Class PyMOLScene

  • All Implemented Interfaces:
    JmolSceneGenerator

    class PyMOLScene
    extends java.lang.Object
    implements JmolSceneGenerator
    A class to allow manipulation of scenes dissociated from file loading. A "scene" in this context is a distillation of PyMOL information into a Hashtable for easier retrieval using RESTORE SCENE name.
    • Constructor Summary

      Constructors 
      Constructor Description
      PyMOLScene​(PymolAtomReader reader, Viewer vwr, javajs.util.Lst<java.lang.Object> settings, java.util.Map<java.lang.Integer,​javajs.util.Lst<java.lang.Object>> uniqueSettings, int pymolVersion, boolean haveScenes, int baseAtomIndex, int baseModelIndex, boolean doCache, java.lang.String filePath)  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      (package private) java.lang.String addCGO​(javajs.util.Lst<java.lang.Object> data, int color)  
      (package private) PyMOLGroup addGroup​(javajs.util.Lst<java.lang.Object> object, java.lang.String parent, int type, javajs.util.BS bsAtoms)
      Create a hierarchical list of named groups as generally seen on the PyMOL app's right-hand object menu.
      (package private) JmolObject addIsosurface​(java.lang.String objectName)  
      private JmolObject addJmolObject​(int id, javajs.util.BS bsAtoms, java.lang.Object info)  
      (package private) void addLabel​(int atomIndex, int uniqueID, int atomColor, float[] labelPos, java.lang.String label)  
      (package private) boolean addMeasurements​(MeasurementData[] mdList, int nCoord, javajs.util.Lst<java.lang.Object> list, javajs.util.BS bsReps, int color, javajs.util.Lst<java.lang.Object> offsets, boolean haveLabels)  
      (package private) void addMesh​(int tok, javajs.util.Lst<java.lang.Object> obj, java.lang.String objName, boolean isMep)  
      private JmolObject addObject​(JmolObject obj)  
      private void addSetting​(int key, int type, java.lang.Object val)  
      (package private) boolean booleanSetting​(int i)  
      (package private) void buildScene​(java.lang.String name, javajs.util.Lst<java.lang.Object> thisScene, java.util.Map<java.lang.String,​javajs.util.Lst<java.lang.Object>> htObjNames, java.util.Map<java.lang.String,​javajs.util.Lst<java.lang.Object>> htSecrets)
      Build a scene at file reading time.
      private void checkNucleicObject​(javajs.util.BS bs, boolean isTrace)  
      private void cleanSingletons​(javajs.util.BS bs)
      PyMOL does not display cartoons or traces for single-residue runs.
      private void clearReaderData()  
      private int colorSetting​(int i)  
      private void createCartoonObject​(java.lang.String key, int sizeID)  
      private void createPuttyObject​(javajs.util.BS bs)
      "Putty" shapes scaled in a variety of ways.
      private void createRibbonObject​(javajs.util.BS bs)
      PyMOL "ribbons" could be Jmol backbone or trace, depending upon the value of PyMOL.ribbon_sampling.
      private void createShapeObject​(int shapeID, javajs.util.BS bs)
      Create JmolObjects for each shape.
      (package private) void createShapeObjects​(javajs.util.BS[] reps, boolean allowSurface, int ac0, int ac)
      create all objects for a given molecule or scene
      private void createSpacefillObjects()
      Create a BALLS JmolObject for each radius.
      private void createTraceObject​(javajs.util.BS bs)
      trace, or cartoon in the case of cartoon ladders.
      private void defineAtoms​(java.lang.String name, javajs.util.BS bs)  
      (package private) void ensureCapacity​(int n)  
      private void finalizeObjects()
      Finally, we turn each JmolObject into its Jmol equivalent.
      private void finalizeUniqueBonds()  
      (package private) void finalizeVisibility()
      Create group JmolObjects, and set hierarchical visibilities
      private java.lang.String fixName​(java.lang.String name)  
      private void fixReps​(javajs.util.BS[] reps)  
      (package private) float floatSetting​(int i)  
      private void generateColors​(java.lang.Object[] colors)
      Set PyMOL "atom-wise" colors -- the colors that are defined initially as element colors but possibly set with the PyMOL 'color' command and are used when representation colors (cartoon, dots, etc.) are not defined (-1).
      void generateScene​(java.util.Map<java.lang.String,​java.lang.Object> scene)
      Generate the saved scene using file settings preserved here and scene-specific information including frame, view, colors, visibilities, .
      private void generateShapes​(java.lang.Object[] reps)
      Create all Jmol shape objects.
