ReferenceSuperimposer (biojava 6.0.0 API)

java.lang.Object
- org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer

All Implemented Interfaces:

MultipleSuperimposer
```
public class ReferenceSuperimposer
extends Object
implements MultipleSuperimposer
```
Superimposes each structure in a MultipleAlignment onto a reference structure.
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:

4.1.0

Author:

Spencer Bliven, Aleix Lafita

- Constructor Summary
  
  Constructors
  Constructor Description
  
  ReferenceSuperimposer()
  Default Constructor.
  
  ReferenceSuperimposer(int reference)
  Constructor using a specified structure as reference.
- Method Summary
  
  All Methods Instance Methods Concrete Methods
  Modifier and Type Method 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
  - ReferenceSuperimposer
```
public ReferenceSuperimposer()
```
    Default Constructor. Uses the first structure as the reference.
  - ReferenceSuperimposer
```
public ReferenceSuperimposer(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