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 _

G

GB - Static variable in class org.jmol.g3d.Xyzd

GB4 - Static variable in class org.jmol.g3d.Xyzd

GBZO - Static variable in class org.jmol.g3d.Xyzd

GBZO4 - Static variable in class org.jmol.g3d.Xyzd

generateCoordinates(int, int) - Method in class msg.ProteinMatrix

Generate the coordinates for the ProteinElement on the lipid matrix.

generateLoaded() - Method in class msg.ProteinMatrix

Generates the ProteinElements loaded with an XML file.

generateMatrix(int, int) - Method in class msg.ProteinMatrix

Generate the matrix of the lipids and executes the calculateRatio() function.

generateNew() - Method in class msg.ProteinMatrix

Generates new ProteinElement objects and add them to this panel.

generateToolTip() - Method in class msg.ProteinElement

Generates the tooltip for this component.

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

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

get(int) - Method in class org.jmol.util.Int2IntHash

get(int) - Method in class org.jmol.util.Int2ObjHash

get(int, int) - Method in class org.jmol.util.IntInt2ObjHash

get2SidedNormix(Vector3f) - Method in class org.jmol.g3d.Graphics3D

get_Line_quantity() - Method in class protein.Protein

get_xz_percentage() - Method in class protein.Protein

getActions() - Method in class org.openscience.jmol.app.DisplayPanel

getActions() - Method in class org.openscience.jmol.app.Jmol

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

getAlles() - Method in class msg.ProteinElement

getAlles() - Method in class msg.ProteinMatrix

getAllProteins() - Method in class membranModel.MembranModel

getAllProteins(String) - Method in interface pdbParser.IPDBreader

getAllProteins(String) - Method in class pdbParser.PDBreader

This function creates for each PDBfile in the given directory a Protein object.

getAlternateLocationID() - Method in class org.jmol.api.JmolAdapter.AtomIterator

getAnimationFps() - Method in class org.jmol.api.JmolViewer

getAnimationFps() - Method in class org.jmol.viewer.Viewer

getAppletInfo() - Method in class org.jmol.applet.Jmol

getAppletInfo() - Method in class org.jmol.applet.JmolAppletControl

getAppletInfo() - Method in class org.jmol.appletwrapper.AppletWrapper

getAppletInfo() - Method in interface org.jmol.appletwrapper.WrappedApplet

getArgbFromString(String) - Static method in class org.jmol.g3d.Graphics3D

getAtom(int) - Method in class org.jmol.smiles.SmilesMolecule

getAtom1() - Method in class org.jmol.smiles.SmilesBond

getAtom2() - Method in class org.jmol.smiles.SmilesBond

getAtom_count() - Method in class protein.Protein

returns the amount of the atom_coordinates

getAtomColor(int) - Method in class org.jmol.api.JmolViewer

getAtomColor(int) - Method in class org.jmol.viewer.Viewer

getAtomCount() - Method in class org.jmol.api.JmolViewer

getAtomCount() - Method in class org.jmol.viewer.Viewer

getAtomicMass() - Method in class org.jmol.smiles.SmilesAtom

getAtomIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter

getAtomIterator(Object) - Method in class org.jmol.api.JmolAdapter

Get an AtomIterator for retrieval of all atoms in the file.

getAtomIterator(Object) - Method in class org.jmol.viewer.FrameExportJmolAdapter

getAtomModelIndex(int) - Method in class org.jmol.api.JmolViewer

getAtomModelIndex(int) - Method in class org.jmol.viewer.Viewer

getAtomName() - Method in class org.jmol.api.JmolAdapter.AtomIterator

getAtomName(int) - Method in class org.jmol.api.JmolViewer

getAtomName(int) - Method in class org.jmol.viewer.Viewer

getAtomNumber(int) - Method in class org.jmol.api.JmolViewer

getAtomNumber(int) - Method in class org.jmol.viewer.Viewer

getAtomPoint3f(int) - Method in class org.jmol.api.JmolViewer

getAtomPoint3f(int) - Method in class org.jmol.viewer.Viewer

getAtomRadius(int) - Method in class org.jmol.api.JmolViewer

getAtomRadius(int) - Method in class org.jmol.viewer.Viewer

getAtomsCount() - Method in class org.jmol.smiles.SmilesMolecule

getAtomSerial() - Method in class org.jmol.api.JmolAdapter.AtomIterator

getAtomSetCollectionName(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter

getAtomSetCollectionName(Object) - Method in class org.jmol.api.JmolAdapter

Get the name of the atom set collection, if known.

