Uses of Class
org.biojava.bio.structure.align.helper.JointFragments

Packages that use JointFragments
org.biojava.bio.structure.align.pairwise Classes for the pairwise alignment of structures. 
 

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

Methods in org.biojava.bio.structure.align.pairwise that return JointFragments
 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.
 

Methods in org.biojava.bio.structure.align.pairwise with parameters of type JointFragments
 void AlternativeAlignment.apairs_from_idxlst(JointFragments jf)
          Set apairs according to a list of (i,j) tuples.
static double FragmentJoiner.getRMS(Atom[] ca1, Atom[] ca2, JointFragments frag)