Field Detail

• vwr

  protected Viewer vwr

• DEFAULT_SPIN_Y

  static final int DEFAULT_SPIN_Y

  See Also:

  Constant Field Values

• DEFAULT_SPIN_FPS

  static final int DEFAULT_SPIN_FPS

  See Also:

  Constant Field Values

• DEFAULT_NAV_FPS

  static final int DEFAULT_NAV_FPS

  See Also:

  Constant Field Values

• DEFAULT_VISUAL_RANGE

  public static final float DEFAULT_VISUAL_RANGE

  See Also:

  Constant Field Values

• DEFAULT_STEREO_DEGREES

  public static final int DEFAULT_STEREO_DEGREES

  See Also:

  Constant Field Values

• MODE_STANDARD

  public static final int MODE_STANDARD

  See Also:

  Constant Field Values

• MODE_NAVIGATION

  public static final int MODE_NAVIGATION

  See Also:

  Constant Field Values

• MODE_PERSPECTIVE_PYMOL

  public static final int MODE_PERSPECTIVE_PYMOL

  See Also:

  Constant Field Values

• DEFAULT_PERSPECTIVE_MODEL

  static final int DEFAULT_PERSPECTIVE_MODEL

  See Also:

  Constant Field Values

• DEFAULT_PERSPECTIVE_DEPTH

  static final boolean DEFAULT_PERSPECTIVE_DEPTH

  See Also:

  Constant Field Values

• DEFAULT_CAMERA_DEPTH

  static final float DEFAULT_CAMERA_DEPTH

  See Also:

  Constant Field Values

• movetoThread

  public JmolThread movetoThread

• vibrationThread

  public JmolThread vibrationThread

• spinThread

  public JmolThread spinThread

• degreesPerRadian

  public static final double degreesPerRadian

  See Also:

  Constant Field Values

• perspectiveModel

  protected int perspectiveModel

• cameraScaleFactor

  protected float cameraScaleFactor

• referencePlaneOffset

  public float referencePlaneOffset

• aperatureAngle

  protected float aperatureAngle

• cameraDistanceFromCenter

  protected float cameraDistanceFromCenter

• modelCenterOffset

  public float modelCenterOffset

• modelRadius

  public float modelRadius

• modelRadiusPixels

  public float modelRadiusPixels

• navigationCenter

  public final javajs.util.P3 navigationCenter

• navigationOffset

  public final javajs.util.P3 navigationOffset

• navigationShiftXY

  public final javajs.util.P3 navigationShiftXY

• navigationDepthPercent

  public float navigationDepthPercent

• matrixTemp

  protected final javajs.util.M4 matrixTemp

• vectorTemp

  protected final javajs.util.V3 vectorTemp

• haveNotifiedNaN

  protected boolean haveNotifiedNaN

• spinX

  public float spinX

• spinY

  public float spinY

• spinZ

  public float spinZ

• spinFps

  public float spinFps

• navX

  public float navX

• navY

  public float navY

• navZ

  public float navZ

• navFps

  public float navFps

• isSpinInternal

  public boolean isSpinInternal

• isSpinFixed

  public boolean isSpinFixed

• isSpinSelected

  boolean isSpinSelected

• doTransform4D

  protected boolean doTransform4D

• fixedRotationOffset

  public final javajs.util.P3 fixedRotationOffset

• fixedRotationCenter

  public final javajs.util.P3 fixedRotationCenter

• perspectiveOffset

  protected final javajs.util.P3 perspectiveOffset

• perspectiveShiftXY

  protected final javajs.util.P3 perspectiveShiftXY

• rotationCenterDefault

  private final javajs.util.P3 rotationCenterDefault

• rotationRadiusDefault

  private float rotationRadiusDefault

• fixedRotationAxis

  public final javajs.util.A4 fixedRotationAxis

• internalRotationAxis

  public final javajs.util.A4 internalRotationAxis

• internalTranslation

  protected javajs.util.V3 internalTranslation

• internalRotationCenter

  final javajs.util.P3 internalRotationCenter

• internalRotationAngle

  private float internalRotationAngle

• matrixRotate

  public final javajs.util.M3 matrixRotate

• matrixTemp3

  protected final javajs.util.M3 matrixTemp3

• matrixTemp4

  private final javajs.util.M4 matrixTemp4

• axisangleT

  private final javajs.util.A4 axisangleT

• vectorT

  private final javajs.util.V3 vectorT

• vectorT2

  private final javajs.util.V3 vectorT2

• pointT2

  private final javajs.util.P3 pointT2

• MAXIMUM_ZOOM_PERCENTAGE

  public static final int MAXIMUM_ZOOM_PERCENTAGE

  See Also:

