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

Interface MultipleSuperimposer

All Known Implementing Classes:

CoreSuperimposer, ReferenceSuperimposer

public interface MultipleSuperimposer

Interface for Multiple Alignment superposition algorithms.

There can be several implementations of a superimposer, because there is not a unique superposition of multiple structures given their residue equivalencies, and their running times are asymptotically different.

Since:

4.1.0

Author:

Spencer Bliven, Aleix Lafita

Method Summary

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

Method Detail

superimpose

void superimpose(MultipleAlignment alignment)
          throws StructureException

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.

Parameters:

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

Throws:

StructureException