Package org.jmol.viewer

Class Viewer

    • Field Detail

      • testAsync

        public boolean testAsync

      • autoExit

        public boolean autoExit

      • haveDisplay

        public boolean haveDisplay

      • isJS

        public static boolean isJS

      • isJSNoAWT

        public static boolean isJSNoAWT

      • isSwingJS

        public static boolean isSwingJS

      • isWebGL

        public static boolean isWebGL

      • isSingleThreaded

        public boolean isSingleThreaded

      • queueOnHold

        public boolean queueOnHold

      • fullName

        public java.lang.String fullName

      • appletDocumentBase

        public static java.lang.String appletDocumentBase

      • appletCodeBase

        public static java.lang.String appletCodeBase

      • appletIdiomaBase

        public static java.lang.String appletIdiomaBase

      • jsDocumentBase

        public static java.lang.String jsDocumentBase

      • compiler

        public java.lang.Object compiler

      • definedAtomSets

        public java.util.Map<java.lang.String,​java.lang.Object> definedAtomSets

      • isApplet

        public boolean isApplet

      • isJNLP

        public boolean isJNLP

      • isSyntaxAndFileCheck

        public boolean isSyntaxAndFileCheck

      • isSyntaxCheck

        public boolean isSyntaxCheck

      • listCommands

        public boolean listCommands

      • mustRender

        boolean mustRender

      • htmlName

        public java.lang.String htmlName

      • appletName

        public java.lang.String appletName

      • tryPt

        public int tryPt

      • insertedCommand

        private java.lang.String insertedCommand

      • gdata

        public GData gdata

      • strJavaVendor

        public static java.lang.String strJavaVendor

      • strOSName

        public static java.lang.String strOSName

      • strJavaVersion

        public static java.lang.String strJavaVersion

      • syncId

        java.lang.String syncId

      • logFilePath

        java.lang.String logFilePath

      • allowScripting

        private boolean allowScripting

      • isPrintOnly

        public boolean isPrintOnly

      • isSignedApplet

        public boolean isSignedApplet

      • isSignedAppletLocal

        private boolean isSignedAppletLocal

      • isSilent

        private boolean isSilent

      • multiTouch

        private boolean multiTouch

      • noGraphicsAllowed

        public boolean noGraphicsAllowed

      • useCommandThread

        private boolean useCommandThread

      • commandOptions

        private java.lang.String commandOptions

      • vwrOptions

        public java.util.Map<java.lang.String,​java.lang.Object> vwrOptions

      • display

        public java.lang.Object display

      • allowArrayDotNotation

        public boolean allowArrayDotNotation

      • async

        public boolean async

      • executor

        public java.lang.Object executor

      • version_date

        private static java.lang.String version_date

      • screenWidth

        int screenWidth

      • screenHeight

        int screenHeight

      • actionStates

        final javajs.util.Lst<java.lang.String> actionStates

      • actionStatesRedo

        final javajs.util.Lst<java.lang.String> actionStatesRedo

      • defaultVdw

        VDW defaultVdw

      • chainMap

        public java.util.Map<java.lang.Object,​java.lang.Object> chainMap

      • chainList

        private javajs.util.Lst<java.lang.String> chainList

      • errorMessage

        private java.lang.String errorMessage

      • errorMessageUntranslated

        private java.lang.String errorMessageUntranslated

      • privateKey

        private double privateKey

      • dataOnly

        private boolean dataOnly

      • maximumSize

        private int maximumSize

      • gRight

        private java.lang.Object gRight
        A graphics from a "slave" stereo display that has been synchronized with this this applet.

      • isStereoSlave

        private boolean isStereoSlave
        A flag to indicate that THIS is the right-side panel of a pair of synced applets running a left-right stereo display (that would be piped into a dual-image polarized projector system such as GeoWall).

      • imageFontScaling

        public float imageFontScaling

      • antialiased

        public boolean antialiased

      • prevFrame

        private int prevFrame

      • prevMorphModel

        private float prevMorphModel

      • haveJDX

        private boolean haveJDX

      • jzt

        private javajs.api.GenericZipTools jzt

      • isPreviewOnly

        public boolean isPreviewOnly

      • headless

        public boolean headless
        determined by GraphicsEnvironment.isHeadless() from java -Djava.awt.headless=true disables command threading disables DELAY, TIMEOUT, PAUSE, LOOP, GOTO, SPIN , ANIMATION ON turns SPIN into just ROTATE

      • movableBitSet

        public javajs.util.BS movableBitSet

      • ligandModels

        java.util.Map<java.lang.String,​java.lang.Object> ligandModels

      • ligandModelSet

        java.util.Map<java.lang.String,​java.lang.Boolean> ligandModelSet

      • lastData

        private java.lang.Object[] lastData

      • motionEventNumber

        private int motionEventNumber

      • inMotion

        private boolean inMotion

      • refreshing

        private boolean refreshing

      • REFRESH_REPAINT_NO_MOTION_ONLY

        public static final int REFRESH_REPAINT_NO_MOTION_ONLY
        See Also:
        Constant Field Values

      • REFRESH_SEND_WEBGL_NEW_ORIENTATION

        public static final int REFRESH_SEND_WEBGL_NEW_ORIENTATION
        See Also:
        Constant Field Values

      • axesAreTainted

        private boolean axesAreTainted

      • captureParams

        public java.util.Map<java.lang.String,​java.lang.Object> captureParams

      • jsParams

        private java.util.Map<java.lang.String,​java.lang.Object> jsParams

      • cirChecked

        boolean cirChecked

      • hoverAtomIndex

        private int hoverAtomIndex

      • hoverText

        private java.lang.String hoverText

      • hoverLabel

        private java.lang.String hoverLabel

      • hoverEnabled

        private boolean hoverEnabled

      • currentCursor

        public int currentCursor

      • ptTemp

        private javajs.util.P3 ptTemp

      • selectionHalosEnabled

        private boolean selectionHalosEnabled

      • frankOn

        public boolean frankOn

      • noFrankEcho

        public boolean noFrankEcho

      • scriptEditorVisible

        public boolean scriptEditorVisible

      • headlessImageParams

        private java.util.Map<java.lang.String,​java.lang.Object> headlessImageParams

      • isTainted

        boolean isTainted

      • movingSelected

        private boolean movingSelected

      • showSelected

        private boolean showSelected

      • atomHighlighted

        public int atomHighlighted

      • creatingImage

        public boolean creatingImage

      • SYNC_GRAPHICS_MESSAGE

        public static final java.lang.String SYNC_GRAPHICS_MESSAGE
        See Also:
        Constant Field Values

      • SYNC_NO_GRAPHICS_MESSAGE

        public static final java.lang.String SYNC_NO_GRAPHICS_MESSAGE
        See Also:
        Constant Field Values

      • bsUserVdws

        javajs.util.BS bsUserVdws

      • userVdws

        float[] userVdws

      • userVdwMars

        int[] userVdwMars

      • currentShapeID

        private int currentShapeID

      • currentShapeState

        private java.lang.String currentShapeState

      • staticFunctions

        static final java.util.Map<java.lang.String,​JmolScriptFunction> staticFunctions

      • isKiosk

        boolean isKiosk

      • nProcessors

        public static int nProcessors

      • displayLoadErrors

        public boolean displayLoadErrors

      • isParallel

        private boolean isParallel

      • stateScriptVersionInt

        public int stateScriptVersionInt

      • timeouts

        public java.util.Map<java.lang.String,​java.lang.Object> timeouts

      • chainCaseSpecified

        private boolean chainCaseSpecified

      • logFileName

        java.lang.String logFileName

      • jsonParser

        private javajs.util.JSJSONParser jsonParser

      • macros

        private java.util.Map<java.lang.String,​java.lang.Object> macros

      • consoleFontScale

        private int consoleFontScale

    • Constructor Detail

      • Viewer

        public Viewer​(java.util.Map<java.lang.String,​java.lang.Object> info)
        new way...
        Parameters:
        info - "display" "adapter" "statusListener" "platform" "options" "fullName" "documentBase" "codeBase" "multiTouch" [options] "noGraphics" "printOnly" "previewOnly" "debug" "applet" "signedApplet" "appletProxy" "useCommandThread" "platform" [option] "backgroundTransparent" "exit" "listCommands" "check" "checkLoad" "silent" "access:READSPT" "access:NONE" "menuFile" "headlessMaxTimeMs" "headlessImage" "isDataOnly" "async"

    • Method Detail

      • finalize

        protected void finalize()
                 throws java.lang.Throwable
        Overrides:
        finalize in class java.lang.Object
        Throws:
        java.lang.Throwable

      • setInsertedCommand

        public void setInsertedCommand​(java.lang.String strScript)

      • getJmolVersion

        public static java.lang.String getJmolVersion()

      • allocateViewer

        protected static JmolViewer allocateViewer​(java.lang.Object display,
                                           JmolAdapter modelAdapter,
                                           java.lang.String fullName,
                                           java.net.URL documentBase,
                                           java.net.URL codeBase,
                                           java.lang.String commandOptions,
                                           JmolStatusListener statusListener,
                                           GenericPlatform implementedPlatform)
        old way...
        Parameters:
        display -
        modelAdapter -
        fullName -
        documentBase -
        codeBase -
        commandOptions -
        statusListener -
        implementedPlatform -
        Returns:
        JmolViewer object

      • getSmartsMatch

        public javajs.util.BS getSmartsMatch​(java.lang.String smarts,
                                     javajs.util.BS bsSelected)
                              throws java.lang.Exception
        Specified by:
        getSmartsMatch in class JmolViewer
        Throws:
        java.lang.Exception

      • getSmartsMatchForNodes

        public javajs.util.BS getSmartsMatchForNodes​(java.lang.String smarts,
                                             Node[] atoms)
                                      throws java.lang.Exception
        Throws:
        java.lang.Exception

      • getSmartsMap

        public int[][] getSmartsMap​(java.lang.String smilesOrSmarts,
                            javajs.util.BS bsSelected,
                            int flags)
                     throws java.lang.Exception
        Parameters:
        smilesOrSmarts -
        bsSelected -
        flags - can be bitwise OR of JC.SMILES_* options, in particular, JC.SMILES_TYPE_SMARTS, JC.SMILES_TYPE_SMILES, and JC.SMILES_MAP_UNIQUE
        Returns:
        map
        Throws:
        java.lang.Exception

      • setOptions

        public void setOptions​(java.util.Map<java.lang.String,​java.lang.Object> info)

      • setMaximumSize

        private void setMaximumSize​(int x)

      • setStereo

        public void setStereo​(boolean isStereoSlave,
                      java.lang.Object gRight)

      • getMenu

        public java.lang.String getMenu​(java.lang.String type)

      • resizeInnerPanel

        public int[] resizeInnerPanel​(int width,
                              int height)
        Specified by:
        resizeInnerPanel in class JmolViewer

      • resizeImage

        void resizeImage​(int width,
                 int height,
                 boolean isImageWrite,
                 boolean isExport,
                 boolean isReset)

      • getScreenDim

        public int getScreenDim()

      • setWidthHeightVar

        public void setWidthHeightVar()

      • getBoundBoxCenterX

        public int getBoundBoxCenterX()

      • getBoundBoxCenterY

        public int getBoundBoxCenterY()

      • updateWindow

        private boolean updateWindow​(int width,
                             int height)

