Package org.biojava.nbio.structure.align.fatcat.calc

Class StructureAlignmentOptimizer

java.lang.Object
org.biojava.nbio.structure.align.fatcat.calc.StructureAlignmentOptimizer
public class StructureAlignmentOptimizer extends Object

  • Constructor Summary

    Constructors
    Constructor
    Description
    StructureAlignmentOptimizer(int b1, int end1, Atom[] c1, int b2, int end2, Atom[] c2, int iniLen, int[][] iniSet)
    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

  • Method Summary

    Modifier and Type
    Method
    Description
    double
    optimizeResult(int[] optLen, int optLenpos, int[][] list)
     
    void
    runOptimization(int maxi)
    run the optimization

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Constructor Details

    • 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 Details

    • 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)