Package org.biojava.nbio.structure.align

Classes for the alignment of structures. This is the unpublished legacy implementation from the time, before BioJava supported CE and FATCAT alignments. See the StructurePairAligner for an example.

Interface Summary

Interface	Description
MultipleStructureAligner	Interface for the Multiple Structure Alignment Algorithms.
StructureAlignment

Class Summary

Class	Description
AbstractStructureAlignment
AFPTwister
BioJavaStructureAlignment	Wrapper for the BioJava Structure Alignment Implementation
CallableStructureAlignment	Simple Callable Class that calculates a pairwise alignment in a different thread, so that multiple pairwise alignments can be run in parallel (examples: all-to-all alignments, DB search alignments).
ClusterAltAligs	A class that clusters alternative alignments according to their similarity.
StrucAligParameters	A class that contains all the parameters of the structure alignment algorithm.
StructureAlignmentFactory
StructurePairAligner	Perform a pairwise protein structure superimposition.