      private void generateVisibilities​(java.util.Map<java.lang.String,​java.lang.Object> vis)
      Hide everything, then just make visible the sets of atoms specified in the visibility (i.e.
      private javajs.util.BS getBS​(javajs.util.Lst<java.lang.Object> list)  
      private void getBsAtoms​(javajs.util.Lst<java.lang.Object> list, int[] atomMap, javajs.util.BS bs)  
      (package private) short getColix​(int colorIndex, float translucency)  
      (package private) PyMOLGroup getGroup​(java.lang.String name)  
      private java.lang.String getJmolName​(java.lang.String name)  
      private JmolObject getJmolObject​(int id, javajs.util.BS bsAtoms, java.lang.Object info)  
      (package private) java.lang.String getObjectID​(java.lang.String name)  
      (package private) javajs.util.Lst<java.lang.Object> getObjectSetting​(int i)  
      private void getObjectSettings()  
      private int getObjectType​(java.lang.String name)  
      private float[] getPymolView​(javajs.util.Lst<java.lang.Object> view, boolean isViewObj)
      adds depth_cue, fog, and fog_start
      private javajs.util.BS getSelectionAtoms​(javajs.util.Lst<java.lang.Object> molecules, int istate, javajs.util.BS bs)
      Add selected atoms to a growing bit set.
      private javajs.util.Lst<java.lang.Object> getSetting​(int i)  
      (package private) javajs.util.BS getSSMapAtom​(java.lang.String ssType)  
      (package private) float getUniqueFloatDef​(int id, int key, float defaultValue)  
      (package private) javajs.util.P3 getUniquePoint​(int id, int key, javajs.util.P3 pt)  
      (package private) javajs.util.SB getViewScript​(javajs.util.Lst<java.lang.Object> view)  
      (package private) float globalSetting​(int i)  
      private void listToSettings​(javajs.util.Lst<java.lang.Object> list, java.util.Map<java.lang.Integer,​javajs.util.Lst<java.lang.Object>> objectSettings)  
      (package private) boolean needSelections()  
      private Text newTextLabel​(java.lang.String label, float[] labelOffset, int colorIndex, int fontID, float fontSize)  
      (package private) void offsetObjects()  
      private javajs.util.P3 pointSetting​(int i)  
      (package private) void processSelection​(javajs.util.Lst<java.lang.Object> selection)
      process the selection sets (sele), (...)
      private void selectAllAtoms​(javajs.util.Lst<java.lang.Object> obj, int istate, javajs.util.BS bs)
      Collect all the atoms specified by an object state into a bit set.
      (package private) void setAtomColor​(int atomColor)  
      (package private) java.util.Map<java.lang.String,​java.lang.Object> setAtomDefs()  
      (package private) void setAtomInfo​(int[] uniqueIDs, int[] cartoonTypes, int[] sequenceNumbers, boolean[] newChain, float[] radii)  
      (package private) javajs.util.BS setAtomMap​(int[] atomMap, int ac0)  
      (package private) void setBondParameters​(Bond b, int modelIndex, float rad, float pymolValence, int argb, float trans)
      used in PyMOL reader to set unique bond settings and for valence
      (package private) void setCarveSets​(java.util.Map<java.lang.String,​javajs.util.Lst<java.lang.Object>> htObjNames)  
      (package private) void setFrameObject​(int type, java.lang.Object info)  
      private void setGroupVisibilities()  
      private void setGroupVisible​(PyMOLGroup g, boolean parentVis)
      Iterate through groups, setting visibility flags.
      (package private) float[] setLabelPosition​(javajs.util.P3 offset, float[] labelPos)  
      (package private) void setReaderObjectInfo​(java.lang.String name, int type, java.lang.String groupName, boolean isHidden, javajs.util.Lst<java.lang.Object> listObjSettings, javajs.util.Lst<java.lang.Object> listStateSettings, java.lang.String ext)  
      (package private) void setReaderObjects()  
      private void setSceneObject​(java.lang.String name, int istate)
      Set scene object/state-specific global fields and settings based on the name and state or stored values from when the file was loaded.
      (package private) void setStateCount​(int stateCount)  
      (package private) void setUniqueBond​(int index, int uniqueID)  
      (package private) void setUniqueBonds​(javajs.util.BS bsBonds, boolean isSticks)  
      private JmolObject setUniqueObjects​(int shape, javajs.util.BS bs, int setColor, int color, int setTrans, float trans, int setSize, float size, float f)  
      private void setVersionSettings()
      Attempt to adjust for PyMOL versions.
      (package private) java.lang.String stringSetting​(int i)  
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Field Detail

