Uses of Class
org.biojava.bio.structure.align.StrucAligParameters

Packages that use StrucAligParameters

org.biojava.bio.structure.align
org.biojava.bio.structure.align.pairwise

Uses of StrucAligParameters in org.biojava.bio.structure.align

Methods in org.biojava.bio.structure.align that return StrucAligParameters

static StrucAligParameters	StrucAligParameters.getDBSearchParameters()
static StrucAligParameters	StrucAligParameters.getDefaultParameters()
StrucAligParameters	StructurePairAligner.getParams() get the parameters.

Methods in org.biojava.bio.structure.align with parameters of type StrucAligParameters

void	StructurePairAligner.align(Atom[] ca1, Atom[] ca2, StrucAligParameters params) calculate the actual protein structure superimposition.
void	StructurePairAligner.align(Structure s1, Structure s2, StrucAligParameters params)
void	StructurePairAligner.setParams(StrucAligParameters params) set the parameters to be used for the algorithm

Uses of StrucAligParameters in org.biojava.bio.structure.align.pairwise

Methods in org.biojava.bio.structure.align.pairwise with parameters of type StrucAligParameters

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)
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.