Uses of Class
org.biojava.nbio.structure.align.pairwise.FragmentPair

Packages that use FragmentPair

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

Methods in org.biojava.nbio.structure.align that return FragmentPair

Modifier and Type	Method and Description
FragmentPair[]	StructurePairAligner.getFragmentPairs() get the results of step 1 - the FragmentPairs used for seeding the alignment

Methods in org.biojava.nbio.structure.align with parameters of type FragmentPair

Modifier and Type	Method and Description
void	StructurePairAligner.setFragmentPairs(FragmentPair[] fragPairs)

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

Methods in org.biojava.nbio.structure.align.pairwise with parameters of type FragmentPair

Modifier and Type	Method and Description
boolean	FragmentJoiner.angleCheckOk(FragmentPair a, FragmentPair b, float distcutoff)
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.nbio.structure.align.pairwise with type arguments of type FragmentPair

Modifier and Type	Method and Description
void	AlignmentProgressListener.calculatedFragmentPairs(List<FragmentPair> fragments)
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.nbio.structure.gui

Methods in org.biojava.nbio.structure.gui that return FragmentPair

Modifier and Type	Method and Description
FragmentPair[]	ScaleableMatrixPanel.getFragmentPairs()
FragmentPair[]	JMatrixPanel.getFragmentPairs()

Methods in org.biojava.nbio.structure.gui with parameters of type FragmentPair

Modifier and Type	Method and Description
void	ScaleableMatrixPanel.setFragmentPairs(FragmentPair[] pairs)
void	JMatrixPanel.setFragmentPairs(FragmentPair[] fragmentPairs)