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