simtk.gui.ProgressDialog

isCancelled() - Method in class org.simtk.gui.ProgressDialogClass

isCancelled() - Method in class org.simtk.gui.ProgressPanel

isDeemedNucleotide(Residue, String) - Method in class org.simtk.rnaml.RnamlDocument

isDNA(String) - Static method in class org.simtk.molecularstructure.ResidueClass

isEmpty() - Method in class org.simtk.util.DoubleRing

isFailed() - Method in interface org.simtk.gui.MonitoredProcess

isFullRank() - Method in class Jama.QRDecomposition

Is the matrix full rank?

isHelix() - Method in interface org.simtk.molecularstructure.Residue

isHelix() - Method in class org.simtk.molecularstructure.ResidueClass

isKnownHetatm(String) - Static method in class org.simtk.molecularstructure.ResidueClass

isNonsingular() - Method in class Jama.LUDecomposition

Is the matrix nonsingular?

isNucleicAcid(String) - Static method in class org.simtk.molecularstructure.ResidueClass

Isoleucine - Class in org.simtk.molecularstructure.protein

Isoleucine() - Constructor for class org.simtk.molecularstructure.protein.Isoleucine

isPopulated() - Method in interface org.simtk.moleculargraphics.cartoon.ActorCartoon

isPopulated - Variable in class org.simtk.moleculargraphics.cartoon.ActorCartoonClass

isPopulated() - Method in class org.simtk.moleculargraphics.cartoon.ActorCartoonClass

isProtein(String) - Static method in class org.simtk.molecularstructure.ResidueClass

isRNA(String) - Static method in class org.simtk.molecularstructure.ResidueClass

isRnaviewNA(Biopolymer) - Method in class org.simtk.rnaml.RnamlDocument

isSolvent() - Method in interface org.simtk.molecularstructure.Molecule

isSolvent() - Method in class org.simtk.molecularstructure.MoleculeClass

isSolvent(String) - Static method in class org.simtk.molecularstructure.ResidueClass

isSPD() - Method in class Jama.CholeskyDecomposition

Is the matrix symmetric and positive definite?

isStrand() - Method in interface org.simtk.molecularstructure.Residue

isStrand() - Method in class org.simtk.molecularstructure.ResidueClass

isSuccessful() - Method in interface org.simtk.gui.MonitoredProcess

isWindowSet() - Method in class org.simtk.moleculargraphics.vtkSwingPanel

iterator() - Method in class org.simtk.geometry3d.MathVectorClass

iterator() - Method in class org.simtk.molecularstructure.nucleicacid.BasePair

iterator() - Method in class org.simtk.molecularstructure.SequenceAlignment

IVORY - Static variable in class org.simtk.util.ColorName

IVORY1 - Static variable in class org.simtk.util.ColorName

IVORY2 - Static variable in class org.simtk.util.ColorName

IVORY3 - Static variable in class org.simtk.util.ColorName

IVORY4 - Static variable in class org.simtk.util.ColorName