      • getImage

        private java.lang.Object getImage​(boolean isDouble,
                                  boolean isImageWrite)
        Parameters:
        isDouble -
        isImageWrite -
        Returns:
        a java.awt.Image in the case of standard Jmol; an int[] in the case of Jmol-Android a canvas in the case of JSmol

      • beginRendering

        private void beginRendering​(boolean isDouble,
                            boolean isImageWrite)

      • render

        private void render()

      • drawImage

        private void drawImage​(java.lang.Object graphic,
                       java.lang.Object img,
                       int x,
                       int y,
                       boolean isDTI)
        Parameters:
        graphic - In JavaScript/HTML5, a Canvas.Context2d
        img -
        x -
        y -
        isDTI - DTI format -- scrunch width by factor of two

      • getScreenImage

        public java.lang.Object getScreenImage()

      • getScreenImageBuffer

        public java.lang.Object getScreenImageBuffer​(java.lang.Object g,
                                             boolean isImageWrite)
        Image.getJpgImage, ImageCreator.clipImage, getImageBytes, Viewer.renderScreenImageStereo
        Specified by:
        getScreenImageBuffer in class JmolViewer

      • evalStringWaitStatusQueued

        public java.lang.Object evalStringWaitStatusQueued​(java.lang.String returnType,
                                                   java.lang.String strScript,
                                                   java.lang.String statusList,
                                                   boolean isQuiet,
                                                   boolean isQueued)

      • popupMenu

        void popupMenu​(int x,
               int y,
               char type)

      • getModelkit

        public ModelKitPopup getModelkit​(boolean andShow)

      • getPopupMenu

        java.lang.Object getPopupMenu()

      • setMenu

        public void setMenu​(java.lang.String fileOrText,
                    boolean isFile)
        Specified by:
        setMenu in class JmolViewer

      • setStatusFrameChanged

        void setStatusFrameChanged​(boolean isVib,
                           boolean doNotify)
        Parameters:
        isVib -
        doNotify - ignored; not implemented

      • doHaveJDX

        private boolean doHaveJDX()

      • getJDXBaseModelIndex

        public int getJDXBaseModelIndex​(int modelIndex)
        get the model designated as "baseModel" in a JCamp-MOL file for example, the model used for bonding for an XYZVIB file or the model used as the base model for a mass spec file. This might then allow pointing off a peak in JSpecView to switch to the model that is involved in HNMR or CNMR
        Parameters:
        modelIndex -
        Returns:
        modelIndex

      • getJspecViewProperties

        public java.lang.Object getJspecViewProperties​(java.lang.Object myParam)

      • scriptEcho

        public void scriptEcho​(java.lang.String strEcho)

      • isScriptQueued

        private boolean isScriptQueued()

      • notifyError

        public void notifyError​(java.lang.String errType,
                        java.lang.String errMsg,
                        java.lang.String errMsgUntranslated)

      • jsEval

        public java.lang.String jsEval​(java.lang.String strEval)

      • jsEvalSV

        public SV jsEvalSV​(java.lang.String strEval)

      • setFileLoadStatus

        private void setFileLoadStatus​(FIL ptLoad,
                               java.lang.String fullPathName,
                               java.lang.String fileName,
                               java.lang.String modelName,
                               java.lang.String strError,
                               java.lang.Boolean isAsync)

      • getZapName

        public java.lang.String getZapName()

      • setStatusMeasuring

        public void setStatusMeasuring​(java.lang.String status,
                               int intInfo,
                               java.lang.String strMeasure,
                               float value)

      • notifyMinimizationStatus

        public void notifyMinimizationStatus()

      • setStatusAtomPicked

        public void setStatusAtomPicked​(int atomIndex,
                                java.lang.String info,
                                java.util.Map<java.lang.String,​java.lang.Object> map,
                                boolean andSelect)

      • getProperty

        public java.lang.Object getProperty​(java.lang.String returnType,
                                    java.lang.String infoType,
                                    java.lang.Object paramInfo)
        Specified by:
        getProperty in class JmolViewer
        Parameters:
        returnType - "JSON", "string", "readable", and anything else returns the Java object.
        Returns:
        property data -- see org.jmol.viewer.PropertyManager.java

      • notifyMouseClicked

        public int notifyMouseClicked​(int x,
                              int y,
                              int action,
                              int mode)

      • getJzt

        public javajs.api.GenericZipTools getJzt()

      • readFileAsMap

        public void readFileAsMap​(java.io.BufferedInputStream bis,
                          java.util.Map<java.lang.String,​java.lang.Object> map,
                          java.lang.String name)

      • getZipDirectoryAsString

        public java.lang.String getZipDirectoryAsString​(java.lang.String fileName)

      • getImageAsBytes

        public byte[] getImageAsBytes​(java.lang.String type,
                              int width,
                              int height,
                              int quality,
                              java.lang.String[] errMsg)
        Specified by:
        getImageAsBytes in class JmolViewer
        errMsg - TODO
        Returns:
        byte[] image, or null and an error message

      • setDisplay

        public void setDisplay​(java.lang.Object canvas)

      • newMeasurementData

        public MeasurementData newMeasurementData​(java.lang.String id,
                                          javajs.util.Lst<java.lang.Object> points)

      • checkOption2

        private boolean checkOption2​(java.lang.String key1,
                             java.lang.String key2)

      • setStartupBooleans

        private void setStartupBooleans()

      • getExportDriverList

        public java.lang.String getExportDriverList()

      • dispose

        public void dispose()
        end of life for this viewer
        Overrides:
        dispose in class JmolViewer

      • reset

        public void reset​(boolean includingSpin)

      • initialize

        public void initialize​(boolean clearUserVariables,
                       boolean isPyMOL)

      • saveModelOrientation

        void saveModelOrientation()

      • restoreModelOrientation

        void restoreModelOrientation​(int modelIndex)

      • restoreModelRotation

        void restoreModelRotation​(int modelIndex)

      • getGLmolView

        public java.lang.Object getGLmolView()
        This method is only called by JmolGLmol applet._refresh();
        Returns:
        enough data to update a WebGL view

      • setRotationRadius

        public void setRotationRadius​(float angstroms,
                              boolean doAll)

      • setCenterBitSet

        public void setCenterBitSet​(javajs.util.BS bsCenter,
                            boolean doScale)

      • setNewRotationCenter

        public void setNewRotationCenter​(javajs.util.P3 center)

      • navigate

        void navigate​(int keyWhere,
              int modifiers)

      • move

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

      • moveTo

        public void moveTo​(JmolScriptEvaluator eval,
                   float floatSecondsTotal,
                   javajs.util.P3 center,
                   javajs.util.V3 rotAxis,
                   float degrees,
                   javajs.util.M3 rotationMatrix,
                   float zoom,
                   float xTrans,
                   float yTrans,
                   float rotationRadius,
                   javajs.util.P3 navCenter,
                   float xNav,
                   float yNav,
                   float navDepth,
                   float cameraDepth,
                   float cameraX,
                   float cameraY)

      • moveUpdate

        public void moveUpdate​(float floatSecondsTotal)

      • navigatePt

        public void navigatePt​(javajs.util.P3 center)

      • navigateAxis

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

      • navTranslatePercent

        public void navTranslatePercent​(float x,
                                float y)

      • zoomBy

        void zoomBy​(int pixels)

      • zoomByFactor

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

      • rotateXYBy

        void rotateXYBy​(float degX,
                float degY)

      • spinXYBy

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

      • rotateZBy

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

      • rotateSelected

        void rotateSelected​(float deltaX,
                    float deltaY,
                    javajs.util.BS bsSelected)

      • setMovableBitSet

        private javajs.util.BS setMovableBitSet​(javajs.util.BS bsSelected,
                                        boolean checkMolecule)

      • translateXYBy

        public void translateXYBy​(int xDelta,
                          int yDelta)

      • translate

        public void translate​(char xyz,
                      float x,
                      char type,
                      javajs.util.BS bsAtoms)

      • slabByPixels

        void slabByPixels​(int pixels)

      • depthByPixels

        void depthByPixels​(int pixels)

      • slabDepthByPixels

        void slabDepthByPixels​(int pixels)

      • finalizeTransformParameters

        public void finalizeTransformParameters()

      • getScalePixelsPerAngstrom

        public float getScalePixelsPerAngstrom​(boolean asAntialiased)

      • setSpin

        public void setSpin​(java.lang.String key,
                    int value)

      • getSpinState

        public java.lang.String getSpinState()

      • getOrientationText

        public java.lang.Object getOrientationText​(int type,
                                           java.lang.String name,
                                           javajs.util.BS bs)
        Parameters:
        type -
        name -
        bs -
        Returns:
        String or Quat or P3[]

      • getCurrentColorRange

        public float[] getCurrentColorRange()

      • setDefaultColors

        private void setDefaultColors​(boolean isRasmol)

      • setElementArgb

        public void setElementArgb​(int elementNumber,
                           int argb)

      • setObjectColor

        void setObjectColor​(java.lang.String name,
                    java.lang.String colorName)

      • setObjectVisibility

        public void setObjectVisibility​(java.lang.String name,
                                boolean b)

      • setObjectArgb

        public void setObjectArgb​(java.lang.String name,
                          int argb)

      • setBackgroundImage

        public void setBackgroundImage​(java.lang.String fileName,
                               java.lang.Object image)

      • getObjectColix

        public short getObjectColix​(int objId)

      • setColorBackground

        public void setColorBackground​(java.lang.String colorName)
        Specified by:
        setColorBackground in class JmolViewer

      • setObjectMad10

        public void setObjectMad10​(int iShape,
                           java.lang.String name,
                           int mad10)
        input here is a JC.SHAPE_xxxx identifier
        Parameters:
        iShape -
        name -
        mad10 -

      • getObjectMad10

        public int getObjectMad10​(int objId)
        Parameters:
        objId -
        Returns:
        mad10

      • setPropertyColorScheme

        public void setPropertyColorScheme​(java.lang.String scheme,
                                   boolean isTranslucent,
                                   boolean isOverloaded)

      • getLightingState

        public java.lang.String getLightingState()

      • getColorPointForPropertyValue

        public javajs.util.P3 getColorPointForPropertyValue​(float val)

      • select

        public void select​(javajs.util.BS bs,
                   boolean isGroup,
                   int addRemove,
                   boolean isQuiet)

      • selectBonds

        public void selectBonds​(javajs.util.BS bs)

      • displayAtoms

        public void displayAtoms​(javajs.util.BS bs,
                         boolean isDisplay,
                         boolean isGroup,
                         int addRemove,
                         boolean isQuiet)

      • getUndeletedGroupAtomBits

        private javajs.util.BS getUndeletedGroupAtomBits​(javajs.util.BS bs)

      • reportSelection

        void reportSelection​(java.lang.String msg)

      • clearAtomSets

        private void clearAtomSets()

      • getDefinedAtomSet

        public javajs.util.BS getDefinedAtomSet​(java.lang.String name)

      • bsA

        public javajs.util.BS bsA()

      • getAtomBitSetEval

        javajs.util.BS getAtomBitSetEval​(JmolScriptEvaluator eval,
                                 java.lang.Object atomExpression)

      • processTwoPointGesture

        public void processTwoPointGesture​(float[][][] touches)