      • pymolVersion

        private int pymolVersion
      • bsHidden

        javajs.util.BS bsHidden
      • bsNucleic

        javajs.util.BS bsNucleic
      • bsNonbonded

        javajs.util.BS bsNonbonded
      • bsLabeled

        javajs.util.BS bsLabeled
      • bsHydrogen

        javajs.util.BS bsHydrogen
      • bsNoSurface

        javajs.util.BS bsNoSurface
      • htSpacefill

        private java.util.Map<java.lang.Float,​javajs.util.BS> htSpacefill
      • ssMapAtom

        private java.util.Map<java.lang.String,​javajs.util.BS> ssMapAtom
      • atomColorList

        private javajs.util.Lst<java.lang.Integer> atomColorList
      • occludedObjects

        private java.util.Map<java.lang.String,​java.lang.Boolean> occludedObjects
      • labels

        private java.util.Map<java.lang.Integer,​Text> labels
      • colixes

        private short[] colixes
      • groups

        private java.util.Map<java.lang.String,​PyMOLGroup> groups
      • objectSettings

        private java.util.Map<java.lang.Integer,​javajs.util.Lst<java.lang.Object>> objectSettings
      • bsCartoon

        private javajs.util.BS bsCartoon
      • htCarveSets

        private java.util.Map<java.lang.String,​javajs.util.BS> htCarveSets
      • htDefinedAtoms

        private java.util.Map<java.lang.String,​javajs.util.BS> htDefinedAtoms
      • htHiddenObjects

        private java.util.Map<java.lang.String,​java.lang.Boolean> htHiddenObjects
      • moleculeNames

        private javajs.util.Lst<java.lang.String> moleculeNames
      • jmolObjects

        private javajs.util.Lst<JmolObject> jmolObjects
      • htAtomMap

        private java.util.Map<java.lang.String,​int[]> htAtomMap
      • htObjectAtoms

        private java.util.Map<java.lang.String,​javajs.util.BS> htObjectAtoms
      • htObjectGroups

        private java.util.Map<java.lang.String,​java.lang.String> htObjectGroups
      • htMeasures

        private java.util.Map<java.lang.String,​MeasurementData[]> htMeasures
      • htObjectSettings

        private java.util.Map<java.lang.String,​java.util.Map<java.lang.Integer,​javajs.util.Lst<java.lang.Object>>> htObjectSettings
      • objectInfo

        private java.util.Map<java.lang.String,​java.lang.Object[]> objectInfo
      • settings