getAtomSetCollectionName(Object) - Method in class org.jmol.viewer.FrameExportJmolAdapter

getAtomSetCollectionProperties(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter

getAtomSetCollectionProperties(Object) - Method in class org.jmol.api.JmolAdapter

Get the properties for this atomSetCollection.

getAtomSetCount(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter

getAtomSetCount(Object) - Method in class org.jmol.api.JmolAdapter

Get number of atomSets in the file.

getAtomSetIndex() - Method in class org.jmol.api.JmolAdapter.AtomIterator

getAtomSetName(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter

getAtomSetName(Object, int) - Method in class org.jmol.api.JmolAdapter

Get the name of an atomSet.

getAtomSetNumber(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter

getAtomSetNumber(Object, int) - Method in class org.jmol.api.JmolAdapter

Get the number identifying each atomSet.

getAtomSetProperties(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter

getAtomSetProperties(Object, int) - Method in class org.jmol.api.JmolAdapter

Get the properties for an atomSet.

getAtomUniqueID1() - Method in class org.jmol.api.JmolAdapter.BondIterator

getAtomUniqueID2() - Method in class org.jmol.api.JmolAdapter.BondIterator

getAutoBond() - Method in class org.jmol.api.JmolViewer

getAutoBond() - Method in class org.jmol.viewer.Viewer

getAwtComponent() - Method in class org.jmol.api.JmolViewer

getAwtComponent() - Method in class org.jmol.viewer.Viewer

getAxesOrientationRasmol() - Method in class org.jmol.api.JmolViewer

getAxesOrientationRasmol() - Method in class org.jmol.viewer.Viewer

getAxisColor() - Method in class org.jmol.jcamp.GraphCharacteristics

getAxisTextColor() - Method in class org.jmol.jcamp.GraphCharacteristics

getBackground_color() - Method in class membranModel.MembranModel

getBar() - Method in class msg.MatrixProgressBar

getBfactor() - Method in class org.jmol.api.JmolAdapter.AtomIterator

getBiLayerSpace() - Method in class membranModel.MembranModel

getBiLayerType() - Method in class membranModel.MembranModel

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

getBond(int) - Method in class org.jmol.smiles.SmilesAtom

getBond(int) - Method in class org.jmol.smiles.SmilesMolecule

getBondColor1(int) - Method in class org.jmol.api.JmolViewer

getBondColor1(int) - Method in class org.jmol.viewer.Viewer

getBondColor2(int) - Method in class org.jmol.api.JmolViewer

getBondColor2(int) - Method in class org.jmol.viewer.Viewer

getBondCount() - Method in class org.jmol.api.JmolViewer

getBondCount() - Method in class org.jmol.viewer.Viewer

getBondingMar(int, int) - Static method in class org.jmol.viewer.JmolConstants

getBondIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter

getBondIterator(Object) - Method in class org.jmol.api.JmolAdapter

Get a BondIterator for retrieval of all bonds in the file.

getBondIterator(Object) - Method in class org.jmol.viewer.FrameExportJmolAdapter

getBondModelIndex(int) - Method in class org.jmol.api.JmolViewer

getBondModelIndex(int) - Method in class org.jmol.viewer.Viewer

getBondOrder(int) - Method in class org.jmol.api.JmolViewer

getBondOrder(int) - Method in class org.jmol.viewer.Viewer

getBondPoint3f1(int) - Method in class org.jmol.api.JmolViewer

getBondPoint3f1(int) - Method in class org.jmol.viewer.Viewer

getBondPoint3f2(int) - Method in class org.jmol.api.JmolViewer

getBondPoint3f2(int) - Method in class org.jmol.viewer.Viewer

getBondRadius(int) - Method in class org.jmol.api.JmolViewer

getBondRadius(int) - Method in class org.jmol.viewer.Viewer

getBondsCount() - Method in class org.jmol.smiles.SmilesAtom

getBondsCount() - Method in class org.jmol.smiles.SmilesMolecule

getBondTolerance() - Method in class org.jmol.api.JmolViewer

getBondTolerance() - Method in class org.jmol.viewer.Viewer

getBondType() - Method in class org.jmol.smiles.SmilesBond

getBondTypeFromCode(char) - Static method in class org.jmol.smiles.SmilesBond

getBooleanProperty(String) - Method in class org.jmol.api.JmolViewer

getBooleanProperty(String) - Method in class org.jmol.viewer.Viewer

mth 2003 05 31 - needs more work this should be implemented using properties or as a hashtable using boxed/wrapped values so that the values could be shared

getBorderSize() - Method in class msg.ProteinElement

getBorderSizeHl() - Method in class msg.ProteinElement

getBsptCount() - Method in class org.jmol.bspt.Bspf

getBuffImage(Image, int, int) - Static method in class org.jmol.viewer.Viewer

This method creates a new BufferedImage by the given image.

