Uses of Class
org.strbio.mol.Monomer

Packages that use Monomer
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 Monomer in org.strbio.mol
 

Subclasses of Monomer in org.strbio.mol
 class Nucleotide
          Class to represent a single nucleotide Version 1.0, 8/17/01 - original version, based on org.strbio.mol.Residue
 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.
 class Residue
          Class to represent a single residue in a protein.
 

Methods in org.strbio.mol that return Monomer
 Monomer Polymer.firstMon()
          Return first monomer if there is one, else null.
 Monomer[] Polymer.getMonomers()
          get an array of the monomers.
 Monomer[] Polymer.getNonGapMonomers()
          get an array of the valid non-gap monomers.
 Monomer[] Polymer.getValidNonGapMonomers()
          get an array of the valid non-gap monomers.
 Monomer Polymer.lastMon()
          Return last monomer if there is one, else null.
 Monomer Polymer.monomer(int n)
          returns the N'th monomer in the sequence.
 Monomer ProfilePSI.newMonomer()
          This returns a new ProfResPSI.
 Monomer Profile.newMonomer()
          Profiles are made of ProfRes-type monomers.
 Monomer Protein.newMonomer()
          This should return a new monomer of whatever type this polymer is made of (i.e.
 Monomer Polymer.newMonomer()
          This should return a new monomer of whatever type this polymer is made of (i.e.
 Monomer ProfilePSI.newMonomer(char t)
          This returns a new ProfResPSI.
 Monomer Profile.newMonomer(char t)
           
 Monomer Protein.newMonomer(char t)
          This should return a new monomer of whatever type this polymer is made of (i.e.
 Monomer Polymer.newMonomer(char t)
          This should return a new monomer of whatever type this polymer is made of (i.e.
 Monomer ProfilePSI.newMonomer(java.lang.String s)
          This returns a new ProfResPSI.
 Monomer Profile.newMonomer(java.lang.String s)
           
 Monomer Protein.newMonomer(java.lang.String s)
          This should return a new monomer of whatever type this polymer is made of (i.e.
 Monomer Polymer.newMonomer(java.lang.String s)
          This should return a new monomer of whatever type this polymer is made of (i.e.
protected  Monomer Polymer.YAPFGetNextMonomer(int n)
          Return the next non-gap residue with number 'n', or null if there is none.
 

Methods in org.strbio.mol with parameters of type Monomer
 void Monomer.copyAtoms(Monomer q)
          copy the atoms from another monomer.
 void ProfRes.copyDataFrom(Monomer q)
          Copy another ProfRes.
 void ProfResPSI.copyDataFrom(Monomer q)
          Copy another ProfResPSI.
 void Residue.copyDataFrom(Monomer q)
          copy another residue, including the atoms.
 void Monomer.copyDataFrom(Monomer q)
          copy another monomer, including the atoms.
 

Constructors in org.strbio.mol with parameters of type Monomer
Monomer(Monomer q)
          copy another monomer, including the atoms.
 

Uses of Monomer in org.strbio.mol.lib
 

Methods in org.strbio.mol.lib with parameters of type Monomer
 double ScoreUFSippl90.score(Monomer a, Monomer b)
           
 double ScoreSippl90.score(Monomer a, Monomer b)
           
 double ScoreScaledID.score(Monomer a, Monomer b)
          Returns EQUAL if monomer types are the same, otherwise NOTEQUAL.
 double ScoreReversePSIBlast.score(Monomer a, Monomer b)
           
 double ScorePredFreq.score(Monomer a, Monomer b)
           
 double ScorePred2ary.score(Monomer a, Monomer b)
           
 double ScorePhiPsi.score(Monomer a, Monomer b)
           
 double ScorePairwiseDistance.score(Monomer a, Monomer b)
           
 double ScorePSIBlast.score(Monomer a, Monomer b)
           
 double ScoreJDB10.score(Monomer a, Monomer b)
           
 double ScoreID.score(Monomer a, Monomer b)
          Returns EQUAL if residue types are the same, otherwise NOTEQUAL.
 double ScoreFischer.score(Monomer a, Monomer b)
           
 double ScoreDefay.score(Monomer a, Monomer b)
           
 double ScoreBlosum62.score(Monomer a, Monomer b)
           
 double ScoreAverageReversePSIBlast.score(Monomer a, Monomer b)
           
 double ScoreAveragePSIBlast.score(Monomer a, Monomer b)
           
 double ScoreAlphaTau.score(Monomer a, Monomer b)
           
 double Score2ary.score(Monomer a, Monomer b)
           
 double ScoreFunction.score(Monomer seqMon, Monomer foldMon)
          This function should return a score for aligning two monomers of a polymer, preferably with low = good, high = bad.
 double ScoreList.totalScore(Monomer a, Monomer b)
          return the total score for a monomer pair, from all scoring functions at this point on.
 

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

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

Methods in org.strbio.mol.lib.pred2ary that return Monomer
 Monomer PredClassProfile.newMonomer()
           
 Monomer PredClassProfile.newMonomer(char t)
           
 Monomer PredClassProfile.newMonomer(java.lang.String s)
           
 

Methods in org.strbio.mol.lib.pred2ary with parameters of type Monomer
 void PCPRes.copyDataFrom(Monomer q)
          Copy another PCPRes.