charite.christo.protein
Class Pymol

java.lang.Object
  charite.christo.protein.Pymol

All Implemented Interfaces:

ChRunnable, CommandInterpreter, Disposable, HasProtein, ProteinViewer, java.awt.event.ActionListener, java.util.EventListener

public class Pymol
extends java.lang.Object
implements ProteinViewer, ChRunnable, java.awt.event.ActionListener

HELP WIKI:PyMOL HOME_PAGE:Pymol is a widely applied protein structure viewer by Warren Delano.

Residue selections: Dragging the mouse over a part of the amino acid sequence in the STRAP alignment creates a residue selection in Pymol. The STRAP cursor position refers to another Pymol selection named "cursor". Users can refer to these selections in Pymol. Using the [S]show or hide [H]hide menus in the side panel of Pymol the representations of the selected atoms can be specified like sphere, cartoon or stick.

Menu The generic 3D-menu for the Pymol view is opened by clicking the Pymol button which will appear in a separate small panel. This menu also allows to add further proteins.

Related links: http://www.rubor.de/bioinf/ http://www.rubor.de/anlagen/PyMOL_Tutorial.pdf

Bugs: Pymol does not treat negative pdb residue numbers correctly. Pymol selection is unspecific if the chain identifier is a space character ' '; PACKAGE:charite.christo.strap. SEE_CLASS:ResidueAnnotation SEE_CLASS:AddAnnotation

Field Summary

static java.lang.String	DEFINE_THIS_COLOR
static java.lang.String	PYMOL_COLOR_NAME

Fields inherited from interface charite.christo.protein.ProteinViewer

COMMAND_HIDE_EVERYTHING, COMMANDbackground, COMMANDbiomolecule, COMMANDcartoon, COMMANDcenter, COMMANDcenter_amino, COMMANDchange_object_color, COMMANDcolor, COMMANDdots, COMMANDhighlight_selected_amino_acids, COMMANDhighlight_selected_atoms, COMMANDlabel, COMMANDlabel_color, COMMANDlines, COMMANDmesh, COMMANDobject_delete, COMMANDribbons, COMMANDrotate, COMMANDsa_surface, COMMANDselect, COMMANDselection_name, COMMANDset_rotation_translation, COMMANDshowScriptPanel, COMMANDspheres, COMMANDsticks, COMMANDsurface, COMMANDsurface_color, COMMANDzoom, GET_ATOM_SELECTION_EXAMPLE, GET_AWTMASK_CONT_SELECTION, GET_AWTMASK_DISC_SELECTION, GET_CANVAS, GET_FLAGS, GET_FRAME_TITLE, GET_JMENUBAR, GET_LAST_CREATED_OBJECT, GET_SUPPORTED_COMMANDS, GET_SURFACEOBJECTS, INTERNAL_USE, INTERPRET_NO_MSG_DIALOGS, mapViewer, NONE, PFX_SURFACE_OBJECT, PROPERTY_EXTERNAL_PROCESS, PROPERTY_HAS_CONTEXTMENU, PROPERTY_HAS_SCRIPT_PANEL, PROPERTY_HEAVY_WEIGHT, PROPERTY_MULTI_MOLECULE, PROPERTY_MULTI_VIEW, PROPERTY_NAMED_SELECTIONS, PROPERTY_NEEDS_UPDATE_SURFACES_WHEN_ROTATED, PROPERTY_OPENGL, PROPERTY_RIBBON_COLOR_NO_CHANGE, PROPERTY_SEQUENCE_CURSOR_DELAYED, PROPERTY_TK, PROTEIN, RESIDUES, SELECTION_CURSOR, SELECTION_PICKED, SET_PROTEIN_VERBOSE, SET_RUN_AFTER_INSTALLATION, SHOW_CURSOR_IF_OTHER_PROTEIN, STYLE_COMMANDS