getBusy() - Method in class msg.ProteinMatrix

getCelltype() - Method in class membranModel.MembranModel

getChainCount() - Method in class org.jmol.api.JmolViewer

getChainCount() - Method in class org.jmol.viewer.Viewer

getChainID() - Method in class org.jmol.api.JmolAdapter.AtomIterator

getChangableColix(short, int) - Method in class org.jmol.g3d.Graphics3D

getChangableColixIndex(short) - Static method in class org.jmol.g3d.Graphics3D

getCharge() - Method in class org.jmol.smiles.SmilesAtom

getChiralClass() - Method in class org.jmol.smiles.SmilesAtom

getChiralOrder() - Method in class org.jmol.smiles.SmilesAtom

getCISPEP() - Method in class protein.Protein

getClientAtomReference() - Method in class org.jmol.api.JmolAdapter.AtomIterator

getClientAtomStringProperty(Object, String) - Method in class org.jmol.api.JmolAdapter

Get a property from a clientAtom.

getClosestVisibleGeodesicVertexIndex(Vector3f, int[], int) - Method in class org.jmol.g3d.Graphics3D

getColix(int) - Static method in class org.jmol.g3d.Graphics3D

getColix(Color) - Static method in class org.jmol.g3d.Graphics3D

getColix(String) - Static method in class org.jmol.g3d.Graphics3D

getColix(Object) - Static method in class org.jmol.g3d.Graphics3D

getColixArgb(short) - Method in class org.jmol.g3d.Graphics3D

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

black or white, whichever contrasts more with the current background

getColixMix(short, short) - Method in class org.jmol.g3d.Graphics3D

getColor(int) - Method in class membranModel.MembranModel

getColor(short) - Method in class org.jmol.g3d.Graphics3D

getColorBackground() - Method in class msg.ProteinElement

getColorBackground() - Method in class msg.ProteinMatrix

getColorBackground() - Method in class org.jmol.api.JmolViewer

getColorBackground() - Method in class org.jmol.viewer.Viewer

getColorBackgroundHl() - Method in class msg.ProteinElement

getColorBackgroundPressed() - Method in class msg.ProteinElement

getColorBond() - Method in class org.jmol.api.JmolViewer

getColorBond() - Method in class org.jmol.viewer.Viewer

getColorBorder() - Method in class msg.ProteinElement

getColorBorderHl() - Method in class msg.ProteinElement

getColorFromString(String) - Static method in class org.jmol.g3d.Graphics3D

getColorLabel() - Method in class org.jmol.api.JmolViewer

getColorLabel() - Method in class org.jmol.viewer.Viewer

getColorMeasurement() - Method in class org.jmol.api.JmolViewer

getColorMeasurement() - Method in class org.jmol.viewer.Viewer

getColors() - Method in class membranModel.MembranModel

getColorText() - Method in class msg.ProteinElement

getColorTextPressed() - Method in class msg.ProteinElement

getColorVector() - Method in class org.jmol.api.JmolViewer

getColorVector() - Method in class org.jmol.viewer.Viewer

getCOMPD() - Method in class protein.Protein

getComponent() - Method in class msg.ProteinElement

getComponent() - Method in class protein.Protein

getCompressionLevel() - Method in class org.openscience.jmol.app.PngEncoder

Retrieve compression level

getCoordinates() - Method in class protein.Protein

getCoordinatesAsString() - Method in class protein.Protein

getCurrentthreadCount() - Method in class pdbParser.PDBwriter

getD(long) - Static method in class org.jmol.g3d.Xyzd

getDate() - Method in class membranModel.MembranModel

getDate() - Method in class protein.Protein

getDBREF() - Method in class protein.Protein

getDescription() - Method in class membranModel.MembranModel

getDescription() - Method in class protein.Protein

getDialog() - Method in class org.openscience.jmol.app.FileChooser

getDimensionValue(int) - Method in interface org.jmol.bspt.Tuple

getDisplayModelIndex() - Method in class org.jmol.api.JmolViewer

getDisplayModelIndex() - Method in class org.jmol.viewer.Viewer

getECN() - Method in class protein.Protein

getElement(int) - Method in class msg.ProteinMatrix

Returns the element at index i.