  Constant Field Values

• MAXIMUM_ZOOM_PERSPECTIVE_DEPTH

  private static final int MAXIMUM_ZOOM_PERSPECTIVE_DEPTH

  See Also:

  Constant Field Values

• rotationAxis

  javajs.util.V3 rotationAxis

• rotationRate

  float rotationRate

• fixedTranslation

  public final javajs.util.P3 fixedTranslation

• camera

  public final javajs.util.P3 camera

• cameraSetting

  public final javajs.util.P3 cameraSetting

• xTranslationFraction

  float xTranslationFraction

• yTranslationFraction

  float yTranslationFraction

• prevZoomSetting

  protected float prevZoomSetting

• previousX

  public float previousX

• previousY

  public float previousY

• zoomEnabled

  public boolean zoomEnabled

• zmPct

  public float zmPct

  zoom percent zmPct is the current displayed zoom value, AFTER rendering; may not be the same as zmPctSet, particularly if zoom is not enabled

• zmPctSet

  float zmPctSet

  zoom percent setting the current setting of zoom; may not be the same as zmPct, particularly if zoom is not enabled

• zoomRatio

  private float zoomRatio

• slabEnabled

  public boolean slabEnabled

• zShadeEnabled

  public boolean zShadeEnabled

• internalSlab

  public boolean internalSlab

• slabPercentSetting

  int slabPercentSetting

• depthPercentSetting

  int depthPercentSetting

• slabValue

  public int slabValue

• depthValue

  public int depthValue

• zSlabPercentSetting

  public int zSlabPercentSetting

• zDepthPercentSetting

  public int zDepthPercentSetting

• zSlabPoint

  public javajs.util.P3 zSlabPoint

• zSlabValue

  public int zSlabValue

• zDepthValue

  public int zDepthValue

• slabRange

  float slabRange

• slabPlane

  javajs.util.P4 slabPlane

• depthPlane

  javajs.util.P4 depthPlane

• perspectiveDepth

  public boolean perspectiveDepth

• scale3D

  protected boolean scale3D

• cameraDepth

  protected float cameraDepth

• cameraDepthSetting

  protected float cameraDepthSetting

• visualRangeAngstroms

  public float visualRangeAngstroms

• cameraDistance

  public float cameraDistance

• width

  public int width

• height

  public int height

• screenPixelCount

  public int screenPixelCount

• scalePixelsPerAngstrom

  float scalePixelsPerAngstrom

• scaleDefaultPixelsPerAngstrom

  public float scaleDefaultPixelsPerAngstrom

• scale3DAngstromsPerInch

  float scale3DAngstromsPerInch

• antialias

  protected boolean antialias

• useZoomLarge

  private boolean useZoomLarge

• zoomHeight

  private boolean zoomHeight

• screenWidth

  int screenWidth

• screenHeight

  int screenHeight

• matrixTransform

  public final javajs.util.M4 matrixTransform

• matrixTransformInv

  public final javajs.util.M4 matrixTransformInv

• fScrPt

  protected final javajs.util.P3 fScrPt

• iScrPt

  protected final javajs.util.P3i iScrPt

• ptVibTemp

  final Point3fi ptVibTemp

• navigating

  public boolean navigating

• mode

  public int mode

• defaultMode

  public int defaultMode

• untransformedPoint

  protected final javajs.util.P3 untransformedPoint

• ptTest1

  protected final javajs.util.P3 ptTest1

• ptTest2

  protected final javajs.util.P3 ptTest2

• ptTest3

  protected final javajs.util.P3 ptTest3

• aaTest1

  protected final javajs.util.A4 aaTest1

• matrixTest

  protected final javajs.util.M3 matrixTest

• spinOn

  public boolean spinOn

• navOn

  public boolean navOn

• spinIsGesture

  private boolean spinIsGesture

• vibrationOn

  public boolean vibrationOn

• vibrationPeriod

  float vibrationPeriod

• vibrationPeriodMs

  public int vibrationPeriodMs

• vibrationScale

  private float vibrationScale

• vibrationT

  private javajs.util.P3 vibrationT

• stereoMode

  STER stereoMode

• stereoColors

  int[] stereoColors

• stereoDoubleDTI

  boolean stereoDoubleDTI

• stereoDoubleFull

  boolean stereoDoubleFull

• stereoDegrees

  float stereoDegrees

• stereoRadians

  float stereoRadians

• stereoFrame

  boolean stereoFrame

• matrixStereo

  protected final javajs.util.M3 matrixStereo

• windowCentered

  public boolean windowCentered

