Class TransformManager

Method Details

• homePosition

  public void homePosition(boolean resetSpin)

• setRotation

  public void setRotation(M3 m)

• resetRotation

  public void resetRotation()

• rotateXYBy

  protected void rotateXYBy(float degX, float degY, BS bsAtoms)

• rotate3DBall

  protected void rotate3DBall(float xDeg, float yDeg, BS bsAtoms)

• rotateXRadians

  public void rotateXRadians(float angleRadians, BS bsAtoms)

• rotateYRadians

  public void rotateYRadians(float angleRadians, BS bsAtoms)

• rotateZRadians

  public void rotateZRadians(float angleRadians)

• rotateAxisAngle

  public void rotateAxisAngle(V3 rotAxis, float radians)

• rotateAxisAngleRadiansFixed

  public void rotateAxisAngleRadiansFixed(float angleRadians, BS bsAtoms)

• rotateAxisAngleRadiansInternal

  public void rotateAxisAngleRadiansInternal(float radians, BS bsAtoms, M4 m4, boolean useModelKit)

• centerAt

  public void centerAt(int x, int y, P3 pt)

• percentToPixels

  public int percentToPixels(char xyz, float percent)

• setCamera

  public void setCamera(float x, float y)

• translateToPercent

  public void translateToPercent(char type, float percent)

• getTranslationXPercent

  public float getTranslationXPercent()

• getTranslationYPercent

  public float getTranslationYPercent()

• getTranslationScript

  public String getTranslationScript()

• getRotationQ

  public Quat getRotationQ()

• getRotation

  public void getRotation(M3 m)

• setZoomHeight

  public void setZoomHeight(boolean zoomHeight, boolean zoomLarge)

• zoomBy

  protected void zoomBy(int pixels)

  standard response to user mouse vertical shift-drag

  Parameters:

  pixels -

• zoomToPercent

  public void zoomToPercent(float percentZoom)

• setSlabRange

  public void setSlabRange(float value)

• slabReset

  public void slabReset()

• getSlabPercentSetting

  public int getSlabPercentSetting()

• slabToPercent

  public void slabToPercent(int percentSlab)

• depthToPercent

  public void depthToPercent(int percentDepth)

• slabInternal

  public void slabInternal(P4 plane, boolean isDepth)

• setSlabDepthInternal

  public void setSlabDepthInternal(boolean isDepth)

  set internal slab or depth from screen-based slab or depth

  Parameters:

  isDepth -

• getCameraFactors

  public P3[] getCameraFactors()

  This method returns data needed by the VRML, X3D, and IDTF/U3D exporters. It also should serve as a valuable resource for anyone adapting Jmol and wanting to know how the Jmol 11+ camera business works.

  Returns:

  a set of camera data

• getPerspectiveDepth

  public boolean getPerspectiveDepth()

• setCameraDepthPercent

  public void setCameraDepthPercent(float percent, boolean resetSlab)

  either as a percent -300, or as a float 3.0 note this percent is of zoom=100 size of model

  Parameters:

  percent -

  resetSlab -

• getCameraDepth

  public float getCameraDepth()

• defaultScaleToScreen

  public float defaultScaleToScreen(float radius)

• scaleToScreen

  public float scaleToScreen(int z, int milliAngstroms)

• unscaleToScreen

  public float unscaleToScreen(float z, float screenDistance)

• scaleToPerspective

  public float scaleToPerspective(int z, float sizeAngstroms)

• isNavigating

  public boolean isNavigating()

• finalizeTransformParameters

  public void finalizeTransformParameters()

• getZoomSetting

  public float getZoomSetting()

• calcSlabAndDepthValues

  public void calcSlabAndDepthValues()

  sets slab and depth, possibly using visual range considerations for setting the slab-clipping plane. (slab on; slab 0) superceded in navigation mode

• zValueFromPercent

  public int zValueFromPercent(int zPercent)

• calcTransformMatrix

  public void calcTransformMatrix()

• rotatePoint

  public void rotatePoint(T3 pt, T3 ptRot)

• getScreenTemp

  protected void getScreenTemp(T3 ptXYZ, P3 fScrPt)

• transformPtScr

  public void transformPtScr(T3 ptXYZ, P3i pointScreen)

  RENDERERS ONLY

  Parameters:

  ptXYZ -

  pointScreen -

• transformPtScrSafe

  public void transformPtScrSafe(T3 ptXYZ, P3i pointScreen)

• transformPtScrT3

  public void transformPtScrT3(T3 ptXYZ, T3 pointScreen)

  RENDERERS ONLY

  Parameters:

  ptXYZ -

  pointScreen -

• transformPt3f

  public void transformPt3f(T3 ptXYZ, P3 screen)

  RENDERERS ONLY

  Parameters:

  ptXYZ -

  screen -

• transformPt3fSafe

  public void transformPt3fSafe(T3 ptXYZ, P3 screen)

• transformPtNoClip

  public void transformPtNoClip(T3 ptXYZ, T3 pointScreen)

