org.biojava.bio.structure.align.fatcat.calc
Class StructureAlignmentOptimizer
java.lang.Object
org.biojava.bio.structure.align.fatcat.calc.StructureAlignmentOptimizer
public class StructureAlignmentOptimizer
- extends Object
Constructor Summary |
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 |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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
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)