## Uses of Class
org.biojava.bio.structure.align.pairwise.FragmentPair

Packages that use FragmentPair
org.biojava.bio.structure.align: Classes for the super-imposition of structures.
org.biojava.bio.structure.align.pairwise: Classes for the pairwise alignment of structures.
org.biojava.bio.structure.gui: A few convenience classes to view protein structures with Jmol (if it is on the classpath), to calculate a protein structure alignment and to investigate the internals of the protein structure alignment algorithm.

Uses of FragmentPair in org.biojava.bio.structure.align

Methods in org.biojava.bio.structure.align that return FragmentPair
`FragmentPair[]` `StructurePairAligner.getFragmentPairs()` get the results of step 1 - the FragmentPairs used for seeding the alignment

Methods in org.biojava.bio.structure.align with parameters of type FragmentPair
`void` `StructurePairAligner.setFragmentPairs(FragmentPair[] fragPairs)`

Uses of FragmentPair in org.biojava.bio.structure.align.pairwise

Methods in org.biojava.bio.structure.align.pairwise with parameters of type FragmentPair
`JointFragments[]` `FragmentJoiner.approach_ap3(Atom[] ca1, Atom[] ca2, FragmentPair[] fraglst, StrucAligParameters params)`
`JointFragments[]` `FragmentJoiner.frag_pairwise_compat(FragmentPair[] fraglst, int angleDiff, float fragCompatDist, int maxRefine)` Calculate the pairwise compatibility of fpairs.
`static boolean` `FragmentJoiner.reduceFragments(List<FragmentPair> fragments, FragmentPair f, Matrix rmsmat)` In helices often many similar fragments can be found.

Method parameters in org.biojava.bio.structure.align.pairwise with type arguments of type FragmentPair
`static boolean` `FragmentJoiner.reduceFragments(List<FragmentPair> fragments, FragmentPair f, Matrix rmsmat)` In helices often many similar fragments can be found.

Uses of FragmentPair in org.biojava.bio.structure.gui

Methods in org.biojava.bio.structure.gui that return FragmentPair
`FragmentPair[]` `ScaleableMatrixPanel.getFragmentPairs()`
`FragmentPair[]` `JMatrixPanel.getFragmentPairs()`

Methods in org.biojava.bio.structure.gui with parameters of type FragmentPair
`void` `ScaleableMatrixPanel.setFragmentPairs(FragmentPair[] pairs)`
`void` `JMatrixPanel.setFragmentPairs(FragmentPair[] fragmentPairs)`