Field Detail

• modelSet

  private ModelSet modelSet

• RET_XYZ

  private static final int RET_XYZ

  See Also:

  Constant Field Values

• RET_XYZORIGINAL

  private static final int RET_XYZORIGINAL

  See Also:

  Constant Field Values

• RET_LABEL

  private static final int RET_LABEL

  See Also:

  Constant Field Values

• RET_DRAW

  private static final int RET_DRAW

  See Also:

  Constant Field Values

• RET_FTRANS

  private static final int RET_FTRANS

  See Also:

  Constant Field Values

• RET_CTRANS

  private static final int RET_CTRANS

  See Also:

  Constant Field Values

• RET_INVCTR

  private static final int RET_INVCTR

  See Also:

  Constant Field Values

• RET_POINT

  private static final int RET_POINT

  See Also:

  Constant Field Values

• RET_AXISVECTOR

  private static final int RET_AXISVECTOR

  See Also:

  Constant Field Values

• RET_ROTANGLE

  private static final int RET_ROTANGLE

  See Also:

  Constant Field Values

• RET_MATRIX

  private static final int RET_MATRIX

  See Also:

  Constant Field Values

• RET_UNITTRANS

  private static final int RET_UNITTRANS

  See Also:

  Constant Field Values

• RET_CTRVECTOR

  private static final int RET_CTRVECTOR

  See Also:

  Constant Field Values

• RET_TIMEREV

  private static final int RET_TIMEREV

  See Also:

  Constant Field Values

• RET_PLANE

  private static final int RET_PLANE

  See Also:

  Constant Field Values

• RET_TYPE

  private static final int RET_TYPE

  See Also:

  Constant Field Values

• RET_ID

  private static final int RET_ID

  See Also:

  Constant Field Values

• RET_CIF2

  private static final int RET_CIF2

  See Also:

  Constant Field Values

• RET_XYZCANON

  private static final int RET_XYZCANON

  See Also:

  Constant Field Values

• RET_XYZNORMALIZED

  private static final int RET_XYZNORMALIZED

  See Also:

  Constant Field Values

• RET_COUNT

  private static final int RET_COUNT

  See Also:

  Constant Field Values

• RET_LIST

  static final int RET_LIST

  See Also:

  Constant Field Values

• RET_INVARIANT

  static final int RET_INVARIANT

  See Also:

  Constant Field Values

• keys

  private static final java.lang.String[] keys

• vtemp

  private static javajs.util.V3 vtemp

• ptemp

  private static javajs.util.P3 ptemp

• ptemp2

  private static javajs.util.P3 ptemp2

• pta01

  private static javajs.util.P3 pta01

• pta02

  private static javajs.util.P3 pta02

• vtrans

  private static javajs.util.V3 vtrans

Constructor Detail

• SymmetryDesc

  public SymmetryDesc()

Method Detail

• set

  public SymmetryDesc set​(ModelSet modelSet)

• getType

  private static int getType​(java.lang.String id)

  Determine the type of this request. Note that label and xyz will be returned as T.xyz and T.label

  Parameters:

  id -

  Returns:

  a code that identifies this request.

• getKeyType

  private static int getKeyType​(java.lang.String id)

• nullReturn

  private static java.lang.Object nullReturn​(int type)

• getInfo

  private static java.lang.Object getInfo​(java.lang.Object[] io,
                                          int type)

  Return information about a symmetry operator by type: array, angle, axis, center, draw, full, info, label, matrix4f, point, time, plane, translation, unitcell, xyz, all, or a negative number (-length, -1]: { "xyz", etc. } where "all" is the info array itself,

  Parameters:

  io -

  type -

  Returns:

  object specified

• getInfoBS

  private static javajs.util.BS getInfoBS​(int type)

• createInfoArray

  private java.lang.Object[] createInfoArray​(SymmetryOperation op,
                                             SymmetryInterface uc,
                                             javajs.util.P3 ptFrom,
                                             javajs.util.P3 ptTarget,
                                             java.lang.String id,
                                             float scaleFactor,
                                             int options,
                                             boolean haveTranslation,
                                             javajs.util.BS bsInfo)

  Parameters:

  op -

  uc -

  ptFrom - optional initial atom point

  ptTarget - optional target atom point

  id -

  scaleFactor - scale for rotation vector only

  options - 0 or T.offset

  haveTranslation - TODO

  bsInfo -

  Returns:

  Object[] containing: [0] xyz (Jones-Faithful calculated from matrix) [1] xyzOriginal (Provided by calling method) [2] info ("C2 axis", for example) [3] draw commands [4] translation vector (fractional) [5] translation vector (Cartesian) [6] inversion point [7] axis point [8] axis vector (defines plane if angle = 0 [9] angle of rotation [10] matrix representation [11] lattice translation [12] centering [13] time reversal [14] plane [15] _type [16] id [17] element [18] invariant

• drawLine

  private static void drawLine​(javajs.util.SB s,
                               java.lang.String id,
                               float diameter,
                               javajs.util.P3 pt0,
                               javajs.util.P3 pt1,
                               java.lang.String color)

