Class PyMOLScene

Method Details

• 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

• getGroup

  PyMOLGroup getGroup(String name)

• 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)

• getJmolName

  private String getJmolName(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, 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)

• fixName

  private String fixName(String name)

• getObjectID

  String getObjectID(String name)

• 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)

• addObject

  private JmolObject addObject(JmolObject obj)

• setGroupVisible

  private void setGroupVisible(PyMOLGroup g, boolean parentVis)

  Iterate through groups, setting visibility flags.

  Parameters:

  g -

  parentVis -

• getSSMapAtom

  javajs.util.BS getSSMapAtom(String ssType)

• setAtomDefs

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

• addIsosurface

  JmolObject addIsosurface(String objectName)