Uses of Class
org.biojava.nbio.structure.align.StrucAligParameters
-
Packages that use StrucAligParameters Package Description org.biojava.nbio.structure.align Classes for the alignment of structures.org.biojava.nbio.structure.align.pairwise Classes for the pairwise alignment of structures. -
-
Uses of StrucAligParameters in org.biojava.nbio.structure.align
Methods in org.biojava.nbio.structure.align that return StrucAligParameters Modifier and Type Method Description static StrucAligParameters
StrucAligParameters. getDBSearchParameters()
static StrucAligParameters
StrucAligParameters. getDefaultParameters()
StrucAligParameters
StructurePairAligner. getParams()
get the parameters.Methods in org.biojava.nbio.structure.align with parameters of type StrucAligParameters Modifier and Type Method Description void
StructurePairAligner. align(Atom[] ca1, Atom[] ca2, StrucAligParameters params)
calculate the protein structure superimposition, between two sets of atoms.void
StructurePairAligner. align(Structure s1, String chainId1, Structure s2, String chainId2, StrucAligParameters params)
Aligns two chains from the structures using user provided parameters.void
StructurePairAligner. align(Structure s1, Structure s2, StrucAligParameters params)
Calculate the alignment between the two full structures with user provided parametersvoid
StructurePairAligner. setParams(StrucAligParameters params)
set the parameters to be used for the algorithm -
Uses of StrucAligParameters in org.biojava.nbio.structure.align.pairwise
Methods in org.biojava.nbio.structure.align.pairwise with parameters of type StrucAligParameters Modifier and Type Method Description static Alignable
AligNPE. align_NPE(Matrix sim, StrucAligParameters params)
Align without penalizing end-gaps.JointFragments[]
FragmentJoiner. approach_ap3(Atom[] ca1, Atom[] ca2, FragmentPair[] fraglst, StrucAligParameters params)
void
FragmentJoiner. extendFragments(Atom[] ca1, Atom[] ca2, JointFragments[] fragments, StrucAligParameters params)
void
FragmentJoiner. extendFragments(Atom[] ca1, Atom[] ca2, JointFragments fragments, 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.
-