charite.christo.strap
Class V3dUtils

java.lang.Object
  charite.christo.strap.V3dUtils

All Implemented Interfaces:

ChRunnable, PaintHook, ProcessEv, TooltipProvider

public class V3dUtils
extends java.lang.Object
implements ChRunnable, ProcessEv, TooltipProvider, PaintHook

HELP

Menu-bar: If the user clicks inside the 3D-view, the default Strap menu-bar disappears and the menu-bar of the 3D-view is shown instead. This menu-bar is independent of the type of 3D-view and will be referred to as the generic menu-bar. Some 3D-programs have their own menu bar. In this case, the user can swap between the native and the generic menu-bar. By clicking the scroll-bar or the sequence of a protein that is not displayed three-dimensionally, the default Strap menu-bar is shown again.

Undock menu items: Menu items like "spheres on" or "sticks on" in the style menu might be frequently used. For convenience, menu items can be dragged to the desktop with the mouse and are easier accessible.

Undock the viewer pane: 3D-viewers that are located inside the STRAP-application frame can be moved outside (undocking). For this purpose the title header needs to be dragged.

Always floating on top of other windows All Strap windows can be set "Always floating on top of all other windows". Type ctrl-T.

Picking Atoms in the 3D-View: When atoms are clicked in the 3D-view, Strap will display a toolbar with buttons that act upon the clicked amino acid. These buttons allow to move the alignment cursor to the clicked residues and to add/remove the clicked amino acid to a residue selection.
By picking an atom, one amino acid is selected. By picking atoms with certain modifier keys, more than one amino acid can be selected. This corresponds to selecting several files in a file browser by Ctrl-left-click or Shift-left-click. The modifier keys depend on the 3D-viewer.

3D-Viewer	Continuous selection	Discontinuous selection
OpenAstex	Ctrl+Shift-Click	Ctrl-Click
JMol	Shift-Click	Ctrl-Click

Selecting a protein. Moving the alignment cursor selects the respective protein in the 3D view and also selects the respective position. The previous atom selection is overridden. There are two options for changing the protein without loosing the previous selection of that protein. Either the protein list can be used which is opened with the menu item "Select protein" or the alignment row header of the protein can be clicked. The previous atom selection of this protein will be activated.

Selecting amino acids in the alignment panel: Using the mouse or using arrow-left/ arrow-right keys together with shift, a number of amino acids can be selected in STRAP. This selection is passed to the 3D viewer. Alternatively, a residue selection can be dragged with the mouse into the 3D-view.

Adding proteins: Proteins can be added by WIKI:Drag_and_drop. See STRING:ChConstants#MOVIE_Drag_to_another_STRAP

Displaying Sequence Features: Sequence Features can highlighted in the 3D-view using WIKI:Drag_and_drop. See STRING:ChConstants#MOVIE_Sequence_Features_in_3D

3D-Superposition: 3D-Superposition allows to compare two or more protein backbones. Two options are available:

1. All peptide chains in the view: One medium structure will be used as a reference. All other proteins are overlayed upon this reference peptide chain.
2. All multiprotein complexes in the view: Different chains of the same PDB entry form a complex and their relative position is sustained. For superimposing two multiprotein complexes, the best structurally matching pair of chains is determined. I.E. for superimposing two trimeric G-proteins, the beta propeller structures may be selected. The superposition is computed for this pair of peptide chains and the transformation is applied to the entire complexes. Complexes might also be defined by the user or by a script - see context menu of proteins.

Field Summary

static int	OPEN_ADD_TAB
static int	OPEN_ASK
static int	OPEN_EACH_PROTEIN_OWN_COLOR
static int	OPEN_INIT_SCRIPT
static int	OPEN_NARROW_OTHERS
static int	OPEN_NOT_ADD_PANEL
static int	OPEN_SEND_ALL_ANNOTATIONS
static int	OPEN_VERBOSE
static int	PV_FOCUSED
static int	PV_FOCUSED_NOT_MB
static int	PV_MENUBAR
static long	RSto3D_AS_ONE_SINGLE
static long	RSto3D_ASK_NAME
static long	RSto3D_COLOR
static long	RSto3D_COMMANDS
static long	RSto3D_GENERIC_NAME
static long	RSto3D_NO_WIRE
static long	RSto3D_NOT_SAME_WIRE
static long	RSto3D_REPORT_ERROR
static long	RSto3D_SAME_PROTEIN
static long	RSto3D_SET_FOCUSED_PV
static long	RSto3D_SPECIFIC_ATOMS

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

V3dUtils()

Method Summary

static void	colorAllAminos(java.awt.Color c, ProteinViewer pv)
static void	enableDisable()
static Selection3D[]	getSelection3D(ProteinViewer pv)
static javax.swing.JComponent	getToolpane()
static ProteinViewer	open3dViewer(long options, Protein[] pp, java.lang.Object clazzOrViewer)
static void	openColorDialog()
boolean	paintHook(javax.swing.JComponent c, java.awt.Graphics g, boolean after)
static javax.swing.JComponent	pnlSurfaceObjects()
void	processEv(java.awt.AWTEvent ev)
java.lang.String	provideTip(java.lang.Object objOrEv)
static void	residueSelectionsTo3D_I(long option, ResidueSelection[] ss, ProteinViewer[] vv)
static boolean	residueSelectionsTo3D(long options, ResidueSelection[] ss, ProteinViewer[] vv)
java.lang.Object	run(java.lang.String id, java.lang.Object arg)
static boolean	sendCommand(long options, java.lang.CharSequence command0, ProteinViewer pv)
static boolean	setFocusedP(boolean menuBar, Protein p)
static java.lang.Thread	thread_open3dViewer(long options, Protein[] pp, java.lang.Object clazzOrViewer, ProteinViewer[] ret)
static void	transform3D(Matrix3D m3d, ProteinViewer pv)
static void	viewerToFront(long options, ProteinViewer pv)