• frameOffset

  final javajs.util.P3 frameOffset

• frameOffsets

  javajs.util.P3[] frameOffsets

• bsFrameOffsets

  public BS bsFrameOffsets

• bsSelectedAtoms

  BS bsSelectedAtoms

• ptOffset

  javajs.util.P3 ptOffset

• NAV_MODE_IGNORE

  public static final int NAV_MODE_IGNORE

  See Also:

  Constant Field Values

• NAV_MODE_ZOOMED

  public static final int NAV_MODE_ZOOMED

  See Also:

  Constant Field Values

• NAV_MODE_NONE

  public static final int NAV_MODE_NONE

  See Also:

  Constant Field Values

• NAV_MODE_RESET

  public static final int NAV_MODE_RESET

  See Also:

  Constant Field Values

• NAV_MODE_NEWXY

  public static final int NAV_MODE_NEWXY

  See Also:

  Constant Field Values

• NAV_MODE_NEWXYZ

  public static final int NAV_MODE_NEWXYZ

  See Also:

  Constant Field Values

• NAV_MODE_NEWZ

  public static final int NAV_MODE_NEWZ

  See Also:

  Constant Field Values

• navMode

  public int navMode

• zoomFactor

  public float zoomFactor

• navigationSlabOffset

  public float navigationSlabOffset

• nav

  private JmolNavigatorInterface nav

Constructor Detail

• TransformManager

  public TransformManager()

Method Detail

• getTransformManager

  static TransformManager getTransformManager​(Viewer vwr,
                                              int width,
                                              int height,
                                              boolean is4D)

• setDefaultPerspective

  void setDefaultPerspective()

• homePosition

  public void homePosition​(boolean resetSpin)

• setRotation

  public void setRotation​(javajs.util.M3 m)

• resetRotation

  public void resetRotation()

• clearThreads

  void clearThreads()

• clear

  void clear()

• setFixedRotationCenter

  private void setFixedRotationCenter​(javajs.util.T3 center)

• setRotationPointXY

  void setRotationPointXY​(javajs.util.P3 center)

• spinXYBy

  void spinXYBy​(int xDelta,
                int yDelta,
                float speed)

• rotateXYBy

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

• rotateZBy

  void rotateZBy​(int zDelta,
                 int x,
                 int y)

• applyRotation

  private void applyRotation​(javajs.util.M3 mNew,
                             boolean isInternal,
                             BS bsAtoms,
                             javajs.util.V3 translation,
                             boolean translationOnly,
                             javajs.util.M4 m4)

• 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​(javajs.util.V3 rotAxis,
                              float radians)

• rotateAxisAngle2

  private void rotateAxisAngle2​(javajs.util.A4 axisAngle,
                                BS bsAtoms)

• rotateAxisAngleAtCenter

  boolean rotateAxisAngleAtCenter​(JmolScriptEvaluator eval,
                                  javajs.util.P3 rotCenter,
                                  javajs.util.V3 rotAxis,
                                  float degreesPerSecond,
                                  float endDegrees,
                                  boolean isSpin,
                                  BS bsAtoms)

• rotateAxisAngleRadiansFixed

  public void rotateAxisAngleRadiansFixed​(float angleRadians,
                                          BS bsAtoms)

• rotateAboutPointsInternal

  boolean rotateAboutPointsInternal​(JmolScriptEvaluator eval,
                                    javajs.util.T3 point1,
                                    javajs.util.T3 point2,
                                    float degreesPerSecond,
                                    float endDegrees,
                                    boolean isClockwise,
                                    boolean isSpin,
                                    BS bsAtoms,
                                    boolean isGesture,
                                    javajs.util.V3 translation,
                                    javajs.util.Lst<javajs.util.P3> finalPoints,
                                    float[] dihedralList,
                                    javajs.util.M4 m4)

