Constructor Detail

• IsoExt

  public IsoExt()

Method Detail

• dispatch

  public java.lang.String dispatch​(int iTok,
                                   boolean b,
                                   T[] st)
                            throws ScriptException

  Specified by:

  dispatch in class ScriptExt

  Throws:

  ScriptException

• dipole

  private void dipole()
               throws ScriptException

  Throws:

  ScriptException

• draw

  private void draw()
             throws ScriptException

  Throws:

  ScriptException

• mo

  private void mo​(boolean isInitOnly,
                  int iShape)
           throws ScriptException

  Throws:

  ScriptException

• setNBOType

  private void setNBOType​(java.util.Map<java.lang.String,​java.lang.Object> moData,
                          java.lang.String type)
                   throws ScriptException

  Throws:

  ScriptException

• moCombo

  private float[] moCombo​(javajs.util.Lst<java.lang.Object[]> propertyList)

• moOffset

  private int moOffset​(int index)
                throws ScriptException

  Throws:

  ScriptException

• setMoData

  private void setMoData​(javajs.util.Lst<java.lang.Object[]> propertyList,
                         int moNumber,
                         float[] lc,
                         int offset,
                         boolean isNegOffset,
                         int modelIndex,
                         java.lang.String title,
                         java.lang.String nboType)
                  throws ScriptException

  Throws:

  ScriptException

• isosurface

  private void isosurface​(int iShape)
                   throws ScriptException

  Throws:

  ScriptException

• lcaoCartoon

  private void lcaoCartoon()
                    throws ScriptException

  Throws:

  ScriptException

• contact

  private boolean contact()
                   throws ScriptException

  Throws:

  ScriptException

• cgo

  private boolean cgo()
               throws ScriptException

  Throws:

  ScriptException

• getAtomicPotentials

  private float[] getAtomicPotentials​(BS bsSelected,
                                      BS bsIgnore,
                                      java.lang.String fileName)

  Parameters:

  bsSelected -

  bsIgnore -

  fileName -

  Returns:

  calculated atom potentials

• getCapSlabObject

  private java.lang.Object getCapSlabObject​(int i,
                                            boolean isLcaoCartoon)
                                     throws ScriptException

  Throws:

  ScriptException

• setColorOptions

  private java.lang.String setColorOptions​(javajs.util.SB sb,
                                           int index,
                                           int iShape,
                                           int nAllowed)
                                    throws ScriptException

  Throws:

  ScriptException

• createFunction

  private java.lang.Object[] createFunction​(java.lang.String fname,
                                            java.lang.String xyz,
                                            java.lang.String ret)

  for the ISOSURFACE command

  Parameters:

  fname -

  xyz -

  ret -

  Returns:

  [ ScriptFunction, Params ]

• getWithinDistanceVector

  private void getWithinDistanceVector​(javajs.util.Lst<java.lang.Object[]> propertyList,
                                       float distance,
                                       javajs.util.P3 ptc,
                                       BS bs,
                                       boolean isShow)

• addShapeProperty

  private void addShapeProperty​(javajs.util.Lst<java.lang.Object[]> propertyList,
                                java.lang.String key,
                                java.lang.Object value)

• floatArraySetXYZ

  private float[][][] floatArraySetXYZ​(int i,
                                       int nX,
                                       int nY,
                                       int nZ)
                                throws ScriptException

  Throws:

  ScriptException

• floatArraySet

  private float[][] floatArraySet​(int i,
                                  int nX,
                                  int nY)
                           throws ScriptException

  Throws:

  ScriptException

• initIsosurface

  private java.lang.String initIsosurface​(int iShape)
                                   throws ScriptException

  Throws:

  ScriptException

• listIsosurface

  private boolean listIsosurface​(int iShape)
                          throws ScriptException

  Throws:

  ScriptException

• getPlaneIntersection

  private javajs.util.Lst<java.lang.Object> getPlaneIntersection​(int type,
                                                                 javajs.util.P4 plane,
                                                                 SymmetryInterface uc,
                                                                 float scale,
                                                                 int flags)

  Parameters:

  type -

  plane - plane to intersect, or null for just the full box

  scale -

  uc -

  flags - 1 -- edges only 2 -- triangles only 3 -- both

  Returns:

  Vector