## 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)` get the RMS of the JointFragments pair frag