Uses of Class
org.biojava.nbio.structure.symmetry.internal.RefinerFailedException

Packages that use RefinerFailedException

Package	Description
org.biojava.nbio.structure.symmetry.internal

Uses of RefinerFailedException in org.biojava.nbio.structure.symmetry.internal

Methods in org.biojava.nbio.structure.symmetry.internal that throw RefinerFailedException

Modifier and Type	Method	Description
int	AngleOrderDetectorPlus.calculateOrder(AFPChain afpChain, Atom[] ca)
int	GraphComponentOrderDetector.calculateOrder(AFPChain selfAlignment, Atom[] ca)
int	OrderDetector.calculateOrder(AFPChain afpChain, Atom[] ca)
int	SequenceFunctionOrderDetector.calculateOrder(AFPChain afpChain, Atom[] ca)
MultipleAlignment	SymmOptimizer.optimize()	Optimization method based in a Monte-Carlo approach.
MultipleAlignment	GraphComponentRefiner.refine(AFPChain selfAlignment, Atom[] atoms, int order)
MultipleAlignment	SequenceFunctionRefiner.refine(AFPChain selfAlignment, Atom[] atoms, int order)
MultipleAlignment	SymmetryRefiner.refine(AFPChain selfAlignment, Atom[] atoms, int order)	Returns a refined symmetry alignment, where the repeat residues are aligned consistently in a MultipleAlignment.
static AFPChain	SequenceFunctionRefiner.refineSymmetry(AFPChain afpChain, Atom[] ca1, Atom[] ca2, int k)	Refines a CE-Symm alignment so that it is perfectly symmetric.