Package org.jmol.adapter.readers.pymol

Class PyMOLScene

  • All Implemented Interfaces:
    JmolSceneGenerator
    class PyMOLScene
extends 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.

    • 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 Map<Float,​javajs.util.BS> htSpacefill

      • ssMapAtom

        private Map<String,​javajs.util.BS> ssMapAtom

      • atomColorList

        private javajs.util.Lst<Integer> atomColorList

      • colixes

        private short[] colixes

      • objectSettings

        private Map<Integer,​javajs.util.Lst<Object>> objectSettings

      • bsCartoon

        private javajs.util.BS bsCartoon

      • htCarveSets

        private Map<String,​javajs.util.BS> htCarveSets

      • htDefinedAtoms

        private Map<String,​javajs.util.BS> htDefinedAtoms

      • moleculeNames

        private javajs.util.Lst<String> moleculeNames

      • jmolObjects

        private javajs.util.Lst<JmolObject> jmolObjects

      • htAtomMap

        private Map<String,​int[]> htAtomMap

      • htObjectAtoms

        private Map<String,​javajs.util.BS> htObjectAtoms

      • settings

        private javajs.util.Lst<Object> settings

      • uniqueSettings

        private Map<Integer,​javajs.util.Lst<Object>> uniqueSettings

      • 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 String objectName

      • objectNameID

        private String objectNameID

      • objectJmolName

        private 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

      • 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

        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<Object> settings,
           Map<Integer,​javajs.util.Lst<Object>> uniqueSettings,
           int pymolVersion,
           boolean haveScenes,
           int baseAtomIndex,
           int baseModelIndex,
           boolean doCache,
           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​(String name,
                         int type,
                         String groupName,
                         boolean isHidden,
                         javajs.util.Lst<Object> listObjSettings,
                         javajs.util.Lst<Object> listStateSettings,
                         String ext)

      • listToSettings

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

      • getObjectSettings

        private void getObjectSettings()

      • setAtomInfo

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

      • setSceneObject

        private void setSceneObject​(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​(String name,
                javajs.util.Lst<Object> thisScene,
                Map<String,​javajs.util.Lst<Object>> htObjNames,
                Map<String,​javajs.util.Lst<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​(Map<String,​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​(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<Object> selection)
        process the selection sets (sele), (...)
        Parameters:
        selection -

      • getSelectionAtoms

        private javajs.util.BS getSelectionAtoms​(javajs.util.Lst<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<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​(Map<String,​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​(Object[] reps)
        Create all Jmol shape objects.
        Parameters:
        reps -

      • getBS

        private javajs.util.BS getBS​(javajs.util.Lst<Object> list)

      • getBsAtoms

        private void getBsAtoms​(javajs.util.Lst<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,
                                 Object info)

      • addJmolObject

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

      • getPymolView

        private float[] getPymolView​(javajs.util.Lst<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<Object> object,
                    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

      • finalizeVisibility

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

      • setCarveSets

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

      • setGroupVisibilities

        private void setGroupVisibilities()

      • defineAtoms

        private void defineAtoms​(String name,
                         javajs.util.BS bs)

      • 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,
              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<Object> getObjectSetting​(int i)

      • booleanSetting

        boolean booleanSetting​(int i)

      • floatSetting

        float floatSetting​(int i)

      • stringSetting

        String stringSetting​(int i)

      • getSetting

        private javajs.util.Lst<Object> getSetting​(int i)

      • setLabelPosition

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

      • addCGO

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

      • addMeasurements

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

      • getViewScript

        javajs.util.SB getViewScript​(javajs.util.Lst<Object> view)

      • getColix

        short getColix​(int colorIndex,
               float translucency)

      • setAtomColor

        void setAtomColor​(int atomColor)

      • setFrameObject

        void setFrameObject​(int type,
                    Object info)

      • getObjectType

        private int getObjectType​(String name)

      • setAtomMap

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

      • newTextLabel

        private Text newTextLabel​(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,
                        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​(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​(String ssType)

      • 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<Object> obj,
             String objName,
             boolean isMep)