charite.christo.protein
Class Protein3dUtils

java.lang.Object
  charite.christo.protein.Protein3dUtils

All Implemented Interfaces:

ChRunnable

public class Protein3dUtils
extends java.lang.Object
implements ChRunnable

Field Summary

static int	ASTEX
static int	GENERIC
static int	JMOL
static int	JV
static java.lang.String	KEY_ADD_TO_NATIVE_MENU
static java.lang.String	LOG_FILE
static java.lang.String	LOG_PROTEIN_PFX
static int	PYMOL
static int	RASMOL
static java.lang.String	SCRIPT_select_3D
static int	SURFACE_ID
static int	SURFACE_ID_COLON
static int	SURFACE_ID_DASH
static int	SURFACE_ID_DOT
static int	SURFACE_ID_KOMMA
static java.lang.String	VARIABLES

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

Protein3dUtils()

Method Summary

static Selection3D[]	addOrRemove(char operation, Selection3D[] ss0, int frst, int last, char ins, char chain)
static void	addPdbId(java.lang.String id_chain, Protein3d p3d, java.lang.Class proteinClass)
static void	addStructure(java.io.File f, Protein3d p3d, java.lang.Class proteinClass)
static java.lang.String[]	allCommands()
static ProteinViewer[]	askViewersSharingView(ProteinViewer pv0, Protein pSuggestion, java.lang.String msg)
static java.lang.String[]	atomsOfAminos()
static Selection3D[]	boolToSelection3D(boolean fullLen, boolean[] bb, int offset, Protein p, java.lang.String atoms)
static void	changeAtoms(boolean isGeneric, Selection3D[] ss, java.lang.String expr)
static ProteinViewer	derefViewer(java.lang.Object o)
static void	dispatchEvtPicked(ProteinViewer pv, int resNum, char chain, char insertion, int awtModi)
static java.lang.String	exampleCommands(int viewerId)
static ProteinViewer	findProteinViewerWithProteins(java.lang.Class clazz, Protein[] pp, boolean exactly)
static long	flags(ProteinViewer v)
static javax.swing.JComponent[]	getNativeMenus(ProteinViewer pv)
static Protein[]	getProteinsInView(ProteinViewer... vv)
static java.util.List<Protein>	getProteinsInViewV(ProteinViewer viewer, java.util.List<Protein> vProts)
static java.util.Map	getSharedHashMap(ProteinViewer pv)
static ProteinViewer	getViewerForProtein(Protein p, ProteinViewer pv)
static ProteinViewer[]	getViewers(Protein[] pp, java.lang.Class clazz)
static ProteinViewer[]	getViewersSharingView(ProteinViewer pv)
static void	highlightAtoms(java.awt.Component c, int x, int y, java.lang.String type)
static void	initCustomizableSettings(ProteinViewer pv)
static boolean	isActive(ProteinViewer v)
static javax.swing.JMenuBar	jMenuBar(ProteinViewer pv)
static BA	log3D(boolean isGeneric, ProteinViewer pv0, java.lang.String command)
static java.lang.String	makeSelId(Selection3D[] atoms, java.lang.String selId)
static Matrix3D	matrixInScript(java.lang.String c)
static java.lang.String	objectIdInScript(java.lang.String c)
static Protein	p(ProteinViewer pv)
static Selection3D[]	rangeToSelection3D(int first, int last, Protein p)
static long	rgbInScript(java.lang.String command)
static byte[]	rplcVars(byte[] txt, Protein p)
java.lang.Object	run(java.lang.String id, java.lang.Object arg)
static boolean[]	selection3dToBoolZ(Selection3D[] atoms, Protein p)
static int	selection3dToFirstIdxZ(boolean fullLength, Selection3D at, Protein p)
static java.lang.String	selection3dToText(int viewerId, Selection3D[] ss)
static void	showLogPanel(boolean isGeneric, ProteinViewer pv)
static java.lang.String[]	splitAtoms(byte[] T, int B, int E)
static java.lang.String[]	splitAtoms(java.lang.String s)
static boolean	supports(java.lang.String command, ProteinViewer v)
static Selection3D[]	textToSelection3D(boolean convert_i2rn, java.lang.Object text, Protein p)
static Selection3D[]	textToSelection3D(java.lang.Object text, Protein p)
static java.lang.Thread	thread_addPdbId(java.lang.String id_chain, Protein3d p3d, java.lang.Class proteinClass)
static java.lang.Thread	thread_addStructure(java.io.File f, Protein3d p3d, java.lang.Class proteinClass)
static java.lang.String	titleFor3dViewers(Protein[] pp)
static Selection3D[]	toSelectionS(ResidueSelection s)
static java.awt.Component	viewerCanvas(ProteinViewer pv)
static java.io.File	withHeterosInOneFile(Protein p)