      • processMouseEvent

        public boolean processMouseEvent​(int id,
                                 int x,
                                 int y,
                                 int modifiers,
                                 long time)

      • getRubberBandSelection

        public Rectangle getRubberBandSelection()

      • isBound

        public boolean isBound​(int mouseAction,
                       int jmolAction)

      • getCursorX

        public int getCursorX()

      • getCursorY

        public int getCursorY()

      • getDefaultDirectory

        public java.lang.String getDefaultDirectory()

      • getLocalUrl

        public java.lang.String getLocalUrl​(java.lang.String fileName)

      • getFileAsString

        public java.lang.String getFileAsString​(java.lang.String fileName)

      • getBufferedInputStream

        public java.io.BufferedInputStream getBufferedInputStream​(java.lang.String fullPathName)
        Specified by:
        getBufferedInputStream in interface AtomDataServer

      • setLoadParameters

        public java.util.Map<java.lang.String,​java.lang.Object> setLoadParameters​(java.util.Map<java.lang.String,​java.lang.Object> htParams,
                                                                                boolean isAppend)

      • openFileAsyncSpecial

        public void openFileAsyncSpecial​(java.lang.String fileName,
                                 int flags)
        opens a file as a model, a script, or a surface via the creation of a script that is queued \t at the beginning disallows script option - used by JmolFileDropper and JmolPanel file-open actions - sets up a script to load the file. Called from (JSmolCore.js)Jmol.$appEvent(,,"drop").reader.onloadend()
        Specified by:
        openFileAsyncSpecial in class JmolViewer
        Parameters:
        fileName -
        flags - 1=pdbCartoons, 2=no scripting, 4=append, 8=fileOpen, 16=fileDropped

      • openFileDropped

        public void openFileDropped​(java.lang.String fname,
                            boolean checkDims)

      • openFile

        public java.lang.String openFile​(java.lang.String fileName)
        for JmolSimpleViewer -- external applications only (and no-script JavaScript)
        Specified by:
        openFile in class JmolViewer
        Parameters:
        fileName -
        Returns:
        null or error

      • openFiles

        public java.lang.String openFiles​(java.lang.String[] fileNames)
        for JmolSimpleViewer -- external applications only
        Specified by:
        openFiles in class JmolViewer
        Parameters:
        fileNames -
        Returns:
        null or error

      • openReader

        public java.lang.String openReader​(java.lang.String fullPathName,
                                   java.lang.String fileName,
                                   java.lang.Object reader)
        Opens the file, given an already-created reader.
        Specified by:
        openReader in class JmolViewer
        Parameters:
        fullPathName -
        fileName - name without path or can just be null
        reader - could be Reader, BufferedInputStream, or byte[]
        Returns:
        null or error message

      • openDOM

        public java.lang.String openDOM​(java.lang.Object DOMNode)
        applet DOM method -- does not preserve state
        Specified by:
        openDOM in class JmolViewer
        Parameters:
        DOMNode -
        Returns:
        null or error

      • loadModelFromFileRepaint

        private java.lang.String loadModelFromFileRepaint​(java.lang.String fullPathName,
                                                  java.lang.String fileName,
                                                  java.lang.String[] fileNames,
                                                  java.lang.Object reader)
        for JmolSimpleViewer -- external applications only (and no-script JavaScript)
        Parameters:
        fullPathName -
        fileName -
        fileNames -
        reader -
        Returns:
        error message or null

      • loadModelFromFile

        public java.lang.String loadModelFromFile​(java.lang.String fullPathName,
                                          java.lang.String fileName,
                                          java.lang.String[] fileNames,
                                          java.lang.Object reader,
                                          boolean isAppend,
                                          java.util.Map<java.lang.String,​java.lang.Object> htParams,
                                          javajs.util.SB loadScript,
                                          javajs.util.SB sOptions,
                                          int tokType,
                                          java.lang.String filecat)
        Used by the ScriptEvaluator LOAD command to open one or more files. Now necessary for EVERY load of a file, as loadScript must be passed to the ModelLoader.
        Parameters:
        fullPathName - may be null; used only when reader != null
        fileName - must not be null
        fileNames - when present, reader is ignored
        reader - may be a Reader, BufferedReader, byte[], or BufferedInputStream
        isAppend -
        htParams -
        loadScript -
        sOptions -
        tokType -
        filecat - + or null, -, or space
        Returns:
        null or error

      • setLigandModel

        public void setLigandModel​(java.lang.String key,
                           java.lang.String data)

      • getLigandModel

        public java.lang.Object getLigandModel​(java.lang.String id,
                                       java.lang.String prefix,
                                       java.lang.String suffix,
                                       java.lang.String terminator)
        obtain CIF data for a ligand for purposes of adding hydrogens or for any other purpose in terms of saving a data set for a file in a state
        Parameters:
        id - unique key; if null, clear "bad" entries from the set.
        prefix -
        suffix - or fileName
        terminator - Only save to this if not null
        Returns:
        a ligand model or a string if just file data or null

      • openFileFull

        private java.lang.Object openFileFull​(java.lang.String fileName,
                                      boolean isAppend,
                                      java.util.Map<java.lang.String,​java.lang.Object> htParams,
                                      javajs.util.SB loadScript)
        does NOT repaint
        Parameters:
        fileName -
        isAppend -
        htParams -
        loadScript - only necessary for string reading
        Returns:
        an AtomSetCollection or a String (error)

      • openStringInline

        public java.lang.String openStringInline​(java.lang.String strModel)
        only used by file dropper.
        Specified by:
        openStringInline in class JmolViewer

      • loadInline

        public java.lang.String loadInline​(java.lang.String strModel)
        from Applet and external applications only
        Specified by:
        loadInline in class JmolViewer

      • loadInline

        public java.lang.String loadInline​(java.lang.String strModel,
                                   char newLine)
        external apps only
        Specified by:
        loadInline in class JmolViewer

      • loadInlineAppend

        public java.lang.String loadInlineAppend​(java.lang.String strModel,
                                         boolean isAppend)
        used by applet and console
        Specified by:
        loadInlineAppend in class JmolViewer

      • loadInlineScriptRepaint

        private java.lang.String loadInlineScriptRepaint​(java.lang.String strModel,
                                                 char newLine,
                                                 boolean isAppend)

      • loadInline

        public java.lang.String loadInline​(java.lang.String[] arrayModels)
        external apps only
        Specified by:
        loadInline in class JmolViewer

      • loadInline

        public java.lang.String loadInline​(java.lang.String[] arrayModels,
                                   boolean isAppend)
        external apps and applet only
        Specified by:
        loadInline in class JmolViewer
        Parameters:
        arrayModels - and array of models, each of which is a String
        Returns:
        null or error message

      • loadInline

        public java.lang.String loadInline​(java.util.List<java.lang.Object> arrayData,
                                   boolean isAppend)
        External applications only; does not preserve state -- intentionally!
        Specified by:
        loadInline in class JmolViewer
        Parameters:
        arrayData -
        isAppend -
        Returns:
        null or error string

      • loadInlineScript

        private java.lang.String loadInlineScript​(java.lang.String strModel,
                                          char newLine,
                                          boolean isAppend,
                                          java.util.Map<java.lang.String,​java.lang.Object> htParams)
        used by loadInline and openFileFull
        Parameters:
        strModel -
        newLine -
        isAppend -
        htParams -
        Returns:
        null or error message

      • fixInlineString

        public static java.lang.String fixInlineString​(java.lang.String strModel,
                                               char newLine)

      • openStringInlineParamsAppend

        public java.lang.String openStringInlineParamsAppend​(java.lang.String strModel,
                                                     java.util.Map<java.lang.String,​java.lang.Object> htParams,
                                                     boolean isAppend)
        Only used for adding hydrogen atoms and adding the model kit methane model; not part of the public interface.
        Parameters:
        strModel -
        htParams -
        isAppend -
        Returns:
        null or error string

      • openStringsInlineParamsAppend

        private java.lang.String openStringsInlineParamsAppend​(java.lang.String[] arrayModels,
                                                       java.util.Map<java.lang.String,​java.lang.Object> htParams,
                                                       boolean isAppend)
        opens multiple files inline; does NOT repaint
        Parameters:
        arrayModels -
        htParams -
        isAppend -
        Returns:
        null or error message

      • getInlineChar

        public char getInlineChar()

      • getDataSeparator

        java.lang.String getDataSeparator()

      • createModelSetAndReturnError

        private java.lang.String createModelSetAndReturnError​(java.lang.Object atomSetCollection,
                                                      boolean isAppend,
                                                      javajs.util.SB loadScript,
                                                      java.util.Map<java.lang.String,​java.lang.Object> htParams)
        finally(!) we are ready to create the "model set" from the "atom set collection" - does NOT repaint
        Parameters:
        atomSetCollection -
        isAppend -
        loadScript - if null, then some special method like DOM; turn of preserveState
        htParams -
        Returns:
        errMsg

      • loadAtomDataAndReturnError

        private java.lang.String loadAtomDataAndReturnError​(java.lang.Object atomSetCollection,
                                                    int tokType)
        or just apply the data to the current model set
        Parameters:
        atomSetCollection -
        tokType -
        Returns:
        error or null

      • getCurrentFileAsString

        public java.lang.String getCurrentFileAsString​(java.lang.String state)

      • getFullPathNameOrError

        public java.lang.String[] getFullPathNameOrError​(java.lang.String filename)
        Parameters:
        filename -
        Returns:
        String[2] where [0] is fullpathname and [1] is error message or null

      • getFileAsString3

        public java.lang.String getFileAsString3​(java.lang.String name,
                                         boolean checkProtected,
                                         java.lang.String state)

      • getFileAsString4

        public java.lang.String getFileAsString4​(java.lang.String name,
                                         int nBytesMax,
                                         boolean doSpecialLoad,
                                         boolean allowBinary,
                                         boolean checkProtected,
                                         java.lang.String state)

      • getAsciiFileOrNull

        public java.lang.String getAsciiFileOrNull​(java.lang.String name)

      • autoCalculate

        public void autoCalculate​(int tokProperty,
                          java.lang.String dataType)

      • calculateStraightness

        public void calculateStraightness()

      • calculateSurface

        public javajs.util.P3[] calculateSurface​(javajs.util.BS bsSelected,
                                         float envelopeRadius)

      • getStructureList

        public java.util.Map<STR,​float[]> getStructureList()

      • setStructureList

        public void setStructureList​(float[] list,
                             STR type)

      • calculateStructures

        public java.lang.String calculateStructures​(javajs.util.BS bsAtoms,
                                            boolean asDSSP,
                                            boolean setStructure,
                                            int version)
        Parameters:
        bsAtoms -
        asDSSP -
        setStructure - to actually change structures
        version -
        Returns:
        structure string from DSSP

      • addStateScript

        public StateScript addStateScript​(java.lang.String script,
                                  boolean addFrameNumber,
                                  boolean postDefinitions)

      • getMinimizer

        public Minimizer getMinimizer​(boolean createNew)

      • clearModelDependentObjects

        public void clearModelDependentObjects()

      • zap

        public void zap​(boolean notify,
                boolean resetUndo,
                boolean zapModelKit)

      • loadDefaultModelKit

        private void loadDefaultModelKit​(java.util.Map<java.lang.String,​java.lang.Object> htParams)

      • zapMsg

        private void zapMsg​(java.lang.String msg)

