Field Detail

• vwr

  private Viewer vwr

• pymolVersion

  private int pymolVersion

• bsHidden

  BS bsHidden

• bsNucleic

  BS bsNucleic

• bsNonbonded

  BS bsNonbonded

• bsLabeled

  BS bsLabeled

• bsHydrogen

  BS bsHydrogen

• bsNoSurface

  BS bsNoSurface

• htSpacefill

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

• ssMapAtom

  private java.util.Map<java.lang.String,​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

• frameObj

  private JmolObject frameObj

• 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 BS bsCartoon

• htCarveSets

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

• htDefinedAtoms

  private java.util.Map<java.lang.String,​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,​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 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 BS bsAtoms

• objectHidden

  private boolean objectHidden

• reader

  private PymolAtomReader reader

• 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 BS bsCarve

• solventAccessible

  private boolean solventAccessible

• bsLineBonds

  private BS bsLineBonds

• bsStickBonds

  private 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 BS getSelectionAtoms​(javajs.util.Lst<java.lang.Object> molecules,
                               int istate,
                               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,
                              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 BS getBS​(javajs.util.Lst<java.lang.Object> list)

• getBsAtoms

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

• addJmolObject

  private JmolObject addJmolObject​(int id,
                                   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,
                      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,
                           BS bs)

• getJmolName

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

• createShapeObjects

  void createShapeObjects​(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,
                          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

  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​(BS[] reps)

• cleanSingletons

  private void cleanSingletons​(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,
                                 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,
                                      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​(BS bs)

  trace, or cartoon in the case of cartoon ladders.

  Parameters:

  bs -

• checkNucleicObject

  private void checkNucleicObject​(BS bs,
                                  boolean isTrace)

• createPuttyObject

  private void createPuttyObject​(BS bs)

  "Putty" shapes scaled in a variety of ways.

  Parameters:

  bs -

• createRibbonObject

  private void createRibbonObject​(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)

• addObject

  private JmolObject addObject​(JmolObject obj)

• setGroupVisible

  private void setGroupVisible​(PyMOLGroup g,
                               boolean parentVis)

  Iterate through groups, setting visibility flags.

  Parameters:

  g -

  parentVis -

• getSSMapAtom

  BS getSSMapAtom​(java.lang.String ssType)

• setAtomDefs

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

• needSelections

  boolean needSelections()

• setUniqueBonds

  void setUniqueBonds​(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)