Methods inherited from class java.lang.Object

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

Field Detail

GENERIC

public static final int GENERIC

See Also:

Constant Field Values

SURFACE_ID

public static final int SURFACE_ID

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Constant Field Values

JMOL

public static final int JMOL

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Constant Field Values

PYMOL

public static final int PYMOL

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Constant Field Values

ASTEX

public static final int ASTEX

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Constant Field Values

RASMOL

public static final int RASMOL

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Constant Field Values

JV

public static final int JV

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Constant Field Values

SURFACE_ID_COLON

public static final int SURFACE_ID_COLON

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Constant Field Values

SURFACE_ID_DASH

public static final int SURFACE_ID_DASH

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Constant Field Values

SURFACE_ID_KOMMA

public static final int SURFACE_ID_KOMMA

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Constant Field Values

SURFACE_ID_DOT

public static final int SURFACE_ID_DOT

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Constant Field Values

KEY_ADD_TO_NATIVE_MENU

public static final java.lang.String KEY_ADD_TO_NATIVE_MENU

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Constant Field Values

SCRIPT_select_3D

public static final java.lang.String SCRIPT_select_3D

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Constant Field Values

VARIABLES

public static final java.lang.String VARIABLES

See Also:

Constant Field Values

LOG_PROTEIN_PFX

public static final java.lang.String LOG_PROTEIN_PFX

See Also:

Constant Field Values

LOG_FILE

public static final java.lang.String LOG_FILE

See Also:

Constant Field Values

Constructor Detail

Protein3dUtils

public Protein3dUtils()

Method Detail

atomsOfAminos

public static java.lang.String[] atomsOfAminos()

getProteinsInView

public static Protein[] getProteinsInView(ProteinViewer... vv)

getProteinsInViewV

public static java.util.List<Protein> getProteinsInViewV(ProteinViewer viewer,
                                                         java.util.List<Protein> vProts)

getViewersSharingView

public static ProteinViewer[] getViewersSharingView(ProteinViewer pv)

titleFor3dViewers

public static java.lang.String titleFor3dViewers(Protein[] pp)

p

public static Protein p(ProteinViewer pv)

isActive

public static boolean isActive(ProteinViewer v)

getViewers

public static ProteinViewer[] getViewers(Protein[] pp,
                                         java.lang.Class clazz)

viewerCanvas

public static java.awt.Component viewerCanvas(ProteinViewer pv)

jMenuBar

public static javax.swing.JMenuBar jMenuBar(ProteinViewer pv)

getNativeMenus

public static javax.swing.JComponent[] getNativeMenus(ProteinViewer pv)

askViewersSharingView

public static ProteinViewer[] askViewersSharingView(ProteinViewer pv0,
                                                    Protein pSuggestion,
                                                    java.lang.String msg)

findProteinViewerWithProteins

public static ProteinViewer findProteinViewerWithProteins(java.lang.Class clazz,
                                                          Protein[] pp,
                                                          boolean exactly)

