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

Packages that use StrucAligParameters
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

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 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

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.