public class CoreSuperimposer extends Object implements MultipleSuperimposer
MultipleAlignmentonto 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
|Constructor and Description|
Constructor using a specified structure as reference.
public CoreSuperimposer(int reference)
reference- Index of the structure to use as a reference (it has to be > 0)
public void superimpose(MultipleAlignment alignment) throws StructureException
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
This method only calculates and sets the transformation 4D Matrices.
If any score is needed it should be calculated and set separately
Copyright © 2000–2016 BioJava. All rights reserved.