getElementList() - Method in class msg.ProteinMatrix

getElementNumber() - Method in class org.jmol.api.JmolAdapter.AtomIterator

getElementsPresentBitSet() - Method in class org.jmol.api.JmolViewer

getElementsPresentBitSet() - Method in class org.jmol.viewer.Viewer

getElementSymbol() - Method in class org.jmol.api.JmolAdapter.AtomIterator

getEncodeAlpha() - Method in class org.openscience.jmol.app.PngEncoder

Retrieve alpha encoding status.

getEncodedOrder() - Method in class org.jmol.api.JmolAdapter.BondIterator

getEndChainID() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator

getEndChainID() - Method in class org.jmol.api.JmolAdapter.StructureIterator

getEndInsertionCode() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator

getEndInsertionCode() - Method in class org.jmol.api.JmolAdapter.StructureIterator

getEndSequenceNumber() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator

getEndSequenceNumber() - Method in class org.jmol.api.JmolAdapter.StructureIterator

getEstimatedAtomCount(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter

getEstimatedAtomCount(Object) - Method in class org.jmol.api.JmolAdapter

Get the estimated number of atoms contained in the file.

getEstimatedAtomCount(Object) - Method in class org.jmol.viewer.FrameExportJmolAdapter

getExtremePointsIndex() - Method in class protein.Protein

getFilename() - Method in interface pdbParser.IPDBwriter

getFilename() - Method in class pdbParser.PDBwriter

getFilepath() - Method in class protein.Protein

getFileTypeName(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter

getFileTypeName(Object) - Method in class org.jmol.api.JmolAdapter

Get the type of this file or molecular model, if known.

getFilter() - Method in class org.openscience.jmol.app.PngEncoder

Retrieve filtering scheme

getFont3D(byte) - Static method in class org.jmol.g3d.Font3D

getFont3D(int) - Method in class org.jmol.g3d.Graphics3D

getFont3D(String, int) - Method in class org.jmol.g3d.Graphics3D

getFont3D(String, String, int) - Method in class org.jmol.g3d.Graphics3D

getFont3DCurrent() - Method in class org.jmol.g3d.Graphics3D

getFontFaceID(String) - Static method in class org.jmol.g3d.Font3D

getFontFid(int) - Method in class org.jmol.g3d.Graphics3D

getFontFid(String, int) - Method in class org.jmol.g3d.Graphics3D

getFontFid(String, String, int) - Method in class org.jmol.g3d.Graphics3D

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

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

getFontStyleID(String) - Static method in class org.jmol.g3d.Font3D

getFormalCharge() - Method in class org.jmol.api.JmolAdapter.AtomIterator

getFORMUL() - Method in class protein.Protein

getFrameRenderer() - Method in class org.jmol.api.JmolViewer

getFrameRenderer() - Method in class org.jmol.viewer.Viewer

getGeodesicFaceCount(int) - Method in class org.jmol.g3d.Graphics3D

getGeodesicFaceNormixes(int) - Method in class org.jmol.g3d.Graphics3D

getGeodesicFaceVertexes(int) - Method in class org.jmol.g3d.Graphics3D

getGeodesicNeighborVertexes(int) - Method in class org.jmol.g3d.Graphics3D

getGeodesicVertexCount(int) - Method in class org.jmol.g3d.Graphics3D

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

getGraphCurveColor() - Method in class org.jmol.jcamp.GraphCharacteristics

getGrid() - Method in class org.jmol.jcamp.GraphCharacteristics

getGroup3() - Method in class org.jmol.api.JmolAdapter.AtomIterator

getGroupCount() - Method in class org.jmol.api.JmolViewer

getGroupCount() - Method in class org.jmol.viewer.Viewer

getGroupsPresentBitSet() - Method in class org.jmol.api.JmolViewer

getGroupsPresentBitSet() - Method in class org.jmol.viewer.Viewer

getHash() - Method in class membranModel.MembranModel

getHeight() - Method in class msg.MatrixProgressBar

getHELIX() - Method in class protein.Protein

getHET() - Method in class protein.Protein

getHETNAM() - Method in class protein.Protein

getHistoryFile() - Static method in class org.openscience.jmol.app.Jmol

getHYDBND() - Method in class protein.Protein

getHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom

getId() - Method in class msg.ProteinElement

getInputStream() - Method in class org.openscience.jmol.app.LoopedStreams

getInsertionCode() - Method in class org.jmol.api.JmolAdapter.AtomIterator

getInstance() - Static method in class membranModel.MembranModelSingleton

If an instance of membrane model does not exist an instance will be generated.

