Uses of Class
org.strbio.mol.Residue

Packages that use Residue
org.strbio.mol These classes represent objects or concepts useful to structural biologists. 
org.strbio.mol.lib These classes represent conceptual objects used in structural biology algorithms. 
org.strbio.mol.lib.pred2ary These classes represent conceptual objects used in the Pred2ary program, which are probably not very useful for other purposes. 
 

Uses of Residue in org.strbio.mol
 

Subclasses of Residue in org.strbio.mol
 class ProfRes
          Class to represent a single residue in a protein with profile information.
 class ProfResPSI
          Class to represent a single residue in a profile, with position specific information (PSI) added.
 

Methods in org.strbio.mol that return Residue
 Residue Protein.AA(int i)
          returns the N'th residue in the sequence.
 Residue Protein.firstRes()
          Return first residue if there is one.
 

Constructors in org.strbio.mol with parameters of type Residue
ProfRes(Residue q)
           
Residue(Residue q)
          copy another residue, including the atoms.
 

Uses of Residue in org.strbio.mol.lib
 

Methods in org.strbio.mol.lib with parameters of type Residue
 double ScoreUFSippl90.score(Residue a, Residue b)
          Restrict scoring to a range of k values.
 double ScoreSippl90.score(Residue a, Residue b)
          This is somewhat hard to read; it is written for speed.
 double ScorePredFreq.score(Residue a, Residue b)
           
 double ScorePred2ary.score(Residue a, Residue b)
           
 double ScorePairwiseDistance.score(Residue a, Residue b)
          Score is the distance between the residues' CA atoms.
 double ScoreJDB10.score(Residue a, Residue b)
           
 double ScoreFischer.score(Residue a, Residue b)
           
 double ScoreDefay.score(Residue a, Residue b)
           
 double ScoreBlosum62.score(Residue a, Residue b)
           
 double Score2ary.score(Residue a, Residue b)
           
 

Uses of Residue in org.strbio.mol.lib.pred2ary
 

Subclasses of Residue in org.strbio.mol.lib.pred2ary
 class PCPRes
          ProfRes with a couple extras useful for 2ary structure prediction.