Methods inherited from class java.lang.Object

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

Field Detail

OPEN_VERBOSE

public static final int OPEN_VERBOSE

See Also:

Constant Field Values

OPEN_ASK

public static final int OPEN_ASK

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Constant Field Values

OPEN_SEND_ALL_ANNOTATIONS

public static final int OPEN_SEND_ALL_ANNOTATIONS

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Constant Field Values

OPEN_NOT_ADD_PANEL

public static final int OPEN_NOT_ADD_PANEL

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Constant Field Values

OPEN_NARROW_OTHERS

public static final int OPEN_NARROW_OTHERS

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Constant Field Values

OPEN_ADD_TAB

public static final int OPEN_ADD_TAB

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Constant Field Values

OPEN_INIT_SCRIPT

public static final int OPEN_INIT_SCRIPT

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Constant Field Values

OPEN_EACH_PROTEIN_OWN_COLOR

public static final int OPEN_EACH_PROTEIN_OWN_COLOR

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Constant Field Values

PV_FOCUSED

public static final int PV_FOCUSED

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Constant Field Values

PV_MENUBAR

public static final int PV_MENUBAR

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Constant Field Values

PV_FOCUSED_NOT_MB

public static final int PV_FOCUSED_NOT_MB

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Constant Field Values

RSto3D_COMMANDS

public static final long RSto3D_COMMANDS

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Constant Field Values

RSto3D_COLOR

public static final long RSto3D_COLOR

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Constant Field Values

RSto3D_AS_ONE_SINGLE

public static final long RSto3D_AS_ONE_SINGLE

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Constant Field Values

RSto3D_SAME_PROTEIN

public static final long RSto3D_SAME_PROTEIN

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Constant Field Values

RSto3D_ASK_NAME

public static final long RSto3D_ASK_NAME

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Constant Field Values

RSto3D_REPORT_ERROR

public static final long RSto3D_REPORT_ERROR

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Constant Field Values

RSto3D_NOT_SAME_WIRE

public static final long RSto3D_NOT_SAME_WIRE

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Constant Field Values

RSto3D_NO_WIRE

public static final long RSto3D_NO_WIRE

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Constant Field Values

RSto3D_GENERIC_NAME

public static final long RSto3D_GENERIC_NAME

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Constant Field Values

RSto3D_SPECIFIC_ATOMS

public static final long RSto3D_SPECIFIC_ATOMS

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Constant Field Values

RSto3D_SET_FOCUSED_PV

public static final long RSto3D_SET_FOCUSED_PV

See Also:

Constant Field Values

Constructor Detail

V3dUtils

public V3dUtils()

Method Detail

thread_open3dViewer

public static java.lang.Thread thread_open3dViewer(long options,
                                                   Protein[] pp,
                                                   java.lang.Object clazzOrViewer,
                                                   ProteinViewer[] ret)

open3dViewer

public static ProteinViewer open3dViewer(long options,
                                         Protein[] pp,
                                         java.lang.Object clazzOrViewer)

run

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

Specified by:

run in interface ChRunnable

setFocusedP

public static boolean setFocusedP(boolean menuBar,
                                  Protein p)

paintHook

public boolean paintHook(javax.swing.JComponent c,
                         java.awt.Graphics g,
                         boolean after)

Specified by:

paintHook in interface PaintHook

after - This method is called once before and once after super.paintComponent.

Returns:

means do not call super.paintComponent

getToolpane

public static javax.swing.JComponent getToolpane()

enableDisable

public static void enableDisable()

processEv

public void processEv(java.awt.AWTEvent ev)

Specified by:

processEv in interface ProcessEv

See Also:

EvAdapter

getSelection3D

public static Selection3D[] getSelection3D(ProteinViewer pv)

residueSelectionsTo3D

public static boolean residueSelectionsTo3D(long options,
                                            ResidueSelection[] ss,
                                            ProteinViewer[] vv)

residueSelectionsTo3D_I

public static void residueSelectionsTo3D_I(long option,
                                           ResidueSelection[] ss,
                                           ProteinViewer[] vv)

viewerToFront

public static void viewerToFront(long options,
                                 ProteinViewer pv)

colorAllAminos

public static void colorAllAminos(java.awt.Color c,
                                  ProteinViewer pv)

sendCommand

public static boolean sendCommand(long options,
                                  java.lang.CharSequence command0,
                                  ProteinViewer pv)

openColorDialog

public static void openColorDialog()

pnlSurfaceObjects

public static javax.swing.JComponent pnlSurfaceObjects()

transform3D

public static void transform3D(Matrix3D m3d,
                               ProteinViewer pv)

provideTip

public java.lang.String provideTip(java.lang.Object objOrEv)

Specified by:

provideTip in interface TooltipProvider