getIntegrate() - Method in class org.jmol.jcamp.GraphCharacteristics

getIntegrateCurveColor() - Method in class org.jmol.jcamp.GraphCharacteristics

getIntegrateTextColor() - Method in class org.jmol.jcamp.GraphCharacteristics

getIntegrationCurveAreaValue(Double) - Method in class org.jmol.jcamp.GraphCharacteristics

getInverseNormix(Vector3f) - Method in class org.jmol.g3d.Graphics3D

getInverseNormix(short) - Method in class org.jmol.g3d.Graphics3D

getIsHetero() - Method in class org.jmol.api.JmolAdapter.AtomIterator

getJavaVendor() - Method in class org.jmol.api.JmolViewer

getJavaVendor() - Method in class org.jmol.viewer.Viewer

getJavaVersion() - Method in class org.jmol.api.JmolViewer

getJavaVersion() - Method in class org.jmol.viewer.Viewer

getJmol(JFrame, int, int) - Static method in class org.openscience.jmol.app.Jmol

getJPreview() - Method in class org.jmol.api.JmolViewer

getJPreview() - Method in class org.jmol.viewer.Viewer

Returns the jPreview.

getKey() - Method in class msg.ProteinElement

getKomponentsCounter() - Method in class gui.dragndrop.TreeDropTargetListener

getLabelHeight() - Method in class msg.MatrixProgressBar

getLength() - Method in class protein.Protein

getLINK() - Method in class protein.Protein

getlipid_extreme_y() - Method in class protein.Protein

getLipidNumber() - Method in class org.jmol.api.JmolViewer

getLipidNumber() - Method in class org.jmol.viewer.Viewer

new: Returns the lipidNumber.

getLipids() - Method in class msg.ProteinElement

getLipids2() - Method in class msg.ProteinElement

getMadBond() - Method in class org.jmol.api.JmolViewer

getMadBond() - Method in class org.jmol.viewer.Viewer

getMatchingAtom() - Method in class org.jmol.smiles.SmilesAtom

getMatrixHeight() - Method in class msg.ProteinMatrix

getMatrixWidth() - Method in class msg.ProteinMatrix

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

getMaxTry() - Method in class msg.ProteinMatrix

getMeasurementCount() - Method in class org.jmol.api.JmolViewer

getMeasurementCount() - Method in class org.jmol.viewer.Viewer

getMeasurementCountPlusIndices(int) - Method in class org.jmol.api.JmolViewer

getMeasurementCountPlusIndices(int) - Method in class org.jmol.viewer.Viewer

getMeasurementStringValue(int) - Method in class org.jmol.api.JmolViewer

getMeasurementStringValue(int) - Method in class org.jmol.viewer.Viewer

getMembraneTitle() - Method in class membranModel.MembranModel

getMembranModel() - Method in class msg.ProteinMatrix

getMenuListener() - Method in class org.openscience.jmol.app.DisplayPanel

getMetabolite() - Method in class protein.Protein

getMHeight() - Method in class msg.ProteinMatrix

getMinBondDistance() - Method in class org.jmol.api.JmolViewer

getMinBondDistance() - Method in class org.jmol.viewer.Viewer

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

getModel_count() - Method in class protein.Protein

getModelCount() - Method in class org.jmol.api.JmolViewer

getModelCount() - Method in class org.jmol.viewer.Viewer

getModelName(int) - Method in class org.jmol.api.JmolViewer

getModelName(int) - Method in class org.jmol.viewer.Viewer

getModelNumber(int) - Method in class org.jmol.api.JmolViewer

getModelNumber(int) - Method in class org.jmol.viewer.Viewer

getModelProperties(int) - Method in class org.jmol.api.JmolViewer

getModelProperties(int) - Method in class org.jmol.viewer.Viewer

getModelProperty(int, String) - Method in class org.jmol.api.JmolViewer

getModelProperty(int, String) - Method in class org.jmol.viewer.Viewer

getModelSetFileName() - Method in class org.jmol.api.JmolViewer

getModelSetFileName() - Method in class org.jmol.viewer.Viewer

getModelSetName() - Method in class org.jmol.api.JmolViewer

getModelSetName() - Method in class org.jmol.viewer.Viewer

getModelSetPathName() - Method in class org.jmol.api.JmolViewer

getModelSetPathName() - Method in class org.jmol.viewer.Viewer

getModelSetProperties() - Method in class org.jmol.api.JmolViewer

getModelSetProperties() - Method in class org.jmol.viewer.Viewer

getMODRES() - Method in class protein.Protein

getMOffsetX() - Method in class msg.ProteinElement

getMOffsetY() - Method in class msg.ProteinElement

getMotionEventNumber() - Method in class org.jmol.api.JmolViewer

getMotionEventNumber() - Method in class org.jmol.viewer.Viewer

getMWidth() - Method in class msg.ProteinMatrix

getMZoom() - Method in class msg.ProteinMatrix

getMZoomFactor() - Method in class msg.ProteinMatrix

getName() - Method in class membranModel.MembranModel

getName() - Method in class protein.Protein

getNodeName() - Method in class protein.Protein

getNormix(Vector3f) - Method in class org.jmol.g3d.Graphics3D

getNormix(Vector3f, int) - Method in class org.jmol.g3d.Graphics3D

getNotionalUnitcell(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter

getNotionalUnitcell(Object) - Method in class org.jmol.api.JmolAdapter

Get the notional unit cell.