      • echoMessage

        void echoMessage​(java.lang.String msg)

      • initializeModel

        private void initializeModel​(boolean isAppend)

      • startHoverWatcher

        public void startHoverWatcher​(boolean tf)

      • getUnitCellInfoText

        public java.lang.String getUnitCellInfoText()

      • getUnitCellInfo

        public float getUnitCellInfo​(int infoType)

      • getV0abc

        public javajs.util.T3[] getV0abc​(int iModel,
                                 java.lang.Object def)
        convert string abc;offset or M3 or M4 to origin and three vectors -- a, b, c. The string can be preceded by ! for "reverse of". For example, "!a-b,-5a-5b,-c;7/8,0,1/8" offset is optional, but it still needs a semicolon: "a/2,b/2,c;"
        Parameters:
        iModel -
        def - a string or an M3 or M4
        Returns:
        vectors [origin a b c]

      • getPolymerPointsAndVectors

        public void getPolymerPointsAndVectors​(javajs.util.BS bs,
                                       javajs.util.Lst<javajs.util.P3[]> vList)

      • getHybridizationAndAxes

        public java.lang.String getHybridizationAndAxes​(int atomIndex,
                                                javajs.util.V3 z,
                                                javajs.util.V3 x,
                                                java.lang.String lcaoType)

      • getAllAtoms

        public javajs.util.BS getAllAtoms()

      • getModelUndeletedAtomsBitSet

        public javajs.util.BS getModelUndeletedAtomsBitSet​(int modelIndex)

      • getModelUndeletedAtomsBitSetBs

        public javajs.util.BS getModelUndeletedAtomsBitSetBs​(javajs.util.BS bsModels)

      • calcBoundBoxDimensions

        public void calcBoundBoxDimensions​(javajs.util.BS bs,
                                   float scale)

      • getModelProperties

        public java.util.Properties getModelProperties​(int modelIndex)
        Specified by:
        getModelProperties in class JmolViewer

      • getModelForAtomIndex

        public Model getModelForAtomIndex​(int iatom)

      • getModelSetAuxiliaryInfo

        public java.util.Map<java.lang.String,​java.lang.Object> getModelSetAuxiliaryInfo()
        Specified by:
        getModelSetAuxiliaryInfo in class JmolViewer

      • getModelFileNumber

        public int getModelFileNumber​(int modelIndex)

      • getModelName

        public java.lang.String getModelName​(int modelIndex)
        Specified by:
        getModelName in class JmolViewer

      • modelHasVibrationVectors

        public boolean modelHasVibrationVectors​(int modelIndex)

      • getBondsForSelectedAtoms

        public javajs.util.BS getBondsForSelectedAtoms​(javajs.util.BS bsAtoms)

      • frankClicked

        public boolean frankClicked​(int x,
                            int y)

      • frankClickedModelKit

        public boolean frankClickedModelKit​(int x,
                                    int y)

      • findNearestAtomIndexMovable

        public int findNearestAtomIndexMovable​(int x,
                                       int y,
                                       boolean mustBeMovable)

      • toCartesian

        public void toCartesian​(javajs.util.T3 pt,
                        boolean ignoreOffset)
        absolute or relative to origin of UNITCELL {x y z}
        Parameters:
        pt -
        ignoreOffset - TODO

      • toFractional

        public void toFractional​(javajs.util.T3 pt,
                         boolean ignoreOffset)
        Parameters:
        pt -
        ignoreOffset - set true for relative to {0 0 0}; otherwise relative to origin of UNITCELL {x y z}

      • toUnitCell

        public void toUnitCell​(javajs.util.P3 pt,
                       javajs.util.P3 offset)
        relative to origin without regard to UNITCELL {x y z}
        Parameters:
        pt -
        offset -

      • setCurrentCage

        public void setCurrentCage​(java.lang.String isosurfaceId)

      • addUnitCellOffset

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

      • setAtomData

        public void setAtomData​(int type,
                        java.lang.String name,
                        java.lang.String coordinateData,
                        boolean isDefault)

      • setApplySymmetryToBonds

        void setApplySymmetryToBonds​(boolean TF)

      • getAtomsNearPt

        public javajs.util.BS getAtomsNearPt​(float distance,
                                     javajs.util.P3 coord)

      • getBranchBitSet

        public javajs.util.BS getBranchBitSet​(int atomIndex,
                                      int atomIndexNot,
                                      boolean allowCyclic)
        given a set of atoms, a subset of atoms to test, two atoms that start the branch, and whether or not to allow the branch to cycle back on itself,deliver the set of atoms constituting this branch.
        Parameters:
        atomIndex -
        atomIndexNot -
        allowCyclic -
        Returns:
        bitset for this branch

      • getFileHeader

        java.lang.String getFileHeader()

      • getFileData

        java.lang.Object getFileData()

      • getCifData

        public java.util.Map<java.lang.String,​java.lang.Object> getCifData​(int modelIndex)

      • readCifData

        public java.util.Map<java.lang.String,​java.lang.Object> readCifData​(java.lang.String fileName,
                                                                          java.lang.String type)

      • readCifData

        public java.util.Map<java.lang.String,​java.lang.Object> readCifData​(java.lang.String fileName,
                                                                          java.lang.Object rdrOrStringData,
                                                                          java.lang.String type)
        Specified by:
        readCifData in interface AtomDataServer

      • getWrappedStateScript

        public java.lang.String getWrappedStateScript()

      • getStateInfo3

        public java.lang.String getStateInfo3​(java.lang.String type,
                                      int width,
                                      int height)

      • getStructureState

        public java.lang.String getStructureState()

      • getCoordinateState

        public java.lang.String getCoordinateState​(javajs.util.BS bsSelected)

      • setCurrentColorRange

        public void setCurrentColorRange​(java.lang.String label)

      • setData

        public void setData​(java.lang.String key,
                    java.lang.Object[] data,
                    int dataType,
                    int matchField,
                    int matchFieldColumnCount,
                    int dataField,
                    int dataFieldColumnCount)
        A general-purpose data storage method. Note that matchFieldCount and dataFieldCount should both be positive or both be negative.
        Parameters:
        key - a simple key name for the data, starting with "property_" if user-defined
        data - data[0] -- label data[1] -- string or float[] or float[][] or float[][][] data[2] -- selection bitset or int[] atomMap when field > 0 data[3] -- arrayDepth 0(String),1(float[]),2(float[][]),3(float[][][]) or -1 to indidate that it is set by data type data[4] -- Boolean.TRUE == saveInState
        dataType - see JmolDataManager interface
        matchField - if positive, data must match atomNo in this column if 0, no match column
        matchFieldColumnCount - if positive, this number of characters in match column if 0, reference is to tokens, not characters
        dataField - if positive, column containing the data if 0, values are a simple list; clear the data if Integer.MAX_VALUE, values are a simple list; don't clear the data if Integer.MIN_VALUE, have one SINGLE data value for all selected atoms
        dataFieldColumnCount - if positive, this number of characters in data column if 0, reference is to tokens, not characters

      • getDataObj

        public java.lang.Object getDataObj​(java.lang.String key,
                                   javajs.util.BS bsSelected,
                                   int dataType)
        Retrieve a data object
        Parameters:
        key -
        bsSelected - selected atoms; for DATA_AF only
        dataType - see JmolDataManager interface
        Returns:
        data object data[0] -- label (same as key) data[1] -- string or float[] or float[][] or float[][][] data[2] -- selection bitset or int[] atomMap when field > 0 data[3] -- arrayDepth 0(String),1(float[]),2(float[][]),3(float[][][]) or -1 to indicate that it is set by data type data[4] -- Boolean.TRUE == saveInState

      • autoHbond

        public int autoHbond​(javajs.util.BS bsFrom,
                     javajs.util.BS bsTo,
                     boolean onlyIfHaveCalculated)

      • getDefaultMeasurementLabel

        public java.lang.String getDefaultMeasurementLabel​(int nPoints)

      • getMeasurementInfoAsString

        public java.lang.String getMeasurementInfoAsString()

      • clearAllMeasurements

        public void clearAllMeasurements()

      • setAnimation

        public void setAnimation​(int tok)

      • setAnimationMode

        private void setAnimationMode​(java.lang.String mode)

      • setAnimationOn

        public void setAnimationOn​(boolean animationOn)

      • setAnimationRange

        public void setAnimationRange​(int modelIndex1,
                              int modelIndex2)

      • getFrameAtoms

        public javajs.util.BS getFrameAtoms()

      • defineAtomSets

        public void defineAtomSets​(java.util.Map<java.lang.String,​java.lang.Object> info)

      • setAnimDisplay

        public void setAnimDisplay​(javajs.util.BS bs)

      • setCurrentModelIndex

        public void setCurrentModelIndex​(int modelIndex)

      • getTrajectoryState

        public java.lang.String getTrajectoryState()

      • setFrameOffsets

        public void setFrameOffsets​(javajs.util.BS bsAtoms,
                            boolean isFull)

      • setCurrentModelIndexClear

        public void setCurrentModelIndexClear​(int modelIndex,
                                      boolean clearBackground)

      • haveFileSet

        public boolean haveFileSet()

      • setBackgroundModelIndex

        public void setBackgroundModelIndex​(int modelIndex)

      • setFrameVariables

        void setFrameVariables()

      • getInMotion

        public boolean getInMotion​(boolean includeAnim)

      • setInMotion

        public void setInMotion​(boolean inMotion)
        Specified by:
        setInMotion in class JmolViewer

      • setRefreshing

        private void setRefreshing​(boolean TF)

      • getRefreshing

        public boolean getRefreshing()

      • pushHoldRepaintWhy

        public void pushHoldRepaintWhy​(java.lang.String why)
        Parameters:
        why -

      • popHoldRepaint

        public void popHoldRepaint​(java.lang.String why)
        Specified by:
        popHoldRepaint in class JmolViewer

      • refresh

        public void refresh​(int mode,
                    java.lang.String strWhy)
        initiate a repaint/update sequence if it has not already been requested. invoked whenever any operation causes changes that require new rendering. The repaint/update sequence will only be invoked if (a) no repaint is already pending and (b) there is no hold flag set in repaintManager. Sequence is as follows: 1) RepaintManager.refresh() checks flags and then calls Viewer.repaint() 2) Viewer.repaint() invokes display.repaint(), provided display is not null (headless) 3) The system responds with an invocation of Jmol.update(Graphics g), which we are routing through Jmol.paint(Graphics g). 4) Jmol.update invokes Viewer.setScreenDimensions(size), which makes the necessary changes in parameters for any new window size. 5) Jmol.update invokes Viewer.renderScreenImage(g, size, rectClip) 6) Viewer.renderScreenImage checks object visibility, invokes render1 to do the actual creation of the image pixel map and send it to the screen, and then invokes repaintView() 7) Viewer.repaintView() invokes RepaintManager.repaintDone(), to clear the flags and then use notify() to release any threads holding on wait().
        Specified by:
        refresh in class JmolViewer
        Parameters:
        mode - REFRESH_REPAINT: ONLY do a repaint -- no syncing REFRESH_SYNC: mouse motion requiring synchronization -- not going through Eval so we bypass Eval and mainline on the other vwr! Also called from j2sApplet.js REFRESH_REPAINT_SYNC_MASK: same as REFRESH_REPAINT, but not WebGL REFRESH_NO_MOTION_ONLY: refresh only if not in motion REFRESH_SEND_WEBGL_NEW_ORIENTATION: send WebGL a "new orientation" command at the end of a script using html5applet._refresh()
        strWhy - debugging or for passing mouse command when using REFRESH_SYNC