Fields inherited from interface charite.christo.ChRunnable

APPEND, COLUMN_TITLE, DOWNLOAD_FINISHED, GET_PANEL, ICON, INTERPRET_LINE, IS_DRAG4XY, ITEM_TEXT, MODIFY_RENDERER_COMPONENT, PROGRESS, REPAINT_CURSOR, SAY_DOWNLOADING, SET_ICON_IMAGE, SET_TREE_VALUE, SHOW_IN_FRAME, TAB_TEXT, TIP_TEXT

Constructor Summary

Pymol()

Method Summary

void	actionPerformed(java.awt.event.ActionEvent ev)
static java.lang.Object	canInstall()
void	dispose()
static java.lang.String	getCustomizableExamples()
static java.lang.String	getCustomizableExecPath()
static java.lang.String	getCustomizableInitCommands()
static java.lang.String	getCustomizableLateCommands()
java.lang.Object	getProperty(java.lang.String getID) The method may return null.
Protein	getProtein()
UniqueList<Pymol>	getViewersSharingViewV(boolean proxies) Each instance is connected with only one protein.
void	interpret(long options, java.lang.String command)
void	loadObject(java.io.File f, java.lang.String n0)
java.lang.Object	run(java.lang.String id, java.lang.Object arg)
void	setProperty(java.lang.String id, java.lang.Object value)
boolean	setProtein(long options, Protein p, ProteinViewer inSameView) The only use of the setProtein and getProtein methods are to to keep a reference to the protein object.
java.lang.String	toString()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

DEFINE_THIS_COLOR

public static final java.lang.String DEFINE_THIS_COLOR

See Also:

Constant Field Values

PYMOL_COLOR_NAME

public static final java.lang.String PYMOL_COLOR_NAME

See Also:

Constant Field Values

Constructor Detail

Pymol

public Pymol()

Method Detail

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

run

public java.lang.Object run(java.lang.String id,
                            java.lang.Object arg)

Specified by:

run in interface ChRunnable

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent ev)

Specified by:

actionPerformed in interface java.awt.event.ActionListener

getProtein

public Protein getProtein()

Specified by:

getProtein in interface HasProtein

setProtein

public boolean setProtein(long options,
                          Protein p,
                          ProteinViewer inSameView)

Description copied from interface: ProteinViewer

The only use of the setProtein and getProtein methods are to to keep a reference to the protein object. Otherwise both methods are not important.

Specified by:

setProtein in interface ProteinViewer

interpret

public void interpret(long options,
                      java.lang.String command)

Specified by:

interpret in interface CommandInterpreter

dispose

public void dispose()

Specified by:

dispose in interface Disposable

loadObject

public void loadObject(java.io.File f,
                       java.lang.String n0)

getCustomizableExamples

public static java.lang.String getCustomizableExamples()

getCustomizableInitCommands

public static java.lang.String getCustomizableInitCommands()

getCustomizableLateCommands

public static java.lang.String getCustomizableLateCommands()

getCustomizableExecPath

public static java.lang.String getCustomizableExecPath()

canInstall

public static java.lang.Object canInstall()

getViewersSharingViewV

public UniqueList<Pymol> getViewersSharingViewV(boolean proxies)

Description copied from interface: ProteinViewer

Each instance is connected with only one protein. But several instances can share the view such that several proteins are displayed in the same panel.

Specified by:

getViewersSharingViewV in interface ProteinViewer

setProperty

public void setProperty(java.lang.String id,
                        java.lang.Object value)

Specified by:

setProperty in interface ProteinViewer

getProperty

public java.lang.Object getProperty(java.lang.String getID)

Description copied from interface: ProteinViewer

The method may return null. GET_JMENUBAR: javax.swing.JMenuBar GET_CANVAS: java.awt.Component GET_SURFACEOBJECTS: List GET_FLAGS: long-bit-mask with properties A generic command like COMMANDcolor: Boolean.TRUE if command is supported

Specified by:

getProperty in interface ProteinViewer