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Packages that use FragmentPair | |
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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. |
Uses of FragmentPair in org.biojava.bio.structure.align |
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Methods in org.biojava.bio.structure.align that return FragmentPair | |
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FragmentPair[] |
StructurePairAligner.getFragmentPairs()
get the results of step 1 - the FragmentPairs used for seeding the alignment |
Methods in org.biojava.bio.structure.align with parameters of type FragmentPair | |
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void |
StructurePairAligner.setFragmentPairs(FragmentPair[] fragPairs)
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Uses of FragmentPair in org.biojava.bio.structure.align.pairwise |
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Methods in org.biojava.bio.structure.align.pairwise with parameters of type FragmentPair | |
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JointFragments[] |
FragmentJoiner.approach_ap3(Atom[] ca1,
Atom[] ca2,
FragmentPair[] fraglst,
StrucAligParameters params)
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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.bio.structure.align.pairwise with type arguments of type FragmentPair | |
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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.bio.structure.gui |
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Methods in org.biojava.bio.structure.gui that return FragmentPair | |
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FragmentPair[] |
JMatrixPanel.getFragmentPairs()
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FragmentPair[] |
ScaleableMatrixPanel.getFragmentPairs()
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Methods in org.biojava.bio.structure.gui with parameters of type FragmentPair | |
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void |
JMatrixPanel.setFragmentPairs(FragmentPair[] fragmentPairs)
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void |
ScaleableMatrixPanel.setFragmentPairs(FragmentPair[] pairs)
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