        private javajs.util.Lst<java.lang.Object> settings
      • htStateSettings

        private java.util.Map<java.lang.String,​java.util.Map<java.lang.Integer,​javajs.util.Lst<java.lang.Object>>> htStateSettings
      • stateSettings

        private java.util.Map<java.lang.Integer,​javajs.util.Lst<java.lang.Object>> stateSettings
      • uniqueSettings

        private java.util.Map<java.lang.Integer,​javajs.util.Lst<java.lang.Object>> uniqueSettings
      • uniqueList

        private java.util.Map<java.lang.Integer,​java.lang.Integer> uniqueList
      • bsUniqueBonds

        private javajs.util.BS bsUniqueBonds
      • bgRgb

        private int bgRgb
      • dotColor

        private int dotColor
      • surfaceMode

        private int surfaceMode
      • surfaceColor

        private int surfaceColor
      • cartoonColor

        private int cartoonColor
      • ribbonColor

        private int ribbonColor
      • sphereColor

        private int sphereColor
      • labelFontId

        private int labelFontId
      • labelColor

        private int labelColor
      • cartoonTranslucency

        private float cartoonTranslucency
      • ribbonTranslucency

        private float ribbonTranslucency
      • labelSize

        private float labelSize
      • meshWidth

        private float meshWidth
      • nonbondedSize

        private float nonbondedSize
      • nonbondedTranslucency

        private float nonbondedTranslucency
      • sphereScale

        private float sphereScale
      • sphereTranslucency

        private float sphereTranslucency
      • stickTranslucency

        private float stickTranslucency
      • transparency

        private float transparency
      • cartoonLadderMode

        private boolean cartoonLadderMode
      • cartoonRockets

        private boolean cartoonRockets
      • haveNucleicLadder

        private boolean haveNucleicLadder
      • labelPosition

        private javajs.util.P3 labelPosition
      • labelPosition0

        private javajs.util.P3 labelPosition0
      • objectName

        private java.lang.String objectName
      • objectNameID

        private java.lang.String objectNameID
      • objectJmolName

        private java.lang.String objectJmolName
      • objectType

        private int objectType
      • bsAtoms

        private javajs.util.BS bsAtoms
      • objectHidden

        private boolean objectHidden
      • uniqueIDs

        private int[] uniqueIDs
      • cartoonTypes

        private int[] cartoonTypes
      • sequenceNumbers

        private int[] sequenceNumbers
      • newChain

        private boolean[] newChain
      • radii

        private float[] radii
      • baseModelIndex

        private int baseModelIndex
      • baseAtomIndex

        private int baseAtomIndex
      • stateCount

        private int stateCount
      • mepList

        java.lang.String mepList
      • doCache

        boolean doCache
      • haveScenes

        private boolean haveScenes
      • bsCarve

        private javajs.util.BS bsCarve
      • solventAccessible

        private boolean solventAccessible
      • bsLineBonds

        private javajs.util.BS bsLineBonds
      • bsStickBonds

        private javajs.util.BS bsStickBonds
      • thisState

        private int thisState
      • currentAtomSetIndex

        int currentAtomSetIndex
      • surfaceInfoName

        java.lang.String surfaceInfoName
      • ptTemp

        private final javajs.util.P3 ptTemp
      • MEAS_DIGITS

        private static final int[] MEAS_DIGITS
    • Constructor Detail

      • PyMOLScene

        PyMOLScene​(PymolAtomReader reader,
                   Viewer vwr,
                   javajs.util.Lst<java.lang.Object> settings,
                   java.util.Map<java.lang.Integer,​javajs.util.Lst<java.lang.Object>> uniqueSettings,
                   int pymolVersion,
                   boolean haveScenes,
                   int baseAtomIndex,
                   int baseModelIndex,
                   boolean doCache,
                   java.lang.String filePath)
    • Method Detail

