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[] JMatrixPanel.getFragmentPairs()
           
 FragmentPair[] ScaleableMatrixPanel.getFragmentPairs()
           
 

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