getViewerForProtein

public static ProteinViewer getViewerForProtein(Protein p,
                                                ProteinViewer pv)

derefViewer

public static ProteinViewer derefViewer(java.lang.Object o)

allCommands

public static java.lang.String[] allCommands()

rgbInScript

public static long rgbInScript(java.lang.String command)

objectIdInScript

public static java.lang.String objectIdInScript(java.lang.String c)

matrixInScript

public static Matrix3D matrixInScript(java.lang.String c)

makeSelId

public static java.lang.String makeSelId(Selection3D[] atoms,
                                         java.lang.String selId)

log3D

public static BA log3D(boolean isGeneric,
                       ProteinViewer pv0,
                       java.lang.String command)

showLogPanel

public static void showLogPanel(boolean isGeneric,
                                ProteinViewer pv)

run

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

Specified by:

run in interface ChRunnable

flags

public static long flags(ProteinViewer v)

supports

public static boolean supports(java.lang.String command,
                               ProteinViewer v)

getSharedHashMap

public static java.util.Map getSharedHashMap(ProteinViewer pv)

thread_addPdbId

public static java.lang.Thread thread_addPdbId(java.lang.String id_chain,
                                               Protein3d p3d,
                                               java.lang.Class proteinClass)

addPdbId

public static void addPdbId(java.lang.String id_chain,
                            Protein3d p3d,
                            java.lang.Class proteinClass)

thread_addStructure

public static java.lang.Thread thread_addStructure(java.io.File f,
                                                   Protein3d p3d,
                                                   java.lang.Class proteinClass)

addStructure

public static void addStructure(java.io.File f,
                                Protein3d p3d,
                                java.lang.Class proteinClass)

dispatchEvtPicked

public static void dispatchEvtPicked(ProteinViewer pv,
                                     int resNum,
                                     char chain,
                                     char insertion,
                                     int awtModi)

selection3dToText

public static java.lang.String selection3dToText(int viewerId,
                                                 Selection3D[] ss)

selection3dToBoolZ

public static boolean[] selection3dToBoolZ(Selection3D[] atoms,
                                           Protein p)

selection3dToFirstIdxZ

public static int selection3dToFirstIdxZ(boolean fullLength,
                                         Selection3D at,
                                         Protein p)

rangeToSelection3D

public static Selection3D[] rangeToSelection3D(int first,
                                               int last,
                                               Protein p)

toSelectionS

public static Selection3D[] toSelectionS(ResidueSelection s)

boolToSelection3D

public static Selection3D[] boolToSelection3D(boolean fullLen,
                                              boolean[] bb,
                                              int offset,
                                              Protein p,
                                              java.lang.String atoms)

rplcVars

public static byte[] rplcVars(byte[] txt,
                              Protein p)

textToSelection3D

public static Selection3D[] textToSelection3D(java.lang.Object text,
                                              Protein p)

textToSelection3D

public static Selection3D[] textToSelection3D(boolean convert_i2rn,
                                              java.lang.Object text,
                                              Protein p)

splitAtoms

public static java.lang.String[] splitAtoms(byte[] T,
                                            int B,
                                            int E)

splitAtoms

public static java.lang.String[] splitAtoms(java.lang.String s)

changeAtoms

public static void changeAtoms(boolean isGeneric,
                               Selection3D[] ss,
                               java.lang.String expr)

addOrRemove

public static Selection3D[] addOrRemove(char operation,
                                        Selection3D[] ss0,
                                        int frst,
                                        int last,
                                        char ins,
                                        char chain)

withHeterosInOneFile

public static java.io.File withHeterosInOneFile(Protein p)

highlightAtoms

public static void highlightAtoms(java.awt.Component c,
                                  int x,
                                  int y,
                                  java.lang.String type)

exampleCommands

public static java.lang.String exampleCommands(int viewerId)

initCustomizableSettings

public static void initCustomizableSettings(ProteinViewer pv)