getNotionalUnitcell(Object) - Method in class org.jmol.viewer.FrameExportJmolAdapter

getNumber() - Method in class org.jmol.smiles.SmilesAtom

getOccupancy() - Method in class org.jmol.api.JmolAdapter.AtomIterator

getOldMouseX() - Method in class msg.ProteinElement

getOldMouseY() - Method in class msg.ProteinElement

getOpaqueColix(short) - Static method in class org.jmol.g3d.Graphics3D

getOpenFileError() - Method in class org.jmol.api.JmolSimpleViewer

getOpenFileError() - Method in class org.jmol.viewer.Viewer

getOperatingSystemName() - Method in class org.jmol.api.JmolViewer

getOperatingSystemName() - Method in class org.jmol.viewer.Viewer

getOriginalCoordinates() - Method in class protein.Protein

getOutputStream() - Method in class org.openscience.jmol.app.LoopedStreams

getParameterInfo() - Method in class org.jmol.applet.JmolAppletControl

getPartialCharge() - Method in class org.jmol.api.JmolAdapter.AtomIterator

getPath() - Method in class xml.XMLWriter

getPdbcode() - Method in class msg.ProteinElement

getPDBcode() - Method in class protein.Protein

getPdbScaleMatrix(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter

getPdbScaleMatrix(Object) - Method in class org.jmol.api.JmolAdapter

Get the PDB scale matrix.

getPdbScaleTranslate(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter

getPdbScaleTranslate(Object) - Method in class org.jmol.api.JmolAdapter

Get the PDB scale translation vector.

getPercent() - Method in class membranModel.MembranModel

getPercentVdwAtom() - Method in class org.jmol.api.JmolViewer

getPercentVdwAtom() - Method in class org.jmol.viewer.Viewer

getPerspectiveDepth() - Method in class org.jmol.api.JmolViewer

getPerspectiveDepth() - Method in class org.jmol.viewer.Viewer

getPolymerCount() - Method in class org.jmol.api.JmolViewer

getPolymerCount() - Method in class org.jmol.viewer.Viewer

getPolymerCountInModel(int) - Method in class org.jmol.api.JmolViewer

getPolymerCountInModel(int) - Method in class org.jmol.viewer.Viewer

getPolymerLeadMidPoints(int, int) - Method in class org.jmol.api.JmolViewer

getPolymerLeadMidPoints(int, int) - Method in class org.jmol.viewer.Viewer

getPopupRotate() - Method in class msg.ProteinElement

getProgbar() - Method in class msg.ProteinMatrix

getProgBarHeight() - Method in class msg.MatrixProgressBar

getProgressPDB() - Method in interface pdbParser.IPDBwriter

getProgressPDB() - Method in class pdbParser.PDBwriter

getProtein(String) - Method in class membranModel.MembranModel

getProtein(String, String) - Method in interface pdbParser.IPDBreader

getProtein(String, String) - Method in class pdbParser.PDBreader

This function creates a Protein object by given PDBname and directory.

getProteinColor() - Method in class protein.Protein

getProteinLabel() - Method in class msg.ProteinElement

getProteinMatrix() - Method in class msg.ProteinElement

getProteinNames() - Method in class membranModel.MembranModel

getProteinPositions() - Method in class protein.Protein

getProteins(Vector, String) - Method in interface pdbParser.IPDBreader

getProteins(Vector, String) - Method in class pdbParser.PDBreader

This function creates for each PDBfile in the given directory a Protein object.

