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 parameters
void	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.