org.biojava.nbio.structure.align.multiple.util

Class CoreSuperimposer

java.lang.Object

org.biojava.nbio.structure.align.multiple.util.CoreSuperimposer

All Implemented Interfaces:

MultipleSuperimposer

public class CoreSuperimposer
extends Object
implements MultipleSuperimposer

Superimposes the core aligned residues of every structure in a MultipleAlignment onto a reference structure. This method can eliminate the pairwise similarities of some structures to the reference, when doing the superposition, taking into account only those shared parts between the structures.

Performs a global superposition of the MultipleAlignment in case there is only one BlockSet, and a superposition for every BlockSet in case there is more than one (flexible alignment).

This class uses the SuperPositionSVD algorithm.

Since:

4.2.0

Author:

Aleix Lafita

Constructor Summary

Constructors

Constructor and Description
CoreSuperimposer() Default Constructor.
CoreSuperimposer(int reference) Constructor using a specified structure as reference.

Method Summary

Modifier and Type	Method and Description
void	superimpose(MultipleAlignment alignment) Superimpose all structures from a MultipleAlignment.

Methods inherited from class java.lang.Object

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

Constructor Detail

CoreSuperimposer

public CoreSuperimposer()

Default Constructor. Uses the first structure as the reference.

CoreSuperimposer

public CoreSuperimposer(int reference)

Constructor using a specified structure as reference.

Parameters:

reference - Index of the structure to use as a reference (it has to be > 0)

Method Detail

superimpose

public void superimpose(MultipleAlignment alignment)
                 throws StructureException

Description copied from interface: MultipleSuperimposer

Superimpose all structures from a MultipleAlignment. The superposition is done for all individual BlockSets. If there is only one BlockSet.

At a minimum, this should set the transformation matrices for the individual BlockSets.

This method only calculates and sets the transformation 4D Matrices. If any score is needed it should be calculated and set separately afterwards with MultipleAlignmentScorer.

Specified by:

superimpose in interface MultipleSuperimposer

Parameters:

alignment - MultipleAlignment specifying the aligned residues (via the blocksets) and the atoms to align (via the ensemble).

Throws:

StructureException