getPX() - Method in class msg.ProteinElement

getPXnew() - Method in class msg.ProteinElement

getPY() - Method in class msg.ProteinElement

getPYnew() - Method in class msg.ProteinElement

getQuality() - Method in class com.obrador.JpegEncoder

getQuality() - Method in class org.openscience.jmol.app.ImageTyper

getQuantity() - Method in class protein.Protein

getRatio() - Method in class msg.ProteinElement

getRatio() - Method in class protein.Protein

getRatioHeight() - Method in class msg.ProteinMatrix

getRatioWidth() - Method in class msg.ProteinMatrix

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

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

getResidueSequenceCount() - Method in class protein.Protein

getResizeValue() - Method in class msg.ProteinMatrix

getReverse() - Method in class org.jmol.jcamp.GraphCharacteristics

getrotatedCoordinatesforWriter(int) - Method in class protein.Protein

getRotateProteinText() - Method in class msg.ProteinElement

getRotation(Matrix3f) - Method in class org.jmol.api.JmolViewer

getRotation(Matrix3f) - Method in class org.jmol.viewer.Viewer

getRotationAngle() - Method in class msg.ProteinElement

getRotationMatrix(Matrix3f) - Method in class protein.Protein

Returns the rotationMatrix of the protein and writes it to the given Matrix3f.

getRotationMatrix() - Method in class protein.Protein

Return an instance of the rotationMatrix.

getRotationRadius() - Method in class org.jmol.api.JmolViewer

getRotationRadius() - Method in class org.jmol.viewer.Viewer

getScalePixelsPerAngstrom() - Method in class org.jmol.api.JmolViewer

getScalePixelsPerAngstrom() - Method in class org.jmol.viewer.Viewer

getScreenHeight() - Method in class org.jmol.api.JmolViewer

getScreenHeight() - Method in class org.jmol.viewer.Viewer

getScreenImage() - Method in class org.jmol.api.JmolViewer

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

getScreenImage() - Method in class org.jmol.viewer.Viewer

getScreenWidth() - Method in class org.jmol.api.JmolViewer

getScreenWidth() - Method in class org.jmol.viewer.Viewer

getSelection_color() - Method in class membranModel.MembranModel

getSelectionSet() - Method in class org.jmol.api.JmolViewer

getSelectionSet() - Method in class org.jmol.viewer.Viewer

getSEQRES() - Method in class protein.Protein

getSequenceNumber() - Method in class org.jmol.api.JmolAdapter.AtomIterator

getShades(short) - Method in class org.jmol.g3d.Graphics3D

getShapeShow(int) - Method in class org.jmol.api.JmolViewer

getShapeShow(int) - Method in class org.jmol.viewer.Viewer

getSHEET() - Method in class protein.Protein

getShowAxes() - Method in class org.jmol.api.JmolViewer

getShowAxes() - Method in class org.jmol.viewer.Viewer

getShowBbcage() - Method in class org.jmol.api.JmolViewer

getShowBbcage() - Method in class org.jmol.viewer.Viewer

getShowHydrogens() - Method in class org.jmol.api.JmolViewer

getShowHydrogens() - Method in class org.jmol.viewer.Viewer

getShowMeasurements() - Method in class org.jmol.api.JmolViewer

getShowMeasurements() - Method in class org.jmol.viewer.Viewer

getShowTransparentLipids() - Method in class org.jmol.viewer.FrameRenderer

getSize() - Method in class protein.Protein

getSizeByLipids() - Method in class protein.Protein

getSizeX() - Method in class msg.ProteinElement

getSizeY() - Method in class msg.ProteinElement

getSLTBRG() - Method in class protein.Protein

getSOURCE() - Method in class protein.Protein

getSpecies() - Method in class membranModel.MembranModel

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

getSphereIterator(int) - Method in class org.jmol.bspt.Bspf

getSSBOND() - Method in class protein.Protein

getStartChainID() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator

getStartChainID() - Method in class org.jmol.api.JmolAdapter.StructureIterator

getStartInsertionCode() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator

getStartInsertionCode() - Method in class org.jmol.api.JmolAdapter.StructureIterator

getStartMouseX() - Method in class msg.ProteinElement

getStartMouseY() - Method in class msg.ProteinElement

getStartSequenceNumber() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator

getStartSequenceNumber() - Method in class org.jmol.api.JmolAdapter.StructureIterator

getStructureIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter

getStructureIterator(Object) - Method in class org.jmol.api.JmolAdapter

Get a StructureIterator.

