public class GraphComponentRefiner extends java.lang.Object implements SymmetryRefiner
Given a set of components and their pairwise compatibilities, iteratively add the most compatible component, which is compatible to all the components already added, to the final alignment.
Constructor and Description |
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GraphComponentRefiner() |
Modifier and Type | Method and Description |
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MultipleAlignment |
refine(AFPChain selfAlignment,
Atom[] atoms,
int order)
Returns a refined symmetry alignment, where the repeat residues are
aligned consistently in a MultipleAlignment.
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public MultipleAlignment refine(AFPChain selfAlignment, Atom[] atoms, int order) throws StructureException, RefinerFailedException
SymmetryRefiner
refine
in interface SymmetryRefiner
selfAlignment
- optimal self-alignment calculated by CeSymmatoms
- coordinates of the structureorder
- order of symmetry to useStructureException
RefinerFailedException