      • requestRepaintAndWait

        public void requestRepaintAndWait​(java.lang.String why)

      • clearShapeRenderers

        public void clearShapeRenderers()

      • isRepaintPending

        public boolean isRepaintPending()

      • areAxesTainted

        public boolean areAxesTainted()

      • generateOutputForExport

        public java.lang.String generateOutputForExport​(java.util.Map<java.lang.String,​java.lang.Object> params)
        Description copied from class: JmolViewer
        for POV-Ray
        Specified by:
        generateOutputForExport in class JmolViewer
        Returns:
        INI file

      • clearRepaintManager

        private void clearRepaintManager​(int iShape)

      • renderScreenImage

        public void renderScreenImage​(java.lang.Object g,
                              int width,
                              int height)
        JmolViewer interface uses this, but that is all
        Specified by:
        renderScreenImage in class JmolViewer

      • renderScreenImageStereo

        public void renderScreenImageStereo​(java.lang.Object gLeft,
                                    boolean checkStereoSlave,
                                    int width,
                                    int height)

      • updateJS

        public void updateJS()
        for JavaScript only

      • updateJSView

        private void updateJSView​(int imodel,
                          int iatom)
        File has been loaded or model has been changed or atom picked. This is a call to Jmol.View for view sets (new in Jmol 14.1.8)
        Parameters:
        imodel -
        iatom -

      • evalFile

        public java.lang.String evalFile​(java.lang.String strFilename)
        Specified by:
        evalFile in class JmolViewer

      • getInsertedCommand

        public java.lang.String getInsertedCommand()

      • script

        public java.lang.String script​(java.lang.String strScript)
        Specified by:
        script in class JmolViewer

      • evalString

        public java.lang.String evalString​(java.lang.String strScript)
        Specified by:
        evalString in class JmolViewer

      • evalStringQuiet

        public java.lang.String evalStringQuiet​(java.lang.String strScript)
        Specified by:
        evalStringQuiet in class JmolViewer

      • evalStringQuietSync

        public java.lang.String evalStringQuietSync​(java.lang.String strScript,
                                            boolean isQuiet,
                                            boolean allowSyncScript)

      • clearScriptQueue

        public void clearScriptQueue()

      • setScriptQueue

        private void setScriptQueue​(boolean TF)

      • checkHalt

        public boolean checkHalt​(java.lang.String str,
                         boolean isInsert)
        Specified by:
        checkHalt in class JmolViewer

      • scriptWait

        public java.lang.String scriptWait​(java.lang.String strScript)
        Specified by:
        scriptWait in class JmolViewer

      • scriptWaitStatus

        public java.lang.Object scriptWaitStatus​(java.lang.String strScript,
                                         java.lang.String statusList)
        Specified by:
        scriptWaitStatus in class JmolViewer

      • evalWait

        private java.lang.Object evalWait​(java.lang.String returnType,
                                  java.lang.String strScript,
                                  java.lang.String statusList)

      • exitJmol

        public void exitJmol()

      • scriptCheckRet

        private java.lang.Object scriptCheckRet​(java.lang.String strScript,
                                        boolean returnContext)

      • scriptCheck

        public java.lang.Object scriptCheck​(java.lang.String strScript)
        Specified by:
        scriptCheck in class JmolViewer

      • pauseScriptExecution

        public void pauseScriptExecution()

      • resolveDatabaseFormat

        java.lang.String resolveDatabaseFormat​(java.lang.String fileName)

      • hasDatabasePrefix

        public static boolean hasDatabasePrefix​(java.lang.String fileName)

      • isDatabaseCode

        public static boolean isDatabaseCode​(char ch)

      • setLoadFormat

        public java.lang.Object setLoadFormat​(java.lang.String name,
                                      char type,
                                      boolean withPrefix)
        Jmol will either specify a type or look for it in the first character, making sure it is found using isDatabaseCode() first. Starting with Jmol 13.1.13, we allow a generalized search using =xxx= where xxx is a known or user-specified database designation.
        Parameters:
        name -
        type - a character to distinguish the type of file, '?' means we are just doing an isosurface check
        withPrefix -
        Returns:
        String or String[]

      • checkCIR

        private void checkCIR​(boolean forceCheck)
        Check to see if the resolver is working
        Parameters:
        forceCheck -

      • getStandardLabelFormat

        public java.lang.String getStandardLabelFormat​(int type)

      • getAdditionalHydrogens

        public javajs.util.P3[] getAdditionalHydrogens​(javajs.util.BS bsAtoms,
                                               javajs.util.Lst<Atom> vConnections,
                                               int flags)

      • setMarBond

        public void setMarBond​(short marBond)
        Specified by:
        setMarBond in class JmolViewer

      • setHoverLabel

        public void setHoverLabel​(java.lang.String strLabel)

      • setHoverEnabled

        private void setHoverEnabled​(boolean tf)

      • hoverOn

        void hoverOn​(int atomIndex,
             boolean isLabel)

      • hoverOnPt

        public void hoverOnPt​(int x,
                      int y,
                      java.lang.String text,
                      java.lang.String id,
                      javajs.util.T3 pt)
        Hover over an arbitrary point.
        Parameters:
        x -
        y -
        text -
        id - optional id to set _objecthovered to
        pt - optional pt to set "hovered" to

      • hoverOff

        void hoverOff()

      • setDebugScript

        public void setDebugScript​(boolean debugScript)
        Specified by:
        setDebugScript in class JmolViewer

      • clearClickCount

        void clearClickCount()

      • setCursor

        public void setCursor​(int cursor)

      • setPickingMode

        void setPickingMode​(java.lang.String strMode,
                    int pickingMode)

      • getPickingMode

        public int getPickingMode()

      • setPickingStyle

        void setPickingStyle​(java.lang.String style,
                     int pickingStyle)

      • getDrawHover

        public boolean getDrawHover()

      • getAtomInfo

        public java.lang.String getAtomInfo​(int atomOrPointIndex)

      • getAtomInfoXYZ

        private java.lang.String getAtomInfoXYZ​(int atomIndex,
                                        boolean useChimeFormat)

      • setSync

        private void setSync()

      • getStatusChanged

        public javajs.util.Lst<javajs.util.Lst<javajs.util.Lst<java.lang.Object>>> getStatusChanged​(java.lang.String statusNameList)

      • menuEnabled

        public boolean menuEnabled()

      • setStatusDragDropped

        public boolean setStatusDragDropped​(int mode,
                                    int x,
                                    int y,
                                    java.lang.String fileName)

      • setStatusResized

        public void setStatusResized​(int width,
                             int height)

      • scriptStatus

        public void scriptStatus​(java.lang.String strStatus)

      • scriptStatusMsg

        public void scriptStatusMsg​(java.lang.String strStatus,
                            java.lang.String statusMessage)

      • setScriptStatus

        public void setScriptStatus​(java.lang.String strStatus,
                            java.lang.String statusMessage,
                            int msWalltime,
                            java.lang.String strErrorMessageUntranslated)

      • showUrl

        public void showUrl​(java.lang.String urlString)
        Specified by:
        showUrl in class JmolViewer

      • setMeshCreator

        public void setMeshCreator​(java.lang.Object meshCreator)
        an external applet or app with class that extends org.jmol.jvxl.MeshCreator might execute: org.jmol.viewer.Viewer vwr = applet.getViewer(); vwr.setMeshCreator(this); then that class's updateMesh(String id) method will be called whenever a mesh is rendered.
        Parameters:
        meshCreator -

      • showConsole

        public void showConsole​(boolean showConsole)

      • getParameter

        public java.lang.Object getParameter​(java.lang.String key)
        Specified by:
        getParameter in class JmolViewer

      • getP

        public java.lang.Object getP​(java.lang.String key)

      • getPOrNull

        public java.lang.Object getPOrNull​(java.lang.String key)

      • unsetProperty

        public void unsetProperty​(java.lang.String key)

      • getInt

        public int getInt​(int tok)
        Specified by:
        getInt in class JmolViewer

      • getDelayMaximumMs

        public int getDelayMaximumMs()

      • getHermiteLevel

        public int getHermiteLevel()

      • getHoverDelay

        public int getHoverDelay()

      • getBoolean

        public boolean getBoolean​(int tok)
        Specified by:
        getBoolean in class JmolViewer

      • allowEmbeddedScripts

        public boolean allowEmbeddedScripts()

      • getDragSelected

        boolean getDragSelected()

      • getBondsPickable

        boolean getBondsPickable()

      • useMinimizationThread

        public boolean useMinimizationThread()

      • getFloat

        public float getFloat​(int tok)
        Specified by:
        getFloat in class JmolViewer

      • setStringProperty

        public void setStringProperty​(java.lang.String key,
                              java.lang.String value)
        Specified by:
        setStringProperty in class JmolViewer

      • setStringPropertyTok

        private void setStringPropertyTok​(java.lang.String key,
                                  int tok,
                                  java.lang.String value)

      • setFloatProperty

        public void setFloatProperty​(java.lang.String key,
                             float value)
        Specified by:
        setFloatProperty in class JmolViewer

      • setFloatPropertyTok

        private void setFloatPropertyTok​(java.lang.String key,
                                 int tok,
                                 float value)

      • setIntProperty

        public void setIntProperty​(java.lang.String key,
                           int value)
        Specified by:
        setIntProperty in class JmolViewer

      • setIntPropertyTok

        private void setIntPropertyTok​(java.lang.String key,
                               int tok,
                               int value)

      • checkIntRange

        private static int checkIntRange​(int value,
                                 int min,
                                 int max)

      • checkFloatRange

        private static float checkFloatRange​(float value,
                                     float min,
                                     float max)

      • setBooleanProperty

        public void setBooleanProperty​(java.lang.String key,
                               boolean value)
        Specified by:
        setBooleanProperty in class JmolViewer

      • setBooleanPropertyTok

        private void setBooleanPropertyTok​(java.lang.String key,
                                   int tok,
                                   boolean value)

      • setModelKitMode

        private void setModelKitMode​(boolean value)

      • setSmilesString

        public void setSmilesString​(java.lang.String s)

      • removeUserVariable

        public void removeUserVariable​(java.lang.String key)

      • jmolTest

        private void jmolTest()

      • showParameter

        public void showParameter​(java.lang.String key,
                          boolean ifNotSet,
                          int nMax)

      • showString

        public void showString​(java.lang.String str,
                       boolean isPrint)

      • getAllSettings

        public java.lang.String getAllSettings​(java.lang.String prefix)

      • getBindingInfo

        public java.lang.String getBindingInfo​(java.lang.String qualifiers)

      • getIsosurfacePropertySmoothing

        public int getIsosurfacePropertySmoothing​(boolean asPower)

      • setNavigationDepthPercent

        public void setNavigationDepthPercent​(float percent)

      • getShowNavigationPoint

        public boolean getShowNavigationPoint()

      • setAxesScale

        private void setAxesScale​(int tok,
                          float val)

      • setAxesMode

        void setAxesMode​(int mode)

      • getSelectionHalosEnabled

        public boolean getSelectionHalosEnabled()