  Parameters:

  eval -

  point1 -

  point2 -

  degreesPerSecond -

  endDegrees -

  isClockwise -

  isSpin -

  bsAtoms -

  isGesture -

  translation -

  finalPoints -

  dihedralList -

  m4 -

  Returns:

  true if synchronous so that JavaScript can restart properly

• rotateAxisAngleRadiansInternal

  public void rotateAxisAngleRadiansInternal​(float radians,
                                             BS bsAtoms,
                                             javajs.util.M4 m4)

• getNewFixedRotationCenter

  void getNewFixedRotationCenter()

• setTranslationFractions

  void setTranslationFractions()

• centerAt

  public void centerAt​(int x,
                       int y,
                       javajs.util.P3 pt)

• percentToPixels

  public int percentToPixels​(char xyz,
                             float percent)

• angstromsToPixels

  int angstromsToPixels​(float distance)

• translateXYBy

  void translateXYBy​(int xDelta,
                     int yDelta)

• 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 java.lang.String getTranslationScript()

• getOrientationText

  java.lang.String getOrientationText​(int type)

• getRotationQ

  public javajs.util.Quat getRotationQ()

• getOrientationInfo

  java.util.Map<java.lang.String,​java.lang.Object> getOrientationInfo()

• getRotation

  public void getRotation​(javajs.util.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 -

• zoomByFactor

  void zoomByFactor​(float factor,
                    int x,
                    int y)

• zoomToPercent

  public void zoomToPercent​(float percentZoom)

• translateZBy

  void translateZBy​(int pixels)

• resetXYCenter

  private void resetXYCenter​(int x,
                             int y)

• zoomByPercent

  void zoomByPercent​(float percentZoom)

• setScaleAngstromsPerInch

  void setScaleAngstromsPerInch​(float angstromsPerInch)

• setSlabRange

  public void setSlabRange​(float value)

• setSlabEnabled

  void setSlabEnabled​(boolean slabEnabled)

• setZShadeEnabled

  void setZShadeEnabled​(boolean zShadeEnabled)

• setZoomEnabled

  void setZoomEnabled​(boolean zoomEnabled)

• slabReset

  public void slabReset()

• getSlabPercentSetting

  public int getSlabPercentSetting()

• slabDepthChanged

  private void slabDepthChanged()

• slabByPercentagePoints

  void slabByPercentagePoints​(int percentage)

• depthByPercentagePoints

  void depthByPercentagePoints​(int percentage)

• slabDepthByPercentagePoints

  void slabDepthByPercentagePoints​(int percentage)

• slabToPercent

  public void slabToPercent​(int percentSlab)

• depthToPercent

  public void depthToPercent​(int percentDepth)

• zSlabToPercent

  void zSlabToPercent​(int percentSlab)

• zDepthToPercent

  void zDepthToPercent​(int percentDepth)

• slabInternal

  public void slabInternal​(javajs.util.P4 plane,
                           boolean isDepth)

• setSlabDepthInternal

  public void setSlabDepthInternal​(boolean isDepth)

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

  Parameters:

  isDepth -

• getSlabDepthPlane

  private javajs.util.P4 getSlabDepthPlane​(boolean isDepth)

• getCameraFactors

  public javajs.util.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

• setPerspectiveDepth

  void setPerspectiveDepth​(boolean perspectiveDepth)

• 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()

• setScreenParameters0

  private void setScreenParameters0​(int screenWidth,
                                    int screenHeight,
                                    boolean useZoomLarge,
                                    boolean antialias,
                                    boolean resetSlab,
                                    boolean resetZoom)

• setAntialias

  void setAntialias​(boolean TF)

• defaultScaleToScreen

  public float defaultScaleToScreen​(float radius)

• resetFitToScreen

  private void resetFitToScreen​(boolean andCenter)

• scaleFitToScreen

  void scaleFitToScreen​(boolean andCenter,
                        boolean zoomLarge,
                        boolean resetSlab,
                        boolean resetZoom)

• scaleToScreen

  public float scaleToScreen​(int z,
                             int milliAngstroms)

• unscaleToScreen

  public float unscaleToScreen​(float z,
                               float screenDistance)

• scaleToPerspective

  public float scaleToPerspective​(int z,
                                  float sizeAngstroms)

