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

Packages that use JointFragments

Package	Description
org.biojava.nbio.structure.align.pairwise	Classes for the pairwise alignment of structures.

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

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

Modifier and Type	Method	Description
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.nbio.structure.align.pairwise with parameters of type JointFragments

Modifier and Type	Method	Description
void	AlternativeAlignment.apairs_from_idxlst(JointFragments jf)	Set apairs according to a list of (i,j) tuples.
void	FragmentJoiner.extendFragments(Atom[] ca1, Atom[] ca2, JointFragments[] fragments, StrucAligParameters params)
void	FragmentJoiner.extendFragments(Atom[] ca1, Atom[] ca2, JointFragments fragments, StrucAligParameters params)
static double	FragmentJoiner.getRMS(Atom[] ca1, Atom[] ca2, JointFragments frag)	Get the RMS of the JointFragments pair frag
void	AlignmentProgressListener.jointFragments(JointFragments[] fragments)