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 _

P

paint(Graphics) - Method in class jmolOutsideApplicationTest.OuterIntegration

paint Jmol

paint(Graphics) - Method in class org.jmol.applet.Jmol

paint(Graphics) - Method in class org.jmol.appletwrapper.AppletWrapper

paint(Graphics) - Method in interface org.jmol.appletwrapper.WrappedApplet

paint(Graphics) - Method in class org.jmol.jcamp.ZoneVisu

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

paint(Graphics) - Method in class org.openscience.jmol.app.Splash

paintComponent(Graphics) - Method in class msg.ProteinElement

Paints the component.

paintComponent(Graphics) - Method in class msg.ProteinMatrix

Paints the component.

paintLipids(Graphics) - Method in class org.jmol.viewer.Viewer

This method paints the tranparent lipids and calculates the size of the painted images.

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

This method paints the tranparent lipids on the left and right border of the JTabbedPane and calculates the size of the painted images.

parseSmiles(String) - Method in class org.jmol.smiles.SmilesParser

Parse a SMILES String

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

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

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

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

PATH_KEY - Static variable in class org.jmol.adapter.smarter.SmarterJmolAdapter

PATH_SEPARATOR - Static variable in class org.jmol.adapter.smarter.SmarterJmolAdapter

pdbParser - package pdbParser

PDBProgressBar - Class in pdbParser

A class that calls functions to generate a membrane model as a .pdb-File.

PDBProgressBar(JFrame) - Constructor for class pdbParser.PDBProgressBar

By initialising this constructor the membrane model will be generated as a pdb.

PDBreader - Class in pdbParser

This class makes functions available to construct a Protein object by given PDBfile.

PDBreader() - Constructor for class pdbParser.PDBreader

initialises the constructor

pdbs - Variable in class gui.dragndrop.TreeDropTargetListener

PDBwriter - Class in pdbParser

PDBwriter() - Constructor for class pdbParser.PDBwriter

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

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

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

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

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

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

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

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

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

picking modes

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

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

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

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

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

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

plotPoints(short, int, int[]) - Method in class org.jmol.g3d.Graphics3D

plotPoints(int, short, byte[], int[]) - Method in class org.jmol.g3d.Graphics3D

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

Creates an array of bytes that is the PNG equivalent of the current image, specifying whether to encode alpha or not.

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

Creates an array of bytes that is the PNG equivalent of the current image.

PngEncoder - Class in org.openscience.jmol.app

PngEncoder takes a Java Image object and creates a byte string which can be saved as a PNG file.

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

Class constructor

PngEncoder(Image) - Constructor for class org.openscience.jmol.app.PngEncoder

Class constructor specifying Image to encode, with no alpha channel encoding.

PngEncoder(Image, boolean) - Constructor for class org.openscience.jmol.app.PngEncoder

Class constructor specifying Image to encode, and whether to encode alpha.

PngEncoder(Image, boolean, int) - Constructor for class org.openscience.jmol.app.PngEncoder

Class constructor specifying Image to encode, whether to encode alpha, and filter to use.

PngEncoder(Image, boolean, int, int) - Constructor for class org.openscience.jmol.app.PngEncoder

Class constructor specifying Image source to encode, whether to encode alpha, filter to use, and compression level.

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

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

PovrayDialog - Class in org.openscience.jmol.app

A dialog for controling the creation of a povray input file from a Chemframe and a display.

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

Creates a dialog for getting info related to output frames in povray format.

PovraySaver - Class in org.openscience.jmol.app

PovraySaver(JmolViewer, OutputStream, boolean, int, int) - Constructor for class org.openscience.jmol.app.PovraySaver

predefinedGroup3Names - Static variable in class org.jmol.viewer.JmolConstants

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

PreferencesDialog - Class in org.openscience.jmol.app

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

print(Graphics, PageFormat, int) - Method in class org.openscience.jmol.app.DisplayPanel

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

added print command, so that it can be used by RasmolScriptHandler

printCords() - Method in class msg.ProteinMatrix

Prints the lipid matrix to the STDOUT.

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

propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.AtomSetChooser

propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.FilePreview

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

protein - package protein

Protein - Class in protein

Protein(String) - Constructor for class protein.Protein

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

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

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

Default table of PdbStructure colors

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

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

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

ProteinElement - Class in msg

ProteinElement(Msg_panel, ProteinMatrix, String, String, String, String, int, int, int, int, Color, int, int, int, int, int, int, int, int, Vector) - Constructor for class msg.ProteinElement

Initializes a new ProteinElement.

ProteinMatrix - Class in msg

ProteinMatrix(Msg_panel, int, int) - Constructor for class msg.ProteinMatrix

Initializes a new ProteinMatrix.

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

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

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

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

put(int, Object) - Method in class org.jmol.util.Int2ObjHash

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