- All Implemented Interfaces:
public class CoreSuperimposer extends Object implements MultipleSuperimposerSuperimposes the core aligned residues of every structure in a
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
- Aleix Lafita
All Methods Instance Methods Concrete Methods Modifier and Type Method Description
superimpose(MultipleAlignment alignment)Superimpose all structures from a
public CoreSuperimposer()Default Constructor. Uses the first structure as the reference.
public CoreSuperimposer(int reference)Constructor using a specified structure as reference.
reference- Index of the structure to use as a reference (it has to be > 0)
public void superimpose(MultipleAlignment alignment) throws StructureExceptionDescription copied from interface:
MultipleSuperimposerSuperimpose 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
This method only calculates and sets the transformation 4D Matrices. If any score is needed it should be calculated and set separately afterwards with