      • clearReaderData

        private void clearReaderData()
      • setUniqueBond

        void setUniqueBond​(int index,
                           int uniqueID)
      • setStateCount

        void setStateCount​(int stateCount)
      • colorSetting

        private int colorSetting​(int i)
      • pointSetting

        private javajs.util.P3 pointSetting​(int i)
      • ensureCapacity

        void ensureCapacity​(int n)
      • setReaderObjectInfo

        void setReaderObjectInfo​(java.lang.String name,
                                 int type,
                                 java.lang.String groupName,
                                 boolean isHidden,
                                 javajs.util.Lst<java.lang.Object> listObjSettings,
                                 javajs.util.Lst<java.lang.Object> listStateSettings,
                                 java.lang.String ext)
      • listToSettings

        private void listToSettings​(javajs.util.Lst<java.lang.Object> list,
                                    java.util.Map<java.lang.Integer,​javajs.util.Lst<java.lang.Object>> objectSettings)
      • getObjectSettings

        private void getObjectSettings()
      • setAtomInfo

        void setAtomInfo​(int[] uniqueIDs,
                         int[] cartoonTypes,
                         int[] sequenceNumbers,
                         boolean[] newChain,
                         float[] radii)
      • setSceneObject

        private void setSceneObject​(java.lang.String name,
                                    int istate)
        Set scene object/state-specific global fields and settings based on the name and state or stored values from when the file was loaded.
        Parameters:
        name -
        istate -
      • buildScene

        void buildScene​(java.lang.String name,
                        javajs.util.Lst<java.lang.Object> thisScene,
                        java.util.Map<java.lang.String,​javajs.util.Lst<java.lang.Object>> htObjNames,
                        java.util.Map<java.lang.String,​javajs.util.Lst<java.lang.Object>> htSecrets)
        Build a scene at file reading time. We only implement frame-specific scenes. Creates a map of information that can be used later and will also be a reference to this instance of PyMOLScene, which is an implementation of JmolSceneGenerator.
        Parameters:
        name -
        thisScene -
        htObjNames -
        htSecrets -
      • generateScene

        public void generateScene​(java.util.Map<java.lang.String,​java.lang.Object> scene)
        Generate the saved scene using file settings preserved here and scene-specific information including frame, view, colors, visibilities, . Called by StateManager via implemented JmolSceneGenerator.
        Specified by:
        generateScene in interface JmolSceneGenerator
        Parameters:
        scene -
      • generateColors

        private void generateColors​(java.lang.Object[] colors)
        Set PyMOL "atom-wise" colors -- the colors that are defined initially as element colors but possibly set with the PyMOL 'color' command and are used when representation colors (cartoon, dots, etc.) are not defined (-1). This is the same as Jmol's inherited atom color.
        Parameters:
        colors -
      • processSelection

        void processSelection​(javajs.util.Lst<java.lang.Object> selection)
        process the selection sets (sele), (...)
        Parameters:
        selection -
      • getSelectionAtoms

        private javajs.util.BS getSelectionAtoms​(javajs.util.Lst<java.lang.Object> molecules,
                                                 int istate,
                                                 javajs.util.BS bs)
        Add selected atoms to a growing bit set.
        Parameters:
        molecules -
        istate -
        bs -
        Returns:
        bs for convenience
      • selectAllAtoms

        private void selectAllAtoms​(javajs.util.Lst<java.lang.Object> obj,
                                    int istate,
                                    javajs.util.BS bs)
        Collect all the atoms specified by an object state into a bit set.
        Parameters:
        obj -
        istate - 0 for "all states"
        bs -
      • generateVisibilities

        private void generateVisibilities​(java.util.Map<java.lang.String,​java.lang.Object> vis)
        Hide everything, then just make visible the sets of atoms specified in the visibility (i.e. "activity") list within scene_dict.
        Parameters:
        vis -
      • generateShapes

        private void generateShapes​(java.lang.Object[] reps)
        Create all Jmol shape objects.
        Parameters:
        reps -
      • getBS

        private javajs.util.BS getBS​(javajs.util.Lst<java.lang.Object> list)
      • getBsAtoms