      • setSelectionHalosEnabled

        public void setSelectionHalosEnabled​(boolean TF)

      • getShowSelectedOnce

        public boolean getShowSelectedOnce()

      • setStrandCount

        private void setStrandCount​(int type,
                            int value)

      • getStrandCount

        public int getStrandCount​(int type)

      • setNavigationMode

        public void setNavigationMode​(boolean TF)

      • makeConnections

        public int[] makeConnections​(float minDistance,
                             float maxDistance,
                             int order,
                             int connectOperation,
                             javajs.util.BS bsA,
                             javajs.util.BS bsB,
                             javajs.util.BS bsBonds,
                             boolean isBonds,
                             boolean addGroup,
                             float energy)

      • rebondState

        public void rebondState​(boolean isStateScript)

      • setShowBbcage

        public void setShowBbcage​(boolean value)

      • getShowBbcage

        public boolean getShowBbcage()

      • setShowUnitCell

        public void setShowUnitCell​(boolean value)

      • getShowUnitCell

        public boolean getShowUnitCell()

      • setShowAxes

        public void setShowAxes​(boolean value)

      • getShowAxes

        public boolean getShowAxes()

      • setFrankOn

        public void setFrankOn​(boolean TF)
        Specified by:
        setFrankOn in class JmolViewer

      • getShowFrank

        public boolean getShowFrank()

      • setUnits

        public void setUnits​(java.lang.String units,
                     boolean isDistance)

      • setDefaultsType

        private void setDefaultsType​(java.lang.String type)

      • setAntialias

        private void setAntialias​(int tok,
                          boolean TF)

      • allocTempPoints

        public javajs.util.P3[] allocTempPoints​(int size)

      • freeTempPoints

        public void freeTempPoints​(javajs.util.P3[] tempPoints)

      • allocTempScreens

        public javajs.util.P3i[] allocTempScreens​(int size)

      • freeTempScreens

        public void freeTempScreens​(javajs.util.P3i[] tempScreens)

      • allocTempEnum

        public STR[] allocTempEnum​(int size)

      • freeTempEnum

        public void freeTempEnum​(STR[] temp)

      • getFont3D

        public Font getFont3D​(java.lang.String fontFace,
                      java.lang.String fontStyle,
                      float fontSize)

      • getAtomGroupQuaternions

        public javajs.util.Quat[] getAtomGroupQuaternions​(javajs.util.BS bsAtoms,
                                                  int nMax)

      • setStereoMode

        public void setStereoMode​(int[] twoColors,
                          STER stereoMode,
                          float degrees)

      • getChimeInfo

        public java.lang.String getChimeInfo​(int tok)

      • getModelFileInfo

        public java.lang.String getModelFileInfo()

      • getModelFileInfoAll

        public java.lang.String getModelFileInfoAll()

      • showEditor

        public void showEditor​(java.lang.String[] file_text)

      • setTainted

        public void setTainted​(boolean TF)

      • checkObjectClicked

        java.util.Map<java.lang.String,​java.lang.Object> checkObjectClicked​(int x,
                                                                          int y,
                                                                          int modifiers)

      • checkObjectHovered

        public boolean checkObjectHovered​(int x,
                                  int y)

      • checkObjectDragged

        boolean checkObjectDragged​(int prevX,
                           int prevY,
                           int x,
                           int y,
                           int action)

      • rotateAxisAngleAtCenter

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

      • rotateAboutPointsInternal

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

      • startSpinningAxis

        public void startSpinningAxis​(javajs.util.T3 pt1,
                              javajs.util.T3 pt2,
                              boolean isClockwise)

      • getModelDipole

        public javajs.util.V3 getModelDipole()

      • calculateMolecularDipole

        public javajs.util.V3 calculateMolecularDipole​(javajs.util.BS bsAtoms)
                                        throws java.lang.Exception
        Throws:
        java.lang.Exception

      • setDefaultLattice

        public void setDefaultLattice​(javajs.util.P3 p)

      • getDefaultLattice

        public javajs.util.P3 getDefaultLattice()

      • getModelExtract

        public java.lang.String getModelExtract​(java.lang.Object atomExpression,
                                        boolean doTransform,
                                        boolean isModelKit,
                                        java.lang.String type)
        V3000, SDF, JSON, CD, XYZ, XYZVIB, XYZRN, CML, PDB, PQR
        Parameters:
        atomExpression -
        doTransform -
        isModelKit -
        type -
        Returns:
        full file data

      • getData

        public java.lang.String getData​(java.lang.String atomExpression,
                                java.lang.String type)
        Specified by:
        getData in class JmolViewer

      • getModelFileData

        public java.lang.String getModelFileData​(java.lang.String atomExpression,
                                         java.lang.String type,
                                         boolean allTrajectories)
        Parameters:
        atomExpression - -- will be wrapped in { } and evaluated
        type - -- lower case means "atom data only; UPPERCASE returns full file data
        allTrajectories -
        Returns:
        full or atom-only data formatted as specified

      • getModelCml

        public java.lang.String getModelCml​(javajs.util.BS bs,
                                    int nAtomsMax,
                                    boolean addBonds,
                                    boolean doTransform)

      • getPdbAtomData

        public java.lang.String getPdbAtomData​(javajs.util.BS bs,
                                       javajs.util.OC out,
                                       boolean asPQR,
                                       boolean doTransform)

      • isJmolDataFrame

        public boolean isJmolDataFrame()

      • setFrameTitle

        public void setFrameTitle​(int modelIndex,
                          java.lang.String title)

      • setFrameTitleObj

        public void setFrameTitleObj​(java.lang.Object title)

      • getFrameTitle

        public java.lang.String getFrameTitle()

      • setAtomProperty

        public void setAtomProperty​(javajs.util.BS bs,
                            int tok,
                            int iValue,
                            float fValue,
                            java.lang.String sValue,
                            float[] values,
                            java.lang.String[] list)

      • checkCoordinatesChanged

        public void checkCoordinatesChanged()

      • setAtomCoords

        public void setAtomCoords​(javajs.util.BS bs,
                          int tokType,
                          java.lang.Object xyzValues)

      • setAtomCoordsRelative

        public void setAtomCoordsRelative​(javajs.util.T3 offset,
                                  javajs.util.BS bs)

      • invertAtomCoordPt

        public void invertAtomCoordPt​(javajs.util.P3 pt,
                              javajs.util.BS bs)

      • invertAtomCoordPlane

        public void invertAtomCoordPlane​(javajs.util.P4 plane,
                                 javajs.util.BS bs)

      • invertRingAt

        public void invertRingAt​(int atomIndex,
                         boolean isClick)

      • invertSelected

        public void invertSelected​(javajs.util.P3 pt,
                           javajs.util.P4 plane,
                           int iAtom,
                           javajs.util.BS bsAtoms)

      • moveAtoms

        public void moveAtoms​(javajs.util.M4 m4,
                      javajs.util.M3 mNew,
                      javajs.util.M3 rotation,
                      javajs.util.V3 translation,
                      javajs.util.P3 center,
                      boolean isInternal,
                      javajs.util.BS bsAtoms,
                      boolean translationOnly)

      • moveSelected

        public void moveSelected​(int deltaX,
                         int deltaY,
                         int deltaZ,
                         int x,
                         int y,
                         javajs.util.BS bsSelected,
                         boolean isTranslation,
                         boolean asAtoms,
                         int modifiers)

      • highlightBond

        public void highlightBond​(int index,
                          int closestAtomIndex,
                          int x,
                          int y)
        from Sticks
        Parameters:
        index -
        closestAtomIndex -
        x -
        y -

      • highlight

        public void highlight​(javajs.util.BS bs)

      • refreshMeasures

        public void refreshMeasures​(boolean andStopMinimization)

      • functionXY

        public float[][] functionXY​(java.lang.String functionName,
                            int nX,
                            int nY)
        fills an array with data -- if nX < 0 and this would involve JavaScript, then this reads a full set of Double[][] in one function call. Otherwise it reads the values using individual function calls, which each return Double. If the functionName begins with "file:" then data are read from a file specified after the colon. The sign of nX is not relevant in that case. The file may contain mixed numeric and non-numeric values; the non-numeric values will be skipped by Parser.parseFloatArray
        Parameters:
        functionName -
        nX -
        nY -
        Returns:
        nX by nY array of floating values

      • functionXYZ

        public float[][][] functionXYZ​(java.lang.String functionName,
                               int nX,
                               int nY,
                               int nZ)

      • extractMolData

        public java.lang.String extractMolData​(java.lang.String what)
        Specified by:
        extractMolData in class JmolViewer

      • getNMRPredict

        public java.lang.String getNMRPredict​(java.lang.String type)
        Parameters:
        type - C13 or H1
        Returns:
        null

      • getHelp

        public void getHelp​(java.lang.String what)

      • getChemicalInfo

        public java.lang.String getChemicalInfo​(java.lang.String smiles,
                                        java.lang.String info,
                                        javajs.util.BS bsAtoms)

      • addCommand

        public void addCommand​(java.lang.String command)
        Adds one or more commands to the command history
        Parameters:
        command - the command to add

      • pushState

        public void pushState()

      • popState

        public void popState()

      • removeCommand

        public java.lang.String removeCommand()
        Removes one command from the command history
        Returns:
        command removed

      • getSetHistory

        public java.lang.String getSetHistory​(int howFarBack)
        Options include: ; all n == Integer.MAX_VALUE ; n prev n >= 1 ; next n == -1 ; set max to -2 - n n <= -3 ; just clear n == -2 ; clear and turn off; return "" n == 0 ; clear and turn on; return "" n == Integer.MIN_VALUE;
        Specified by:
        getSetHistory in class JmolViewer
        Parameters:
        howFarBack - number of lines (-1 for next line)
        Returns:
        one or more lines of command history

      • historyFind

        public java.lang.String historyFind​(java.lang.String cmd,
                                    int dir)

      • setHistory

        public void setHistory​(java.lang.String fileName)

      • getOutputChannel

        public javajs.util.OC getOutputChannel​(java.lang.String localName,
                                       java.lang.String[] fullPath)

      • writeTextFile

        public java.lang.String writeTextFile​(java.lang.String fileName,
                                      java.lang.String data)
        Specified by:
        writeTextFile in class JmolViewer

      • clipImageOrPasteText

        public java.lang.String clipImageOrPasteText​(java.lang.String text)
        Specified by:
        clipImageOrPasteText in class JmolViewer
        Parameters:
        text - null here clips image; String pastes text
        Returns:
        "OK image to clipboard: [width] * [height] or "OK text to clipboard: [length]

      • processWriteOrCapture

        public java.lang.String processWriteOrCapture​(java.util.Map<java.lang.String,​java.lang.Object> params)
        from eval write command only includes option to write set of files
        Parameters:
        params -
        Returns:
        message starting with "OK" or an error message

      • createZip

        public java.lang.Object createZip​(java.lang.String fileName,
                                  java.lang.String type,
                                  java.util.Map<java.lang.String,​java.lang.Object> params)

      • outputToFile

        public java.lang.String outputToFile​(java.util.Map<java.lang.String,​java.lang.Object> params)
        Specified by:
        outputToFile in class JmolViewer
        Parameters:
        params - include type, fileName, text, bytes, quality, width, height
        Returns:
        null (canceled) or a message starting with OK or an error message

