Class StructureAlignmentOptimizer
- java.lang.Object
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- org.biojava.nbio.structure.align.fatcat.calc.StructureAlignmentOptimizer
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public class StructureAlignmentOptimizer extends Object
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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
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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
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Constructor Detail
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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
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Method Detail
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runOptimization
public void runOptimization(int maxi) throws StructureException
run the optimization- Parameters:
maxi
- maximum nr. of iterations- Throws:
StructureException
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optimizeResult
public double optimizeResult(int[] optLen, int optLenpos, int[][] list)
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