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.
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Modifier and Type | Method and Description |
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static StrucAligParameters |
StrucAligParameters.getDBSearchParameters() |
static StrucAligParameters |
StrucAligParameters.getDefaultParameters() |
StrucAligParameters |
StructurePairAligner.getParams()
get the parameters.
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Modifier and Type | Method and Description |
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void |
StructurePairAligner.align(Atom[] ca1,
Atom[] ca2,
StrucAligParameters params)
calculate the protein structure superimposition, between two sets of atoms.
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void |
StructurePairAligner.align(Structure s1,
Structure s2,
StrucAligParameters params)
calculate the alignment between the two full structures with user provided parameters
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void |
StructurePairAligner.setParams(StrucAligParameters params)
set the parameters to be used for the algorithm
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Modifier and Type | Method and Description |
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static Alignable |
AligNPE.align_NPE(Matrix sim,
StrucAligParameters params)
Align w/o penalizing endpags.
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JointFragments[] |
FragmentJoiner.approach_ap3(Atom[] ca1,
Atom[] ca2,
FragmentPair[] fraglst,
StrucAligParameters params) |
void |
AlternativeAlignment.finish(StrucAligParameters params,
Atom[] ca1,
Atom[] ca2) |
void |
AlternativeAlignment.refine(StrucAligParameters params,
Atom[] ca1,
Atom[] ca2)
Refinement procedure based on superposition and dynamic programming.
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