Constructor Detail

• StructureAlignmentDisplay

  public StructureAlignmentDisplay()

Method Detail

• display

  public static StructureAlignmentJmol display​(AFPChain afpChain,
                                               Atom[] ca1,
                                               Atom[] ca2)
                                        throws StructureException

  Display an AFPChain alignment

  Parameters:

  afpChain -

  ca1 -

  ca2 -

  Returns:

  a StructureAlignmentJmol instance

  Throws:

  StructureException

• prepareGroupsForDisplay

  public static Group[] prepareGroupsForDisplay​(AFPChain afpChain,
                                                Atom[] ca1,
                                                Atom[] ca2)
                                         throws StructureException

  Rotate the Atoms/Groups so they are aligned for the 3D visualisation

  Parameters:

  afpChain -

  ca1 -

  ca2 -

  Returns:

  an array of Groups that are transformed for 3D display

  Throws:

  StructureException

• shiftCA2

  public static void shiftCA2​(AFPChain afpChain,
                              Atom[] ca2,
                              Matrix m,
                              Atom shift,
                              Group[] twistedGroups)

  only shift CA positions.