Package 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 SVDSuperimposer algorithm.

Since:
4.2.0
Author:
Aleix Lafita

  • Constructor Details

    • 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 Details