• drawFrameLine

  private static void drawFrameLine​(java.lang.String xyz,
                                    javajs.util.P3 pt,
                                    javajs.util.V3 v,
                                    float width,
                                    javajs.util.P3 ptemp,
                                    javajs.util.SB draw1,
                                    java.lang.String key,
                                    java.lang.String color)

• drawVector

  private static void drawVector​(javajs.util.SB draw1,
                                 java.lang.String drawid,
                                 java.lang.String label,
                                 java.lang.String type,
                                 javajs.util.T3 pt1,
                                 javajs.util.T3 v,
                                 java.lang.String color)

• setFractional

  private static void setFractional​(SymmetryInterface uc,
                                    javajs.util.T3 pt00,
                                    javajs.util.P3 pt01,
                                    javajs.util.P3 offset)

  Set pt01 to pt00, possibly adding offset into unit cell

  Parameters:

  uc -

  pt00 -

  pt01 -

  offset -

• rotTransCart

  private static javajs.util.P3 rotTransCart​(SymmetryOperation op,
                                             SymmetryInterface uc,
                                             javajs.util.P3 pt00,
                                             javajs.util.V3 vtrans)

• strCoord

  private static java.lang.String strCoord​(SymmetryOperation op,
                                           javajs.util.T3 p,
                                           boolean isBio)

• approx0

  private static javajs.util.T3 approx0​(javajs.util.T3 pt)

• approx

  private static javajs.util.T3 approx​(javajs.util.T3 pt)

• getSymmetryInfo

  private java.lang.Object getSymmetryInfo​(SymmetryInterface sym,
                                           int iModel,
                                           int iatom,
                                           SymmetryInterface uc,
                                           java.lang.String xyz,
                                           int op,
                                           javajs.util.P3 translation,
                                           javajs.util.P3 pt,
                                           javajs.util.P3 pt2,
                                           java.lang.String id,
                                           int type,
                                           float scaleFactor,
                                           int nth,
                                           int options)

  multipurpose function handling a variety of tasks, including: processing of "lattice", "list", "atom", "point", and some "draw" output types finding the operator in the given space group creating a temporary space group for an xyz operator

  Parameters:

  sym -

  iModel -

  iatom -

  uc -

  xyz -

  op -

  translation - [i j k] to be added to operator

  pt -

  pt2 - second point or offset

  id -

  type -

  scaleFactor -

  nth -

  options - 0 or T.offset

  Returns:

  a string or an Object[] containing information

• getAtom

  private javajs.util.BS getAtom​(SymmetryInterface uc,
                                 int iModel,
                                 int iAtom,
                                 javajs.util.T3 sympt)

• getSymopInfoForPoints

  java.lang.Object getSymopInfoForPoints​(SymmetryInterface sym,
                                         int modelIndex,
                                         int symOp,
                                         javajs.util.P3 translation,
                                         javajs.util.P3 pt1,
                                         javajs.util.P3 pt2,
                                         java.lang.String drawID,
                                         java.lang.String stype,
                                         float scaleFactor,
                                         int nth,
                                         int options,
                                         javajs.util.BS bsInfo)

  get information about a symmetry operation relating two specific points or atoms

  Parameters:

  sym -

  modelIndex -

  symOp -

  translation - TODO

  pt1 -

  pt2 -

  drawID -

  stype -

  scaleFactor -

  nth -

  options - 0 or T.offset

  bsInfo -

  Returns:

  Object[] or String or Object[Object[]] (nth = 0, "array")

• getSymopInfo

  java.lang.Object getSymopInfo​(int iAtom,
                                java.lang.String xyz,
                                int op,
                                javajs.util.P3 translation,
                                javajs.util.P3 pt,
                                javajs.util.P3 pt2,
                                java.lang.String id,
                                int type,
                                float scaleFactor,
                                int nth,
                                int options)

  Parameters:

  iAtom -

  xyz -

  op -

  translation - TODO

  pt -

  pt2 -

  id -

  type -

  scaleFactor -

  nth -

  options - 0 or T.offset

  Returns:

  "" or a bitset of matching atoms, or

• getSpaceGroupInfo

  java.util.Map<java.lang.String,​java.lang.Object> getSpaceGroupInfo​(SymmetryInterface sym,
                                                                           int modelIndex,
                                                                           java.lang.String sgName,
                                                                           int symOp,
                                                                           javajs.util.P3 pt1,
                                                                           javajs.util.P3 pt2,
                                                                           java.lang.String drawID,
                                                                           float scaleFactor,
                                                                           int nth,
                                                                           boolean isFull,
                                                                           boolean isForModel,
                                                                           int options,
                                                                           SymmetryInterface cellInfo,
                                                                           javajs.util.BS bsInfo)

• getTransform

  public javajs.util.M4 getTransform​(UnitCell uc,
                                     SymmetryOperation[] ops,
                                     javajs.util.P3 fracA,
                                     javajs.util.P3 fracB,
                                     boolean best)