• setNavigationMode

  void setNavigationMode​(boolean TF)

• 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​(javajs.util.T3 pt,
                          javajs.util.T3 ptRot)

• getScreenTemp

  protected void getScreenTemp​(javajs.util.T3 ptXYZ)

• transformPtScr

  public void transformPtScr​(javajs.util.T3 ptXYZ,
                             javajs.util.P3i pointScreen)

• transformPtScrT3

  public void transformPtScrT3​(javajs.util.T3 ptXYZ,
                               javajs.util.T3 pointScreen)

• transformPt3f

  public void transformPt3f​(javajs.util.T3 ptXYZ,
                            javajs.util.P3 screen)

• transformPtNoClip

  public void transformPtNoClip​(javajs.util.T3 ptXYZ,
                                javajs.util.T3 pointScreen)

• transformPt

  public javajs.util.P3i transformPt​(javajs.util.T3 ptXYZ)

  CAUTION! returns a POINTER TO A TEMPORARY VARIABLE

  Parameters:

  ptXYZ -

  Returns:

  POINTER TO point3iScreenTemp

• transformPtVib

  public javajs.util.P3i transformPtVib​(javajs.util.P3 ptXYZ,
                                        Vibration v)

  Parameters:

  ptXYZ -

  v -

  Returns:

  POINTER TO TEMPORARY VARIABLE (caution!) point3iScreenTemp

• getVibrationPoint

  public javajs.util.T3 getVibrationPoint​(Vibration v,
                                          javajs.util.T3 pt,
                                          float scale)

  return

  Parameters:

  v -

  pt - temporary value; also returned

  scale -

  Returns:

  pt

• transformPt2D

  public javajs.util.P3i transformPt2D​(javajs.util.T3 ptXyp)

• applyPerspective

  private javajs.util.P3i applyPerspective​(javajs.util.T3 ptXYZ,
                                           javajs.util.T3 ptRef)

  adjusts the temporary point for perspective and offsets

  Parameters:

  ptXYZ -

  ptRef -

  Returns:

  temporary point!!!

• xyzIsSlabbedInternal

  public boolean xyzIsSlabbedInternal​(javajs.util.T3 ptRef)

• move

  void move​(JmolScriptEvaluator eval,
            javajs.util.V3 dRot,
            float dZoom,
            javajs.util.V3 dTrans,
            float dSlab,
            float floatSecondsTotal,
            int fps)

• isInPosition

  public boolean isInPosition​(javajs.util.V3 axis,
                              float degrees)

• moveToPyMOL

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

• moveTo

  void moveTo​(JmolScriptEvaluator eval,
              float floatSecondsTotal,
              javajs.util.P3 center,
              javajs.util.T3 rotAxis,
              float degrees,
              javajs.util.M3 matrixEnd,
              float zoom,
              float xTrans,
              float yTrans,
              float newRotationRadius,
              javajs.util.P3 navCenter,
              float xNav,
              float yNav,
              float navDepth,
              float cameraDepth,
              float cameraX,
              float cameraY)

• setAll

  public void setAll​(javajs.util.P3 center,
                     javajs.util.M3 m,
                     javajs.util.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()

• getRotationText

  java.lang.String getRotationText()

• getMoveToText

  public java.lang.String getMoveToText​(float timespan,
                                        boolean addComments)

• getCenterText

  private java.lang.String getCenterText()

• getRotateXyzText

  private java.lang.String getRotateXyzText()

• addZoomTranslationNavigationText

  private void addZoomTranslationNavigationText​(javajs.util.SB sb)

• getRotateZyzText

  private java.lang.String getRotateZyzText​(boolean iAddComment)

• truncate0

  private static void truncate0​(javajs.util.SB sb,
                                float val)

• truncate2

  private static void truncate2​(javajs.util.SB sb,
                                float val)

• setSpinXYZ

  void setSpinXYZ​(float x,
                  float y,
                  float z)

• setSpinFps

  void setSpinFps​(int value)

• setNavXYZ

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

• clearSpin

  private void clearSpin()

• setSpinOn

  public void setSpinOn()

• setSpinOff

  public void setSpinOff()

• setSpin

  private void setSpin​(JmolScriptEvaluator eval,
                       boolean spinOn,
                       float endDegrees,
                       javajs.util.Lst<javajs.util.P3> endPositions,
                       float[] dihedralList,
                       BS bsAtoms,
                       boolean isGesture)