      • setSyncTarget

        private void setSyncTarget​(int mode,
                           boolean TF)

      • syncScript

        public void syncScript​(java.lang.String script,
                       java.lang.String applet,
                       int port)
        Specified by:
        syncScript in class JmolViewer

      • getModelIndexFromId

        public int getModelIndexFromId​(java.lang.String id)
        Specified by:
        getModelIndexFromId in class JmolViewer
        Parameters:
        id - some_id, filename#id, or ~fileNo.modelNo added ".basemodel" indicates to get the first model in a series from a JDX-MOL file.
        Returns:
        model index if found; -2 if file found but model not found -2 if no file indicated and no model found -1 if no such file

      • setSyncDriver

        public void setSyncDriver​(int mode)

      • setProteinType

        public void setProteinType​(STR type,
                           javajs.util.BS bs)

      • getVanderwaalsMar

        public int getVanderwaalsMar​(int i)

      • getVanderwaalsMarType

        public int getVanderwaalsMarType​(int atomicAndIsotopeNumber,
                                 VDW type)

      • setVdwStr

        void setVdwStr​(java.lang.String name)

      • setUserVdw

        void setUserVdw​(VDW mode)

      • getDefaultVdwNameOrData

        public java.lang.String getDefaultVdwNameOrData​(int mode,
                                                VDW type,
                                                javajs.util.BS bs)

      • deleteAtoms

        public int deleteAtoms​(javajs.util.BS bsAtoms,
                       boolean fullModels)

      • deleteModels

        public int deleteModels​(int modelIndex,
                        javajs.util.BS bsAtoms)
        called by ZAP {atomExpression} when atoms are present or the command is specific for a model, such as ZAP 2.1
        Parameters:
        modelIndex -
        bsAtoms -
        Returns:
        number of atoms deleted

      • deleteBonds

        public void deleteBonds​(javajs.util.BS bsDeleted)

      • deleteModelAtoms

        public void deleteModelAtoms​(int modelIndex,
                             int firstAtomIndex,
                             int nAtoms,
                             javajs.util.BS bsModelAtoms)

      • getQuaternionFrame

        public char getQuaternionFrame()

      • loadImageData

        public boolean loadImageData​(java.lang.Object image,
                             java.lang.String nameOrError,
                             java.lang.String echoName,
                             java.lang.Object sco)
        NOTE: This method is called from within a j2sNative block in awtjs2d.Platform.java as well as from FileManager.loadImage
        Parameters:
        image - could be a byte array
        nameOrError -
        echoName - if this is an echo rather than the background
        sco - delivered in JavaScript from Platform.java
        Returns:
        false

      • cd

        public java.lang.String cd​(java.lang.String dir)

      • setErrorMessage

        public java.lang.String setErrorMessage​(java.lang.String errMsg,
                                        java.lang.String errMsgUntranslated)

      • setShapeErrorState

        public void setShapeErrorState​(int shapeID,
                               java.lang.String state)

      • getShapeErrorState

        public java.lang.String getShapeErrorState()

      • handleError

        public void handleError​(java.lang.Error er,
                        boolean doClear)

      • getFunctions

        public java.util.Map<java.lang.String,​JmolScriptFunction> getFunctions​(boolean isStatic)

      • removeFunction

        public void removeFunction​(java.lang.String name)

      • isStaticFunction

        static boolean isStaticFunction​(java.lang.String name)

      • isFunction

        public boolean isFunction​(java.lang.String name)

      • clearFunctions

        public void clearFunctions()

      • getFunctionCalls

        public java.lang.String getFunctionCalls​(java.lang.String selectedFunction)

      • checkPrivateKey

        public boolean checkPrivateKey​(double privateKey)
        Simple method to ensure that the image creator (which writes files) was in fact opened by this vwr and not by some manipulation of the applet. When the image creator is used it requires both a vwr object and that vwr's private key. But the private key is private, so it is not possible to create a useable image creator without working through a vwr's own methods. Bob Hanson, 9/20/2009
        Parameters:
        privateKey -
        Returns:
        true if privateKey matches

      • bindAction

        public void bindAction​(java.lang.String desc,
                       java.lang.String name)

      • unBindAction

        public void unBindAction​(java.lang.String desc,
                         java.lang.String name)

      • calculateStruts

        public int calculateStruts​(javajs.util.BS bs1,
                           javajs.util.BS bs2)

      • getPreserveState

        public boolean getPreserveState()
        This flag if set FALSE: 1) turns UNDO off for the application 2) turns history off 3) prevents saving of inlinedata for later LOAD "" commands 4) turns off the saving of changed atom properties 5) does not guarantee accurate state representation 6) disallows generation of the state It is useful in situations such as web sites where memory is an issue and there is no need for such.
        Returns:
        TRUE or FALSE

      • isKiosk

        boolean isKiosk()

      • hasFocus

        public boolean hasFocus()

      • setFocus

        public void setFocus()

      • stopMinimization

        void stopMinimization()

      • clearMinimization

        void clearMinimization()

      • getMinimizationInfo

        public java.lang.String getMinimizationInfo()

      • checkMinimization

        private void checkMinimization()

      • minimize

        public void minimize​(JmolScriptEvaluator eval,
                     int steps,
                     float crit,
                     javajs.util.BS bsSelected,
                     javajs.util.BS bsFixed,
                     float rangeFixed,
                     int flags)
              throws java.lang.Exception
        Parameters:
        eval -
        steps - Integer.MAX_VALUE --> use defaults
        crit - -1 --> use defaults
        bsSelected -
        bsFixed -
        rangeFixed -
        flags -
        Throws:
        java.lang.Exception

      • setHydrogens

        private void setHydrogens​(javajs.util.BS bsAtoms)

      • setMotionFixedAtoms

        public void setMotionFixedAtoms​(javajs.util.BS bs)

      • getMotionFixedAtoms

        public javajs.util.BS getMotionFixedAtoms()

      • getAtomicPropertyState

        void getAtomicPropertyState​(javajs.util.SB commands,
                            byte type,
                            javajs.util.BS bs,
                            java.lang.String name,
                            float[] data)

      • getCenterAndPoints

        public javajs.util.P3[][] getCenterAndPoints​(javajs.util.Lst<java.lang.Object[]> atomSets,
                                             boolean addCenter)

      • writeFileData

        public java.lang.String writeFileData​(java.lang.String fileName,
                                      java.lang.String type,
                                      int modelIndex,
                                      java.lang.Object[] parameters)

      • getPdbData

        public java.lang.String getPdbData​(int modelIndex,
                                   java.lang.String type,
                                   javajs.util.BS bsAtoms,
                                   java.lang.Object[] parameters,
                                   javajs.util.OC oc,
                                   boolean getStructure)

      • getGroupsWithin

        public javajs.util.BS getGroupsWithin​(int nResidues,
                                      javajs.util.BS bs)

      • setShapeSize

        public void setShapeSize​(int shapeID,
                         int madOrMad10,
                         javajs.util.BS bsSelected)
        Parameters:
        shapeID -
        madOrMad10 - for axes, unitcell, and boundbox 10*mad; otherwise milliangstrom diameter
        bsSelected -

      • setShapeProperty

        public void setShapeProperty​(int shapeID,
                             java.lang.String propertyName,
                             java.lang.Object value)

      • getShapeProperty

        public java.lang.Object getShapeProperty​(int shapeType,
                                         java.lang.String propertyName)

      • getShapePropertyAsInt

        private int getShapePropertyAsInt​(int shapeID,
                                  java.lang.String propertyName)

      • setModelVisibility

        public void setModelVisibility()

      • resetShapes

        public void resetShapes​(boolean andCreateNew)

      • setParallel

        public boolean setParallel​(boolean TF)

      • isParallel

        public boolean isParallel()

      • undoClear

        void undoClear()

      • undoMoveAction

        public void undoMoveAction​(int action,
                           int n)
        Parameters:
        action - Token.undo or Token.redo
        n - number of steps to go back/forward; 0 for all; -1 for clear; -2 for clear BOTH

      • undoMoveActionClear

        public void undoMoveActionClear​(int taintedAtom,
                                int type,
                                boolean clearRedo)

      • moveAtomWithHydrogens

        protected void moveAtomWithHydrogens​(int atomIndex,
                                     int deltaX,
                                     int deltaY,
                                     int deltaZ,
                                     javajs.util.BS bsAtoms)

      • isModelPDB

        public boolean isModelPDB​(int i)

      • getSmiles

        public java.lang.String getSmiles​(javajs.util.BS bs)
                           throws java.lang.Exception
        Specified by:
        getSmiles in class JmolViewer
        Throws:
        java.lang.Exception

      • getOpenSmiles

        public java.lang.String getOpenSmiles​(javajs.util.BS bs)
                               throws java.lang.Exception
        Specified by:
        getOpenSmiles in class JmolViewer
        Throws:
        java.lang.Exception

      • getBioSmiles

        public java.lang.String getBioSmiles​(javajs.util.BS bs)
                              throws java.lang.Exception
        Throws:
        java.lang.Exception

      • getSmilesOpt

        public java.lang.String getSmilesOpt​(javajs.util.BS bsSelected,
                                     int index1,
                                     int index2,
                                     int flags,
                                     java.lang.String options)
                              throws java.lang.Exception
        returns the SMILES string for a sequence or atom set does not include attached protons on groups
        Parameters:
        bsSelected - selected atom set or null for current or specified range
        index1 - when bsSeleced == null, first atomIndex or -1 for current
        index2 - when bsSeleced == null, end atomIndex or -1 for current
        flags - see JC.SMILES_xxxx
        options - e.g. /strict,open/
        Returns:
        SMILES string
        Throws:
        java.lang.Exception

      • isModel2D

        private boolean isModel2D​(javajs.util.BS bs)

      • alert

        public void alert​(java.lang.String msg)

      • prompt

        public java.lang.String prompt​(java.lang.String label,
                               java.lang.String data,
                               java.lang.String[] list,
                               boolean asButtons)

      • dialogAsk

        public java.lang.String dialogAsk​(java.lang.String type,
                                  java.lang.String fileName,
                                  java.util.Map<java.lang.String,​java.lang.Object> params)
        Ask for new file name when saving or opening a file in Java and saving a file in JavaScript. JavaScript use of FileReader goes through loadFileAsync
        Parameters:
        type -
        fileName -
        params -
        Returns:
        new file name

      • initializeExporter

        public JmolRendererInterface initializeExporter​(java.util.Map<java.lang.String,​java.lang.Object> params)

      • getMouseEnabled

        public boolean getMouseEnabled()

      • getObjectMap

        public void getObjectMap​(java.util.Map<java.lang.String,​?> map,
                         char c)
        used in autocompletion in console using TAB
        Parameters:
        map -
        c -

      • setPicked

        public void setPicked​(int atomIndex,
                      boolean andReset)

      • runScript

        public java.lang.String runScript​(java.lang.String script)
        Run a script using the script function script("xxxxxx") using direct script tokens for script ( "xxxxxxx" )
        Specified by:
        runScript in class JmolViewer
        Returns:
        string from ScriptEvaluator#outputBuffer

      • runScriptCautiously

        public java.lang.String runScriptCautiously​(java.lang.String script)
        formerly runScript(), this method really can ONLY be called by the viewer being run from an already-running script. If it is invoked by a separate thread, it can wreak havoc on any queued thread, since they are not thread safe.
        Overrides:
        runScriptCautiously in class JmolViewer
        Parameters:
        script -
        Returns:
        output of the script.

