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

H

Hairpin - Class in org.simtk.molecularstructure.nucleicacid

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

handleMoleculeUrl(URL) - Method in class org.simtk.pdb.MoleculeAcquisitionMethodDialog

HardCopy(String, int) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

hasChanged() - Method in class org.simtk.gui.ProgressManager

hasChanged() - Method in interface org.simtk.mvc.ObservableInterface

Hash3D<V> - Class in org.simtk.geometry3d

Container class to speed up finding objects that are near one another in 3D Cartesian space.

Hash3D(double) - Constructor for class org.simtk.geometry3d.Hash3D

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

hashCode() - Method in class org.simtk.geometry3d.Vector2DClass

hashCode() - Method in class org.simtk.geometry3d.Vector3DClass

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

hasVisibleColor() - Method in class org.simtk.moleculargraphics.cartoon.ToonColors

hBondNormal(Residue, int) - Static method in class org.simtk.moleculargraphics.cartoon.ProteinRibbonSegment

headLength - Variable in class org.simtk.moleculargraphics.cartoon.vtkArrowWidthFilter

headWidth - Variable in class org.simtk.moleculargraphics.cartoon.vtkArrowWidthFilter

height - Variable in class org.simtk.moleculargraphics.cartoon.BasePairOval

Helix - Class in org.simtk.molecularstructure.protein

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

helixString() - Method in class org.simtk.molecularstructure.nucleicacid.Duplex

helixWidth - Variable in class org.simtk.moleculargraphics.cartoon.RichardsonProteinRibbon

Hidable - Interface in org.simtk.moleculargraphics.cartoon

HidableActorClass - Class in org.simtk.moleculargraphics.cartoon

HidableActorClass(vtkActor) - Constructor for class org.simtk.moleculargraphics.cartoon.HidableActorClass

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

hide() - Method in interface org.simtk.moleculargraphics.cartoon.Hidable

hide() - Method in class org.simtk.moleculargraphics.cartoon.HidableActorClass

hide() - Method in class org.simtk.moleculargraphics.cartoon.ProteinRibbon

hide(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.ProteinRibbon

hideDialog() - Method in class org.simtk.gui.ProgressManager

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

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

HighlightColorScheme - Class in org.simtk.moleculargraphics.cartoon

Color scheme that blends a particular highlight color with that of another color scheme.

HighlightColorScheme(Color, ColorScheme) - Constructor for class org.simtk.moleculargraphics.cartoon.HighlightColorScheme

highlightedResidues - Variable in class org.simtk.moleculargraphics.SequenceCartoonCanvas

highlightFactor - Variable in class org.simtk.moleculargraphics.cartoon.GlyphCartoon

highlightGap - Variable in class org.simtk.moleculargraphics.cartoon.NewBackboneCurveActor

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

highlightPosition(Graphics, int, Color) - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

highlightResidue(Residue, Color) - Method in class org.simtk.moleculargraphics.cartoon.ActorCartoonClass

highlightResidue(Residue, Color) - Method in class org.simtk.moleculargraphics.cartoon.AtomSphereActor

highlightResidue(Residue, Color) - Method in class org.simtk.moleculargraphics.cartoon.BondStickCartoon

highlightResidue(Residue, Color) - Method in class org.simtk.moleculargraphics.cartoon.WireFrameActor

highlightResidue(Residue, Color) - Method in interface org.simtk.moleculargraphics.ResidueHighlightListener

highlightResidue(Residue, Color) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

highlightResidue(Residue, Color) - Method in class org.simtk.moleculargraphics.SequencePane

highlightResidue(Residue, Color) - Method in class org.simtk.moleculargraphics.Tornado

highlightResidue(Residue, Color) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

highlightResidue(Residue, Color) - Method in class org.simtk.moleculargraphics.TornadoSequenceCanvas

highlightResidue(Residue, Color) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

highlightResidueByAtomScalars(Residue, Color) - Method in class org.simtk.moleculargraphics.cartoon.ActorCartoonClass

highlightResidueByResidueScalars(Residue, Color) - Method in class org.simtk.moleculargraphics.cartoon.ActorCartoonClass

highlightResidues - Variable in class org.simtk.moleculargraphics.Tornado3DCanvas

highlightResidues - Variable in class org.simtk.moleculargraphics.TornadoSequenceCanvas

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

Histidine - Class in org.simtk.molecularstructure.protein

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

HomogeneousTransform - Interface in org.simtk.geometry3d

HomogeneousTransformClass - Class in org.simtk.geometry3d

HomogeneousTransformClass() - Constructor for class org.simtk.geometry3d.HomogeneousTransformClass

HomogeneousTransformClass(MathMatrix) - Constructor for class org.simtk.geometry3d.HomogeneousTransformClass

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

HONEYDEW1 - Static variable in class org.simtk.util.ColorName

HONEYDEW2 - Static variable in class org.simtk.util.ColorName

HONEYDEW3 - Static variable in class org.simtk.util.ColorName

HONEYDEW4 - Static variable in class org.simtk.util.ColorName

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

HOT_PINK1 - Static variable in class org.simtk.util.ColorName

HOT_PINK2 - Static variable in class org.simtk.util.ColorName

HOT_PINK3 - Static variable in class org.simtk.util.ColorName

HOT_PINK4 - Static variable in class org.simtk.util.ColorName

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

hypot(double, double) - Static method in class Jama.util.Maths

sqrt(a^2 + b^2) without under/overflow.