        private void getBsAtoms​(javajs.util.Lst<java.lang.Object> list,
                                int[] atomMap,
                                javajs.util.BS bs)
      • setReaderObjects

        void setReaderObjects()
      • finalizeObjects

        private void finalizeObjects()
        Finally, we turn each JmolObject into its Jmol equivalent.
      • offsetObjects

        void offsetObjects()
      • getJmolObject

        private JmolObject getJmolObject​(int id,
                                         javajs.util.BS bsAtoms,
                                         java.lang.Object info)
      • addJmolObject

        private JmolObject addJmolObject​(int id,
                                         javajs.util.BS bsAtoms,
                                         java.lang.Object info)
      • getPymolView

        private float[] getPymolView​(javajs.util.Lst<java.lang.Object> view,
                                     boolean isViewObj)
        adds depth_cue, fog, and fog_start
        Parameters:
        view -
        isViewObj -
        Returns:
        22-element array
      • globalSetting

        float globalSetting​(int i)
      • addGroup

        PyMOLGroup addGroup​(javajs.util.Lst<java.lang.Object> object,
                            java.lang.String parent,
                            int type,
                            javajs.util.BS bsAtoms)
        Create a hierarchical list of named groups as generally seen on the PyMOL app's right-hand object menu.
        Parameters:
        object -
        parent -
        type -
        bsAtoms -
        Returns:
        group
      • getGroup

        PyMOLGroup getGroup​(java.lang.String name)
      • finalizeVisibility

        void finalizeVisibility()
        Create group JmolObjects, and set hierarchical visibilities
      • setCarveSets

        void setCarveSets​(java.util.Map<java.lang.String,​javajs.util.Lst<java.lang.Object>> htObjNames)
      • setGroupVisibilities

        private void setGroupVisibilities()
      • defineAtoms

        private void defineAtoms​(java.lang.String name,
                                 javajs.util.BS bs)
      • getJmolName

        private java.lang.String getJmolName​(java.lang.String name)
      • createShapeObjects

        void createShapeObjects​(javajs.util.BS[] reps,
                                boolean allowSurface,
                                int ac0,
                                int ac)
        create all objects for a given molecule or scene
        Parameters:
        reps -
        allowSurface -
        ac0 - > 0 for a molecule; -1 for a scene
        ac -
      • addLabel

        void addLabel​(int atomIndex,
                      int uniqueID,
                      int atomColor,
                      float[] labelPos,
                      java.lang.String label)
      • getUniqueFloatDef

        float getUniqueFloatDef​(int id,
                                int key,
                                float defaultValue)
      • getUniquePoint

        javajs.util.P3 getUniquePoint​(int id,
                                      int key,
                                      javajs.util.P3 pt)
      • getObjectSetting

        javajs.util.Lst<java.lang.Object> getObjectSetting​(int i)
      • booleanSetting

        boolean booleanSetting​(int i)
      • floatSetting

        float floatSetting​(int i)
      • stringSetting

        java.lang.String stringSetting​(int i)
      • getSetting

        private javajs.util.Lst<java.lang.Object> getSetting​(int i)
      • setLabelPosition

        float[] setLabelPosition​(javajs.util.P3 offset,
                                 float[] labelPos)
      • addCGO

        java.lang.String addCGO​(javajs.util.Lst<java.lang.Object> data,
                                int color)
      • addMeasurements

        boolean addMeasurements​(MeasurementData[] mdList,
                                int nCoord,
                                javajs.util.Lst<java.lang.Object> list,
                                javajs.util.BS bsReps,
                                int color,
                                javajs.util.Lst<java.lang.Object> offsets,
                                boolean haveLabels)
      • getViewScript

        javajs.util.SB getViewScript​(javajs.util.Lst<java.lang.Object> view)
      • getColix

        short getColix​(int colorIndex,
                       float translucency)
      • setAtomColor

