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

A

AboutDialog - Class in org.openscience.jmol.app

AboutDialog(JFrame) - Constructor for class org.openscience.jmol.app.AboutDialog

action(Event, Object) - Method in class org.jmol.applet.JmolAppletControl

actionPerformed(ActionEvent) - Method in class msg.ProteinElement

Performs the action of the action command.

actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.AtomSetChooser

actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.PreferencesDialog

actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.ScriptWindow

activate() - Method in class org.openscience.jmol.app.MeasurementTable

activateHighlight() - Method in class msg.ProteinElement

Highlights all components with the same id.

addBond(SmilesBond) - Method in class org.jmol.smiles.SmilesAtom

addComponent(String, String) - Method in class membranModel.MembranModel

This function adds a protein to a subcomponent of the mebrane model

addComponents(Vector) - Method in class membranModel.MembranModel

This function adds proteins to the membrane model

addElement(ProteinElement) - Method in class msg.ProteinMatrix

Adds a ProteinElement.

addPropertyChangeListener(PropertyChangeListener) - Method in class org.openscience.jmol.app.FileDropper

addProtein(Protein) - Method in class membranModel.MembranModel

This function adds one protein to the membrane model

addProteinPositions(int[]) - Method in class protein.Protein

addSelectionListener(JmolSelectionListener) - Method in class org.jmol.api.JmolViewer

addSelectionListener(JmolSelectionListener) - Method in class org.jmol.viewer.Viewer

addTuple(int, Tuple) - Method in class org.jmol.bspt.Bspf

addTuple(Tuple) - Method in class org.jmol.bspt.Bspt

Iterate through all of your data points, calling addTuple

allocateBitmap(int) - Static method in class org.jmol.util.Bmp

allocateSetAllBits(int) - Static method in class org.jmol.util.Bmp

allocateSimpleViewer(Component, JmolAdapter) - Static method in class org.jmol.api.JmolSimpleViewer

allocateSphereIterator() - Method in class org.jmol.bspt.Bspt

allocateViewer(Component, JmolAdapter) - Static method in class org.jmol.api.JmolViewer

allocateViewer(Component, JmolAdapter) - Static method in class org.jmol.viewer.Viewer

allocateViewer(Component, JmolAdapter, boolean, JPanel, Protein) - Static method in class org.jmol.viewer.Viewer

allocFont3D(short, int, int, int) - Static method in class org.jmol.g3d.Font3D

allocMinimalCopy(int[]) - Static method in class org.jmol.util.Bmp

alternateElementNames - Static variable in class org.jmol.viewer.JmolConstants

alternateElementNumbers - Static variable in class org.jmol.viewer.JmolConstants

and(int[], int[]) - Static method in class org.jmol.util.Bmp

and(int[], int[], int[]) - Static method in class org.jmol.util.Bmp

antecedent(double) - Method in class org.jmol.jcamp.ZoneVisu

applets() - Method in class org.jmol.applet.JmolAppletRegistry

AppletWrapper - Class in org.jmol.appletwrapper

AppletWrapper(String, String, String, int, String[]) - Constructor for class org.jmol.appletwrapper.AppletWrapper

applyBlueOrGreenAnaglyph(boolean) - Method in class org.jmol.g3d.Graphics3D

applyCyanAnaglyph() - Method in class org.jmol.g3d.Graphics3D

AQUA - Static variable in class org.jmol.g3d.Graphics3D

argbsAmino - Static variable in class org.jmol.viewer.JmolConstants

argbsChainAtom - Static variable in class org.jmol.viewer.JmolConstants

some pastel colors C0D0FF - pastel blue B0FFB0 - pastel green B0FFFF - pastel cyan FFC0C8 - pink FFC0FF - pastel magenta FFFF80 - pastel yellow FFDEAD - navajowhite FFD070 - pastel gold FF9898 - light coral B4E444 - light yellow-green C0C000 - light olive FF8060 - light tomato 00FF7F - springgreen cpk on; select atomno>100; label %i; color chain; select selected & hetero; cpk off

argbsChainHetero - Static variable in class org.jmol.viewer.JmolConstants

argbsCpk - Static variable in class org.jmol.viewer.JmolConstants

Default table of CPK atom colors.

argbsCpkRasmol - Static variable in class org.jmol.viewer.JmolConstants

argbsFormalCharge - Static variable in class org.jmol.viewer.JmolConstants

argbShapelyBackbone - Static variable in class org.jmol.viewer.JmolConstants

argbShapelyDefault - Static variable in class org.jmol.viewer.JmolConstants

argbShapelySpecial - Static variable in class org.jmol.viewer.JmolConstants

argbsHbondType - Static variable in class org.jmol.viewer.JmolConstants

argbsIsosurfaceNegative - Static variable in class org.jmol.viewer.JmolConstants

argbsIsosurfacePositive - Static variable in class org.jmol.viewer.JmolConstants

argbsRoygbScale - Static variable in class org.jmol.viewer.JmolConstants

argbsRwbScale - Static variable in class org.jmol.viewer.JmolConstants

argbsShapely - Static variable in class org.jmol.viewer.JmolConstants

argbsStructure - Static variable in class org.jmol.viewer.JmolConstants

In DRuMS, RasMol, and Chime, quoting from http://www.umass.edu/microbio/rasmol/rascolor.htm The RasMol structure color scheme colors the molecule by protein secondary structure.

ATOMID_ALPHA_CARBON - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_ALPHA_ONLY_MASK - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_AMINO_NITROGEN - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_BACKBONE_MAX - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_C2 - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_C3_PRIME - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_C4 - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_C5 - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_C5_PRIME - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_C5M - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_C6 - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_C8 - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_CARBONYL_CARBON - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_CARBONYL_OXYGEN - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_DISTINGUISHING_ATOM_MAX - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_H3T_TERMINUS - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_H5T_TERMINUS - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_MAX - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_N1 - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_N2 - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_N3 - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_N4 - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_N6 - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_N7 - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_N9 - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_NUCLEIC_MASK - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_NUCLEIC_PHOSPHORUS - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_NUCLEIC_WING - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_O1 - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_O2 - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_O3_PRIME - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_O4 - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_O5_PRIME - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_O5T_TERMINUS - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_O6 - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_PHOSPHORUS_ONLY_MASK - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_PROTEIN_MASK - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_RNA_O2PRIME - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_S4 - Static variable in class org.jmol.viewer.JmolConstants

ATOMID_TERMINATING_OXT - Static variable in class org.jmol.viewer.JmolConstants

AtomSetChooser - Class in org.openscience.jmol.app

A JFrame that allows for choosing an Atomset to view.

AtomSetChooser(JmolViewer, JFrame) - Constructor for class org.openscience.jmol.app.AtomSetChooser

atomSetChooser - Variable in class org.openscience.jmol.app.Jmol

AXES_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JmolConstants