Class ReferenceSuperimposer
java.lang.Object
org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer
- All Implemented Interfaces:
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 SVDSuperimposer algorithm.
- Since:
- 4.1.0
- Author:
- Spencer Bliven, Aleix Lafita
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Constructor Summary
ConstructorsConstructorDescriptionDefault Constructor.ReferenceSuperimposer(int reference) Constructor using a specified structure as reference. -
Method Summary
Modifier and TypeMethodDescriptionvoidsuperimpose(MultipleAlignment alignment) Superimpose all structures from aMultipleAlignment.
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Constructor Details
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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)
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Method Details
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superimpose
Description copied from interface:MultipleSuperimposerSuperimpose all structures from aMultipleAlignment. 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:
superimposein interfaceMultipleSuperimposer- Parameters:
alignment- MultipleAlignment specifying the aligned residues (via theblocksets) and the atoms to align (via theensemble).- Throws:
StructureException
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