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 _

C

calcIntensity(float, float, float) - Static method in class org.jmol.g3d.Graphics3D

calcIntensityScreen(Point3f, Point3f, Point3f) - Method in class org.jmol.g3d.Graphics3D

calcNormalizedNormal(Point3f, Point3f, Point3f, Vector3f) - Method in class org.jmol.g3d.Graphics3D

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

calcSurfaceShade(short, Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D

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

Calculates the start size of the lipid matrix.

calculateProteinNumber() - Method in class msg.ProteinMatrix

Calculates the number of Proteins.

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

Calculates the quantity value of a ProteinElement in the lipid matrix.

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

Calculates the ratio of a singe lipid according to the panel size.

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

canonizeAlphaDigit(char) - Static method in class org.jmol.api.JmolAdapter

canonizeAlternateLocationID(char) - Static method in class org.jmol.api.JmolAdapter

canonizeChainID(char) - Static method in class org.jmol.api.JmolAdapter

canonizeInsertionCode(char) - Static method in class org.jmol.api.JmolAdapter

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

Changes the busy coordinates in the lipid matrix.

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

changeElements() - Method in class msg.ProteinMatrix

Change the properties of the component.

changeKey(String, String) - Method in class msg.ProteinMatrix

Change the key of all elements that belong to the old key.

changeLipidCubeRotation(int, int, int) - Method in class msg.ProteinElement

Changes the values in the matrix of the lipids for a rotation of 90° of the matrix.

changeResize() - Method in class msg.ProteinMatrix

Changes the component if the window is resized.

changeZoomDefault() - Method in class msg.ProteinMatrix

Change the size of the component to fit the size of the panel.

changeZoomIn() - Method in class msg.ProteinMatrix

Change the size of the component to zoom in.

changeZoomOut() - Method in class msg.ProteinMatrix

Change the size of the component to zoom out.

checkRotate(int) - Method in class msg.ProteinMatrix

Checks if the ProteinElement is rotated with 90° or 270°.

chemFileProperty - Static variable in class org.openscience.jmol.app.Jmol

CHIRALITY_ALLENE - Static variable in class org.jmol.smiles.SmilesAtom

CHIRALITY_OCTAHEDRAL - Static variable in class org.jmol.smiles.SmilesAtom

CHIRALITY_SQUARE_PLANAR - Static variable in class org.jmol.smiles.SmilesAtom

CHIRALITY_TETRAHEDRAL - Static variable in class org.jmol.smiles.SmilesAtom

CHIRALITY_TRIGONAL_BIPYRAMIDAL - Static variable in class org.jmol.smiles.SmilesAtom

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

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

clearCords() - Method in class msg.ProteinMatrix

Clear the busy coordinates in the lipid matrix.

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

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

delegated to MeasurementManager

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

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

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

CODE_AROMATIC - Static variable in class org.jmol.smiles.SmilesBond

CODE_DIRECTIONAL_1 - Static variable in class org.jmol.smiles.SmilesBond

CODE_DIRECTIONAL_2 - Static variable in class org.jmol.smiles.SmilesBond

CODE_DOUBLE - Static variable in class org.jmol.smiles.SmilesBond

CODE_NONE - Static variable in class org.jmol.smiles.SmilesBond

CODE_SINGLE - Static variable in class org.jmol.smiles.SmilesBond

CODE_TRIPLE - Static variable in class org.jmol.smiles.SmilesBond

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

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

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

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

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

com.obrador - package com.obrador

compareStrings(String, String) - Static method in class org.jmol.jcamp.utils.StringDataUtils

Compares two strings provided and returns an expected integer value based on the comparison

complete_scaling_proteins() - Method in class membranModel.MembranModel

Does the completeScaling() function for any Protein the membrane consists of

completeScaling() - Method in class protein.Protein

Scales the protein by applying the matrix to the original Coordinates.

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

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

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

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

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

ConsoleTextArea - Class in org.openscience.jmol.app

ConsoleTextArea(InputStream[]) - Constructor for class org.openscience.jmol.app.ConsoleTextArea

ConsoleTextArea() - Constructor for class org.openscience.jmol.app.ConsoleTextArea

convertDoubleArrayToString(double[], String) - Method in class xml.XMLWriter

Converts an array of double values into a string.

convertIntArrayToString(int[], String) - Method in class xml.XMLWriter

Converts an int array into a string.

convertMatrix3fToString(Matrix3f, String) - Method in class xml.XMLWriter

Converts a Matrix3f into a string.

convertStringArrayToString(String[], String) - Method in class xml.XMLWriter

Converts an array of strings into a single string.

convertStringToDoubleArray(String, String) - Method in class xml.XMLReader

Converts a string into an array of double values.

convertStringToIntArray(String, String) - Method in class xml.XMLReader

Converts a string into an array of int values.

convertStringToMatrix3f(String, String) - Method in class xml.XMLReader

Converts a string into a Matrix3f.

convertStringToStringArray(String, String) - Method in class xml.XMLReader

Converts a string into an array of strings.

convertVectorIntArrayToString(Vector, String) - Method in class xml.XMLWriter

Converts a vector of int arrays into a string.

convToIntelDouble(long) - Static method in class org.jmol.jcamp.utils.NumericDataUtils

convToIntelFloat(int) - Static method in class org.jmol.jcamp.utils.NumericDataUtils

convToIntelInt(int) - Static method in class org.jmol.jcamp.utils.NumericDataUtils

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

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

Get the boolean whether coordinates are fractional.

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

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

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

countProteins() - Method in class membranModel.MembranModel

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

createBond(SmilesAtom, SmilesAtom, int) - Method in class org.jmol.smiles.SmilesMolecule

createElements() - Method in class msg.ProteinMatrix

Creates the new ProteinElements components.

createFile(String, MembranModel) - Method in class xml.XMLWriter

Parse the data of the MembranModel object and create an document.

createMissingHydrogen(SmilesMolecule) - Method in class org.jmol.smiles.SmilesAtom

Creates missing hydrogen

createProgBar() - Method in class msg.ProteinMatrix

Creates and initializes a MatrixProgressBar.

createProteinElement(String, int, int, int, int) - Method in class msg.ProteinElement

Creates a new ProteinElement.

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

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