Package | Description |
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org.biojava.bio.structure.align |
Classes for the super-imposition of structures.
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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.
|
Modifier and Type | Method and Description |
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FragmentPair[] |
StructurePairAligner.getFragmentPairs()
get the results of step 1 - the FragmentPairs used for seeding the alignment
|
Modifier and Type | Method and Description |
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void |
StructurePairAligner.setFragmentPairs(FragmentPair[] fragPairs) |
Modifier and Type | Method and Description |
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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.
|
Modifier and Type | Method and Description |
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static boolean |
FragmentJoiner.reduceFragments(java.util.List<FragmentPair> fragments,
FragmentPair f,
Matrix rmsmat)
In helices often many similar fragments can be found.
|
Modifier and Type | Method and Description |
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FragmentPair[] |
ScaleableMatrixPanel.getFragmentPairs() |
FragmentPair[] |
JMatrixPanel.getFragmentPairs() |
Modifier and Type | Method and Description |
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void |
ScaleableMatrixPanel.setFragmentPairs(FragmentPair[] pairs) |
void |
JMatrixPanel.setFragmentPairs(FragmentPair[] fragmentPairs) |