      • setFrameDelayMs

        public void setFrameDelayMs​(long millis)

      • getBaseModelBitSet

        public javajs.util.BS getBaseModelBitSet()

      • clearTimeouts

        public void clearTimeouts()

      • setTimeout

        public void setTimeout​(java.lang.String name,
                       int mSec,
                       java.lang.String script)

      • triggerTimeout

        public void triggerTimeout​(java.lang.String name)

      • clearTimeout

        public void clearTimeout​(java.lang.String name)

      • showTimeout

        public java.lang.String showTimeout​(java.lang.String name)

      • setCurrentModelID

        public void setCurrentModelID​(java.lang.String id)

      • cacheClear

        public void cacheClear()

      • cachePut

        public void cachePut​(java.lang.String key,
                     java.lang.Object data)
        JSInterface -- allows saving files in memory for later retrieval
        Parameters:
        key -
        data -

      • cacheFileByName

        public int cacheFileByName​(java.lang.String fileName,
                           boolean isAdd)

      • clearThreads

        public void clearThreads()

      • getDefaultPropertyParam

        public java.lang.String getDefaultPropertyParam​(int propertyID)

      • getPropertyNumber

        public int getPropertyNumber​(java.lang.String name)

      • checkPropertyParameter

        public boolean checkPropertyParameter​(java.lang.String name)

      • extractProperty

        public java.lang.Object extractProperty​(java.lang.Object property,
                                        java.lang.Object args,
                                        int pt)

      • addHydrogens

        public javajs.util.BS addHydrogens​(javajs.util.BS bsAtoms,
                                   int flags)

      • addHydrogensInline

        public javajs.util.BS addHydrogensInline​(javajs.util.BS bsAtoms,
                                         javajs.util.Lst<Atom> vConnections,
                                         javajs.util.P3[] pts)
                                  throws java.lang.Exception
        Throws:
        java.lang.Exception

      • evalFunctionFloat

        public float evalFunctionFloat​(java.lang.Object func,
                               java.lang.Object params,
                               float[] values)
        Specified by:
        evalFunctionFloat in interface AtomDataServer

      • evaluateExpression

        public java.lang.Object evaluateExpression​(java.lang.Object stringOrTokens)
        synchronized here trapped the eventQueue; see also evaluateExpressionAsVariable
        Specified by:
        evaluateExpression in class JmolViewer
        Returns:
        a String representation of the evaluated expression

      • evaluateExpressionAsVariable

        public SV evaluateExpressionAsVariable​(java.lang.Object stringOrTokens)
        Specified by:
        evaluateExpressionAsVariable in class JmolViewer
        Returns:
        a String representation of the evaluated expression as a script variable (org.jmol.script.SV)

      • getAtomBitSet

        public javajs.util.BS getAtomBitSet​(java.lang.Object atomExpression)

      • getScriptContext

        public ScriptContext getScriptContext​(java.lang.String why)

      • getAtomDefs

        public java.lang.String getAtomDefs​(java.util.Map<java.lang.String,​java.lang.Object> names)

      • setCGO

        public void setCGO​(javajs.util.Lst<java.lang.Object> info)

      • setModelSet

        public void setModelSet​(ModelSet modelSet)

      • setObjectProp

        public java.lang.String setObjectProp​(java.lang.String id,
                                      int tokCommand)

      • setDihedrals

        public void setDihedrals​(float[] dihedralList,
                         javajs.util.BS[] bsBranches,
                         float rate)

      • getChainID

        public int getChainID​(java.lang.String id,
                      boolean isAssign)
        Create a unique integer for any chain string. Note that if there are any chains that are more than a single character, chainCaseSensitive is automatically set TRUE
        Parameters:
        id - < 256 is just the character of a single-character upper-case chain id, upper or lower case query; >= 256 < 300 is lower case found in structure
        isAssign - from a file reader, not a select query
        Returns:
        i

      • getChainIDStr

        public java.lang.String getChainIDStr​(int id)

      • getScriptQueueInfo

        public java.lang.Boolean getScriptQueueInfo()

      • getDistanceUnits

        public java.lang.String getDistanceUnits​(java.lang.String s)

      • calculateFormalCharges

        public int calculateFormalCharges​(javajs.util.BS bs)

      • setModulation

        public void setModulation​(javajs.util.BS bs,
                          boolean isOn,
                          javajs.util.P3 t1,
                          boolean isQ)

      • checkInMotion

        public void checkInMotion​(int state)

      • checkMotionRendering

        public boolean checkMotionRendering​(int tok)
        check motion for rendering during mouse movement, spin, vibration, and animation
        Parameters:
        tok -
        Returns:
        TRUE if allowed

      • openExportChannel

        public javajs.util.OC openExportChannel​(double privateKey,
                                        java.lang.String fileName,
                                        boolean asWriter)
                                 throws java.io.IOException
        Throws:
        java.io.IOException

      • log

        public void log​(java.lang.String data)
        Specified by:
        log in interface AtomDataServer

      • getLogFileName

        public java.lang.String getLogFileName()

      • getCommands

        public java.lang.String getCommands​(java.util.Map<java.lang.String,​javajs.util.BS> htDefine,
                                    java.util.Map<java.lang.String,​javajs.util.BS> htMore,
                                    java.lang.String select)

      • allowCapture

        public boolean allowCapture()

      • compileExpr

        public T[] compileExpr​(java.lang.String expr)

      • checkSelect

        public boolean checkSelect​(java.util.Map<java.lang.String,​SV> h,
                           T[] value)

      • getAnnotationInfo

        public java.lang.String getAnnotationInfo​(SV d,
                                          java.lang.String match,
                                          int type)

      • getAtomValidation

        public javajs.util.Lst<java.lang.Float> getAtomValidation​(java.lang.String type,
                                                          Atom atom)

      • dragMinimizeAtom

        void dragMinimizeAtom​(int iAtom)

      • checkMenuUpdate

        public void checkMenuUpdate()

      • getAuxiliaryInfoForAtoms

        public java.util.Map<java.lang.String,​java.lang.Object> getAuxiliaryInfoForAtoms​(java.lang.Object atomExpression)

      • getJSJSONParser

        private javajs.util.JSJSONParser getJSJSONParser()

      • parseJSON

        public java.lang.Object parseJSON​(java.lang.String str)

      • parseJSONMap

        public java.util.Map<java.lang.String,​java.lang.Object> parseJSONMap​(java.lang.String jsonMap)

      • parseJSONArray

        public javajs.util.Lst<java.lang.Object> parseJSONArray​(java.lang.String jsonArray)

      • getSymTemp

        public SymmetryInterface getSymTemp()
        Retrieve a Symmetry object, possibly re-using an old one.
        Returns:
        org.jmol.symmetry.Symmetry object

      • setWindowDimensions

        public void setWindowDimensions​(float[] dims)

      • getCurrentModelAuxInfo

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

      • startNBO

        public void startNBO​(java.lang.String options)

      • startPlugin

        public void startPlugin​(java.lang.String plugin)
        startup -U nbo option
        Parameters:
        plugin -

      • connectNBO

        public void connectNBO​(java.lang.String type)

      • getNBOParser

        private NBOParser getNBOParser()

      • getNBOAtomLabel

        public java.lang.String getNBOAtomLabel​(Atom atom)

      • calculateChirality

        public java.lang.String calculateChirality​(javajs.util.BS bsAtoms)

      • getSubstructureSetArray

        public javajs.util.BS[] getSubstructureSetArray​(java.lang.String pattern,
                                                javajs.util.BS bsSelected,
                                                int flags)
                                         throws java.lang.Exception
        Throws:
        java.lang.Exception

      • getSubstructureSetArrayForNodes

        public javajs.util.BS[] getSubstructureSetArrayForNodes​(java.lang.String pattern,
                                                        Node[] nodes,
                                                        int flags)
                                                 throws java.lang.Exception
        Throws:
        java.lang.Exception

      • getSmilesAtoms

        public Node[] getSmilesAtoms​(java.lang.String smiles)
                      throws java.lang.Exception
        Throws:
        java.lang.Exception

      • calculateChiralityForSmiles

        public java.lang.String[] calculateChiralityForSmiles​(java.lang.String smiles)

      • getPdbID

        public java.lang.String getPdbID()

      • getModelInfo

        public java.lang.Object getModelInfo​(java.lang.String key)
        get a value from the current model's Model.auxiliaryInfo
        Parameters:
        key -
        Returns:
        value, or null if there is no SINGLE current model

      • notifyScriptEditor

        public void notifyScriptEditor​(int msWalltime,
                               java.lang.Object[] data)

      • sendConsoleMessage

        public void sendConsoleMessage​(java.lang.String msg)

      • getModelkitProperty

        public java.lang.Object getModelkitProperty​(java.lang.Object nameOrData)
        Parameters:
        nameOrData - could be name or [name,value]
        Returns:
        value

      • setModelkitProperty

        public java.lang.Object setModelkitProperty​(java.lang.String key,
                                            java.lang.Object value)

      • getSymmetryInfo

        public java.lang.Object getSymmetryInfo​(int iatom,
                                        java.lang.String xyz,
                                        int iOp,
                                        javajs.util.P3 translation,
                                        javajs.util.P3 pt1,
                                        javajs.util.P3 pt2,
                                        int type,
                                        java.lang.String desc,
                                        float scaleFactor,
                                        int nth,
                                        int options)
        A general method for retrieving symmetry information with full capability of the symop() scripting function.
        Parameters:
        iatom - atom index specifying the model set and used for pt1 if that is null and also for matching element type.
        xyz - the desired Jones-Faithful representation of the symmetry operation or null
        iOp - the desired symmetry operation [1-n] or 0
        translation - [i j k] translational addition to symop
        pt1 - the starting point, or null if to use iatom or otherwise unnecessary
        pt2 - the target point, if this is a point-to-point determination, or the offset if not and options is nonzero
        type - a token type such as T.list or T.array
        desc - if type == T.nada (0), a name evaluating to a type, or one of the special names: "info", "description", "matrix", "axispoint", or "time" (as in time-reversal); otherwise, if type == T.draw, the root id given to a returned DRAW command set
        scaleFactor - if nonzero and type == T.draw, a scaling factor to be applied to the rotational vector
        nth - in the case of a point-to-point determination, the nth matching operator, or 0 for "all"
        options - if nonzero, a option, currently just T.offset, indicating that pt1 is an {i j k} offset from cell 555
        Returns:
        string, Object[], or Lst

      • setModelKitRotateBondIndex

        public void setModelKitRotateBondIndex​(int i)
        Parameters:
        i - Integer.MIN_VALUE initializes the bond index

      • getMacro

        public java.lang.String getMacro​(java.lang.String key)
        retrieve macros.json from the directory
        Parameters:
        key -
        Returns:
        the macro path

      • getInchi

        public java.lang.String getInchi​(javajs.util.BS atoms,
                                 java.lang.String molData,
                                 java.lang.String options)

      • getConsoleFontScale

        public int getConsoleFontScale()

      • setConsoleFontScale

        public void setConsoleFontScale​(int scale)

      • confirm

        public int confirm​(java.lang.String msg,
                   java.lang.String msgNo)