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

All Methods Instance Methods Concrete Methods
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 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)

Class StructureAlignmentOptimizer