        void setAtomColor​(int atomColor)
      • setFrameObject

        void setFrameObject​(int type,
                            java.lang.Object info)
      • fixName

        private java.lang.String fixName​(java.lang.String name)
      • getObjectID

        java.lang.String getObjectID​(java.lang.String name)
      • getObjectType

        private int getObjectType​(java.lang.String name)
      • setAtomMap

        javajs.util.BS setAtomMap​(int[] atomMap,
                                  int ac0)
      • newTextLabel

        private Text newTextLabel​(java.lang.String label,
                                  float[] labelOffset,
                                  int colorIndex,
                                  int fontID,
                                  float fontSize)
      • setVersionSettings

        private void setVersionSettings()
        Attempt to adjust for PyMOL versions. See PyMOL layer3.Executive.c
      • addSetting

        private void addSetting​(int key,
                                int type,
                                java.lang.Object val)
      • fixReps

        private void fixReps​(javajs.util.BS[] reps)
      • cleanSingletons

        private void cleanSingletons​(javajs.util.BS bs)
        PyMOL does not display cartoons or traces for single-residue runs. This two-pass routine first sets bits in a residue bitset, then it clears out all singletons, and in a second pass all atom bits for not-represented residues are cleared.
        Parameters:
        bs -
      • createShapeObject

        private void createShapeObject​(int shapeID,
                                       javajs.util.BS bs)
        Create JmolObjects for each shape. Note that LINES and STICKS are done initially, then all the others are processed.
        Parameters:
        shapeID -
        bs -
      • setUniqueObjects

        private JmolObject setUniqueObjects​(int shape,
                                            javajs.util.BS bs,
                                            int setColor,
                                            int color,
                                            int setTrans,
                                            float trans,
                                            int setSize,
                                            float size,
                                            float f)
      • createSpacefillObjects

        private void createSpacefillObjects()
        Create a BALLS JmolObject for each radius.
      • createTraceObject

        private void createTraceObject​(javajs.util.BS bs)
        trace, or cartoon in the case of cartoon ladders.
        Parameters:
        bs -
      • checkNucleicObject

        private void checkNucleicObject​(javajs.util.BS bs,
                                        boolean isTrace)
      • createPuttyObject

        private void createPuttyObject​(javajs.util.BS bs)
        "Putty" shapes scaled in a variety of ways.
        Parameters:
        bs -
      • createRibbonObject

        private void createRibbonObject​(javajs.util.BS bs)
        PyMOL "ribbons" could be Jmol backbone or trace, depending upon the value of PyMOL.ribbon_sampling.
        Parameters:
        bs -
      • createCartoonObject

        private void createCartoonObject​(java.lang.String key,
                                         int sizeID)
      • setGroupVisible

        private void setGroupVisible​(PyMOLGroup g,
                                     boolean parentVis)
        Iterate through groups, setting visibility flags.
        Parameters:
        g -
        parentVis -
      • getSSMapAtom

        javajs.util.BS getSSMapAtom​(java.lang.String ssType)
      • setAtomDefs

        java.util.Map<java.lang.String,​java.lang.Object> setAtomDefs()
      • needSelections

        boolean needSelections()
      • setUniqueBonds

        void setUniqueBonds​(javajs.util.BS bsBonds,
                            boolean isSticks)
      • finalizeUniqueBonds

        private void finalizeUniqueBonds()
      • setBondParameters

        void setBondParameters​(Bond b,
                               int modelIndex,
                               float rad,
                               float pymolValence,
                               int argb,
                               float trans)
        used in PyMOL reader to set unique bond settings and for valence
        Parameters:
        modelIndex -
        b -
        rad -
        pymolValence - 1 for "show multiple bonds"
        argb -
        trans -
      • addMesh

        void addMesh​(int tok,
                     javajs.util.Lst<java.lang.Object> obj,
                     java.lang.String objName,
                     boolean isMep)
      • addIsosurface

        JmolObject addIsosurface​(java.lang.String objectName)