getStructureType() - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter.StructureIterator

getStructureType() - Method in class org.jmol.api.JmolAdapter.StructureIterator

getSubcomponent() - Method in class msg.ProteinElement

getSubcomponent() - Method in class protein.Protein

getSuperAtom() - Method in class protein.Protein

getSymbol() - Method in class org.jmol.smiles.SmilesAtom

getTextColor() - Method in class org.jmol.jcamp.GraphCharacteristics

getTransferData(DataFlavor) - Method in class gui.dragndrop.TransferableTreeNode

getTransferDataFlavors() - Method in class gui.dragndrop.TransferableTreeNode

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

getTranslucentColix(short, boolean) - Static method in class org.jmol.g3d.Graphics3D

getTranslucentColix(short) - Static method in class org.jmol.g3d.Graphics3D

getTURN() - Method in class protein.Protein

getType() - Method in class org.openscience.jmol.app.FileTyper

getType() - Method in class org.openscience.jmol.app.ImageTyper

getUniqueID() - Method in class org.jmol.api.JmolAdapter.AtomIterator

getUnscaledTransformMatrix() - Method in class org.jmol.api.JmolViewer

getUnscaledTransformMatrix() - Method in class org.jmol.viewer.Viewer

getUserDirectory() - Static method in class org.openscience.jmol.app.Jmol

Returns a new File referenced by the property 'user.dir', or null if the property is not defined.

getVectorX() - Method in class org.jmol.api.JmolAdapter.AtomIterator

getVectorY() - Method in class org.jmol.api.JmolAdapter.AtomIterator

getVectorZ() - Method in class org.jmol.api.JmolAdapter.AtomIterator

getVHeight() - Method in class msg.ProteinElement

getViewer() - Method in class jmolOutsideApplicationTest.OuterIntegration

returns the JmolViewer

getVRMLFile() - Method in class membranModel.MembranModel

getVWidth() - Method in class msg.ProteinElement

getWHeight() - Method in class msg.ProteinMatrix

getWidth() - Method in class msg.MatrixProgressBar

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

gets g3d height

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

gets g3d width

getWireframeRotation() - Method in class org.jmol.api.JmolViewer

getWireframeRotation() - Method in class org.jmol.viewer.Viewer

getWWidth() - Method in class msg.ProteinMatrix

getX() - Method in class org.jmol.api.JmolAdapter.AtomIterator

getX(long) - Static method in class org.jmol.g3d.Xyzd

getXa() - Method in class msg.ProteinElement

getXTranslationNormalized() - Method in class org.jmol.api.JmolViewer

getXTranslationNormalized() - Method in class org.jmol.viewer.Viewer

getXyzd(int, int, int, int) - Static method in class org.jmol.g3d.Xyzd

getXz_area() - Method in class membranModel.MembranModel

getxz_area() - Method in class protein.Protein

getY() - Method in class org.jmol.api.JmolAdapter.AtomIterator

getY(long) - Static method in class org.jmol.g3d.Xyzd

getYa() - Method in class msg.ProteinElement

getYTranslation() - Method in class org.jmol.api.JmolViewer

getYTranslation() - Method in class org.jmol.viewer.Viewer

getYTranslation() - Method in class protein.Protein

Returns the yTranslation of the protein.

getYTranslation4Jmol() - Method in class protein.Protein

Returns the yTranslation of the protein for Jmol, multiplicated by 2.8.

getYTranslationNormalized() - Method in class org.jmol.api.JmolViewer

getYTranslationNormalized() - Method in class org.jmol.viewer.Viewer

getZ() - Method in class org.jmol.api.JmolAdapter.AtomIterator

getZ(long) - Static method in class org.jmol.g3d.Xyzd

getZoomIn() - Method in class org.jmol.jcamp.GraphCharacteristics

getZoomPercent() - Method in class org.jmol.api.JmolViewer

getZoomPercent() - Method in class org.jmol.viewer.Viewer

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

GraphCharacteristics - Class in org.jmol.jcamp

GraphCharacteristics() - Constructor for class org.jmol.jcamp.GraphCharacteristics

GraphCharacteristics(boolean, boolean, boolean, boolean, String, String, String, String, String, String, String) - Constructor for class org.jmol.jcamp.GraphCharacteristics

GraphControlData - Class in org.jmol.jcamp.data

GraphControlData() - Constructor for class org.jmol.jcamp.data.GraphControlData

Graphics3D - Class in org.jmol.g3d

Provides high-level graphics primitives for 3D visualization.

Graphics3D(Component) - Constructor for class org.jmol.g3d.Graphics3D

Allocates a g3d object

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

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

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

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

GROUPID_GUANINE_1_LAST - Static variable in class org.jmol.viewer.JmolConstants

GROUPID_GUANINE_1_MIN - Static variable in class org.jmol.viewer.JmolConstants

GROUPID_GUANINE_2_LAST - Static variable in class org.jmol.viewer.JmolConstants

GROUPID_GUANINE_2_MIN - Static variable in class org.jmol.viewer.JmolConstants

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

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

PDB file format spec says that the 'residue name' must be right-justified.

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

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

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

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

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

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

GT - Class in org.jmol.i18n

gui.dragndrop - package gui.dragndrop

gui.messages - package gui.messages