Uses of Class
org.biojava.bio.structure.align.pairwise.FragmentPair
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Packages that use FragmentPair Package Description 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. -
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Uses of FragmentPair in org.biojava.bio.structure.align
Methods in org.biojava.bio.structure.align that return FragmentPair Modifier and Type Method Description FragmentPair[]
StructurePairAligner. getFragmentPairs()
get the results of step 1 - the FragmentPairs used for seeding the alignmentMethods in org.biojava.bio.structure.align with parameters of type FragmentPair Modifier and Type Method Description void
StructurePairAligner. setFragmentPairs(FragmentPair[] fragPairs)
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Uses of FragmentPair in org.biojava.bio.structure.align.pairwise
Methods in org.biojava.bio.structure.align.pairwise with parameters of type FragmentPair 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.static boolean
FragmentJoiner. reduceFragments(java.util.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 Modifier and Type Method Description static boolean
FragmentJoiner. reduceFragments(java.util.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 Modifier and Type Method Description FragmentPair[]
JMatrixPanel. getFragmentPairs()
FragmentPair[]
ScaleableMatrixPanel. getFragmentPairs()
Methods in org.biojava.bio.structure.gui with parameters of type FragmentPair Modifier and Type Method Description void
JMatrixPanel. setFragmentPairs(FragmentPair[] fragmentPairs)
void
ScaleableMatrixPanel. setFragmentPairs(FragmentPair[] pairs)
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