Constructor Detail

• StructureAlignmentOptimizer

  public StructureAlignmentOptimizer​(int b1,
                                     int end1,
                                     Atom[] c1,
                                     int b2,
                                     int end2,
                                     Atom[] c2,
                                     int iniLen,
                                     int[][] iniSet)
                              throws StructureException

  optimize the structural alignment by update the equivalent residues and then run dynamic programming input: len1 the length of structure 1; c1: the structure information of 1 len2 the length of structure 2; c2: the structure information of 2 iniLen and iniSet is the length and list of initial equivalent residues

  Throws:

  StructureException

Method Detail

• runOptimization

  public void runOptimization​(int maxi)
                       throws StructureException

  run the optimization

  Parameters:

  maxi - maximum nr. of iterations

  Throws:

  StructureException

• optimizeResult

  public double optimizeResult​(int[] optLen,
                               int optLenpos,
                               int[][] list)