SymmetryRefiner
public class SequenceFunctionRefiner extends java.lang.Object implements SymmetryRefiner
Constructor | Description |
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SequenceFunctionRefiner() |
Modifier and Type | Method | 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.
|
static java.util.Map<java.lang.Integer,java.lang.Integer> |
refineSymmetry(java.util.Map<java.lang.Integer,java.lang.Integer> alignment,
int k) |
Refines a CE-Symm alignment so that it is perfectly symmetric.
|
static AFPChain |
refineSymmetry(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2,
int k) |
Refines a CE-Symm alignment so that it is perfectly symmetric.
|
public MultipleAlignment refine(AFPChain selfAlignment, Atom[] atoms, int order) throws RefinerFailedException, StructureException
SymmetryRefiner
refine
in interface SymmetryRefiner
selfAlignment
- optimal self-alignment calculated by CeSymmatoms
- coordinates of the structureorder
- order of symmetry to useRefinerFailedException
StructureException
public static AFPChain refineSymmetry(AFPChain afpChain, Atom[] ca1, Atom[] ca2, int k) throws StructureException, RefinerFailedException
afpChain
- Input alignment from CE-Symmk
- Symmetry order. This can be guessed by CeSymm#getSymmetryOrder(AFPChain)
StructureException
RefinerFailedException
public static java.util.Map<java.lang.Integer,java.lang.Integer> refineSymmetry(java.util.Map<java.lang.Integer,java.lang.Integer> alignment, int k) throws StructureException
alignment
- The input alignment, as a map. This will be modified.k
- Symmetry order. This can be guessed by CeSymm#getSymmetryOrder(AFPChain)
StructureException