  RENDERERS ONLY

  Parameters:

  ptXYZ -

  pointScreen -

• transformPt

  public P3i transformPt(T3 ptXYZ)

  RENDERERS ONLY CAUTION! returns a POINTER TO A TEMPORARY VARIABLE

  Parameters:

  ptXYZ -

  Returns:

  POINTER TO point3iScreenTemp

• transformPtSafe

  public P3i transformPtSafe(T3 ptXYZ)

• transformPtVib

  public P3i transformPtVib(P3 ptXYZ, Vibration v)

  RENDERERS ONLY

  Parameters:

  ptXYZ -

  v -

  Returns:

  POINTER TO TEMPORARY VARIABLE (caution!) point3iScreenTemp

• transformPtVibSafe

  public P3i transformPtVibSafe(P3 ptXYZ, Vibration v)

• getVibrationPoint

  public T3 getVibrationPoint(Vibration v, T3 pt, float scale)

  return

  Parameters:

  v -

  pt - temporary value; also returned

  scale -

  Returns:

  pt

• transformPt2D

  public P3i transformPt2D(T3 ptXyp)

  RENDERERS ONLY

  Parameters:

  ptXyp -

  Returns:

  P3i

• xyzIsSlabbedInternal

  public boolean xyzIsSlabbedInternal(T3 ptRef)

• isInPosition

  public boolean isInPosition(V3 axis, float degrees)

• moveToPyMOL

  public boolean moveToPyMOL(JmolScriptEvaluator eval, float floatSecondsTotal, float[] pymolView)

• setAll

  public void setAll(P3 center, M3 m, P3 navCenter, float zoom, float xTrans, float yTrans, float rotationRadius, float pixelScale, float navDepth, float xNav, float yNav, float cameraDepth, float cameraX, float cameraY)

• stopMotion

  public void stopMotion()

• getMoveToText

  public String getMoveToText(float timespan, boolean addComments)

• setNavXYZ

  public void setNavXYZ(float x, float y, float z)

• setSpinOn

  public void setSpinOn()

• setSpinOff

  public void setSpinOff()

• setNavOn

  public void setNavOn(boolean navOn)

• setVibrationPeriod

  public void setVibrationPeriod(float period)

  sets the period of vibration -- period > 0: sets the period and turns -- period invalid input: '<' 0: sets the period but does not turn vibration on -- period = 0: sets the period to zero and turns vibration off -- period Double.NaN: uses current setting (frame change)

  Parameters:

  period -

• setVibrationT

  public void setVibrationT(float t)

• isWindowCentered

  public boolean isWindowCentered()

• setRotationRadius

  public float setRotationRadius(float angstroms, boolean doAll)

• moveRotationCenter

  public void moveRotationCenter(P3 center, boolean toXY)

• setCenterAt

  public void setCenterAt(int relativeTo, P3 pt)

• setNavFps

  protected void setNavFps(int navFps)

• calcCameraFactors

  public void calcCameraFactors()

  sets all camera and scale factors needed by the specific perspective model instantiated

• getPerspectiveFactor

  public float getPerspectiveFactor(float z)

  calculate the perspective factor based on z

  Parameters:

  z -

  Returns:

  perspectiveFactor

• unTransformPoint

  public void unTransformPoint(T3 screenPt, T3 coordPt)

• resetNavigationPoint

  protected void resetNavigationPoint(boolean doResetSlab)

  something has arisen that requires resetting of the navigation point.

  Parameters:

  doResetSlab -

• setNavigatePt

  public void setNavigatePt(P3 pt)

  scripted entry point for navigation

  Parameters:

  pt -

• getNavigationOffset

  public P3 getNavigationOffset()

• getNavPtHeight

  public float getNavPtHeight()

• getNavigationOffsetPercent

  public float getNavigationOffsetPercent(char XorY)

• getNavigationText

  protected String getNavigationText(boolean addComments)

• navigateList

  public void navigateList(JmolScriptEvaluator eval, Lst<Object[]> list)

• navigateAxis

  public void navigateAxis(V3 rotAxis, float degrees)

  scripted entry point for navigation

  Parameters:

  rotAxis -

  degrees -

• setNavigationOffsetRelative

  public void setNavigationOffsetRelative()

• setNavigationDepthPercent

  public void setNavigationDepthPercent(float percent)

  sets the position of the navigation offset relative to the model (50% center; 0% rear, 100% front; can be invalid input: '<'0 or >100)

  Parameters:

  percent -

• navTranslatePercentOrTo

  public void navTranslatePercentOrTo(float seconds, float x, float y)

  seconds invalid input: '<' 0 means "to (x,y)"; >= 0 mean "to (x%, y%)"

  Parameters:

  seconds -

  x -

  y -

• calcNavigationPoint

  protected void calcNavigationPoint()

  All the magic happens here. all navigation effects go through this method

• getNavigationState

  protected String getNavigationState()

  Returns:

  the script that defines the current navigation state