org.biojava.nbio.structure.symmetry.internal

Class SequenceFunctionRefiner

java.lang.Object

org.biojava.nbio.structure.symmetry.internal.SequenceFunctionRefiner

All Implemented Interfaces:

SymmetryRefiner

public class SequenceFunctionRefiner
extends Object
implements SymmetryRefiner

Creates a refined alignment with the CE-Symm alternative self-alignment. Needs the order of symmetry and assumes that the last repeat aligns with the first, being thus a CLOSE symmetry.

Since:

4.2.0

Author:

Spencer Bliven, Aleix Lafita

Constructor Summary

Constructors

Constructor and Description
SequenceFunctionRefiner()

Method Summary

Modifier and Type	Method and Description
MultipleAlignment	refine(AFPChain selfAlignment, Atom[] atoms, int order) Returns a refined symmetry alignment, where the repeat residues are aligned consistently in a MultipleAlignment.
static AFPChain	refineSymmetry(AFPChain afpChain, Atom[] ca1, Atom[] ca2, int k) Refines a CE-Symm alignment so that it is perfectly symmetric.
static Map<Integer,Integer>	refineSymmetry(Map<Integer,Integer> alignment, int k) Refines a CE-Symm alignment so that it is perfectly symmetric.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SequenceFunctionRefiner

public SequenceFunctionRefiner()

Method Detail

refine

public MultipleAlignment refine(AFPChain selfAlignment,
                                Atom[] atoms,
                                int order)
                         throws RefinerFailedException,
                                StructureException

Description copied from interface: SymmetryRefiner

Returns a refined symmetry alignment, where the repeat residues are aligned consistently in a MultipleAlignment.

Specified by:

refine in interface SymmetryRefiner

Parameters:

selfAlignment - optimal self-alignment calculated by CeSymm

atoms - coordinates of the structure

order - order of symmetry to use

Returns:

MultipleAlignment refined symmetry alignment

Throws:

RefinerFailedException

StructureException

refineSymmetry

public static AFPChain refineSymmetry(AFPChain afpChain,
                                      Atom[] ca1,
                                      Atom[] ca2,
                                      int k)
                               throws StructureException,
                                      RefinerFailedException

Refines a CE-Symm alignment so that it is perfectly symmetric. The resulting alignment will have a one-to-one correspondance between aligned residues of each symmetric part.

Parameters:

afpChain - Input alignment from CE-Symm

k - Symmetry order. This can be guessed by CeSymm#getSymmetryOrder(AFPChain)

Returns:

The refined alignment

Throws:

StructureException

RefinerFailedException

refineSymmetry

public static Map<Integer,Integer> refineSymmetry(Map<Integer,Integer> alignment,
                                                  int k)
                                           throws StructureException

Refines a CE-Symm alignment so that it is perfectly symmetric. The resulting alignment will have a one-to-one correspondance between aligned residues of each symmetric part.

Parameters:

alignment - The input alignment, as a map. This will be modified.

k - Symmetry order. This can be guessed by CeSymm#getSymmetryOrder(AFPChain)

Returns:

A modified map with the refined alignment

Throws:

StructureException