• setNavOn

  public void setNavOn​(boolean navOn)

• setVibrationScale

  void setVibrationScale​(float scale)

• setVibrationPeriod

  public void setVibrationPeriod​(float period)

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

  Parameters:

  period -

• setVibrationT

  public void setVibrationT​(float t)

• isVibrationOn

  boolean isVibrationOn()

• setVibrationOn

  private void setVibrationOn​(boolean vibrationOn)

• clearVibration

  private void clearVibration()

• setStereoMode2

  void setStereoMode2​(int[] twoColors)

• setStereoMode

  void setStereoMode​(STER stereoMode)

• setStereoDegrees

  void setStereoDegrees​(float stereoDegrees)

• getStereoRotationMatrix

  javajs.util.M3 getStereoRotationMatrix​(boolean stereoFrame)

• isWindowCentered

  public boolean isWindowCentered()

• setWindowCentered

  void setWindowCentered​(boolean TF)

• setRotationRadius

  public float setRotationRadius​(float angstroms,
                                 boolean doAll)

• setRotationCenterAndRadiusXYZ

  private void setRotationCenterAndRadiusXYZ​(javajs.util.T3 newCenterOfRotation,
                                             boolean andRadius)

• setNewRotationCenter

  void setNewRotationCenter​(javajs.util.P3 center,
                            boolean doScale)

• moveRotationCenter

  public void moveRotationCenter​(javajs.util.P3 center,
                                 boolean toXY)

• setCenter

  void setCenter()

• setCenterAt

  public void setCenterAt​(int relativeTo,
                          javajs.util.P3 pt)

• setFrameOffset

  void setFrameOffset​(int modelIndex)

• setSelectedTranslation

  void setSelectedTranslation​(BS bsAtoms,
                              char xyz,
                              int xy)

• setNavFps

  protected void setNavFps​(int navFps)

• calcCameraFactors

  public void calcCameraFactors()

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

• calcNavCameraFactors

  private void calcNavCameraFactors​(float offset100)

• getPerspectiveFactor

  public float getPerspectiveFactor​(float z)

  calculate the perspective factor based on z

  Parameters:

  z -

  Returns:

  perspectiveFactor

• unTransformPoint

  public void unTransformPoint​(javajs.util.T3 screenPt,
                               javajs.util.T3 coordPt)

• resetNavigationPoint

  protected void resetNavigationPoint​(boolean doResetSlab)

  something has arisen that requires resetting of the navigation point.

  Parameters:

  doResetSlab -

• setNavigatePt

  public void setNavigatePt​(javajs.util.P3 pt)

  scripted entry point for navigation

  Parameters:

  pt -

• setNavigationSlabOffsetPercent

  void setNavigationSlabOffsetPercent​(float percent)

• getNavigationOffset

  public javajs.util.P3 getNavigationOffset()

• getNavPtHeight

  public float getNavPtHeight()

• getNavigationOffsetPercent

  public float getNavigationOffsetPercent​(char XorY)

• getNavigationText

  protected java.lang.String getNavigationText​(boolean addComments)

• setScreenParameters

  void setScreenParameters​(int screenWidth,
                           int screenHeight,
                           boolean useZoomLarge,
                           boolean antialias,
                           boolean resetSlab,
                           boolean resetZoom)

• navInterrupt

  private void navInterrupt()

• getNav

  private boolean getNav()

• navigateList

  public void navigateList​(JmolScriptEvaluator eval,
                           javajs.util.Lst<java.lang.Object[]> list)

• navigateAxis

  public void navigateAxis​(javajs.util.V3 rotAxis,
                           float degrees)

  scripted entry point for navigation

  Parameters:

  rotAxis -

  degrees -

• setNavigationOffsetRelative

  public void setNavigationOffsetRelative()

• navigateKey

  void navigateKey​(int keyCode,
                   int modifiers)

  entry point for keyboard-based navigation

  Parameters:

  keyCode - 0 indicates key released

  modifiers - shift,alt,ctrl

• 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 <0 or >100)

  Parameters:

  percent -

• navTranslatePercentOrTo

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

  seconds < 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 java.lang.String getNavigationState()

  Returns:

  the script that defines the current navigation state