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 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.