Uses of Class
org.strbio.mol.PolymerSet

Packages that use PolymerSet
org.strbio.local These classes are for running or exchanging data with local programs (other programs installed on your computer). 
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 PolymerSet in org.strbio.local
 

Methods in org.strbio.local that return PolymerSet
 PolymerSet Muscle.runOnPolymerSet(PolymerSet p)
           
 PolymerSet Muscle.runOnPolymerSet(PolymerSet p, java.lang.String options)
          return a protein set resulting from running muscle on a protein set, with optional options to Muscle
 

Methods in org.strbio.local with parameters of type PolymerSet
 PolymerSet Muscle.runOnPolymerSet(PolymerSet p)
           
 PolymerSet Muscle.runOnPolymerSet(PolymerSet p, java.lang.String options)
          return a protein set resulting from running muscle on a protein set, with optional options to Muscle
 

Uses of PolymerSet in org.strbio.mol
 

Subclasses of PolymerSet in org.strbio.mol
 class ProfilePSISet
          Class to represent a set of profiles with position specific information (PSI), such as PSI-BLAST info and JMC's backbone potential.
 class ProfileSet
          Class to represent a set of proteins with profile information.
 class ProteinSet
          Class to represent a set of proteins to be acted on in a group.
 

Fields in org.strbio.mol declared as PolymerSet
 PolymerSet ThreadSet.folds
          Folds being threaded.
 PolymerSet ThreadSet.seqs
          Sequences being threaded.
 

Methods in org.strbio.mol with parameters of type PolymerSet
 void PolymerSet.add(PolymerSet q)
          add in another set of Polymers, without duplicating them.
 boolean PolymerSet.isEqual(PolymerSet y)
          do 2 sets of Polymers contain the same Polymers?
 void AlignmentSet.load(java.io.BufferedReader infile, PolymerSet seqs, PolymerSet folds)
          Load alignment out of new format file.
 void AlignmentSet.load(java.lang.String in_file, PolymerSet seqs, PolymerSet folds)
          Load alignment out of new format file.
 

Constructors in org.strbio.mol with parameters of type PolymerSet
PolymerSet.PolymerEnumeration(java.io.BufferedReader inf, Printf outf, PolymerSet ps)
          create an enumeration on a given file, with a given polymer set.
PolymerSet(PolymerSet y)
          Create a set by copying another set, but not the polymers in it.
 

Uses of PolymerSet in org.strbio.mol.lib
 

Subclasses of PolymerSet in org.strbio.mol.lib
 class FoldLibrary
          A standard fold library for threading; i.e. the TOM fold library, or the Fischer fold library.
 class TOMFoldLibrary
          The TOM fold library.
 class UserFoldLibrary
          A standard fold library for threading, loaded in by the user.
 

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

Subclasses of PolymerSet in org.strbio.mol.lib.pred2ary
 class PCPSet
          Class to represent a set of profiles with information for 2ary structure prediction.
 class PredictionSet
          Class to represent a set of profiles being used in 2ary structure prediction as a prediction set.
 class TPSet
          Class to represent a set of profiles being used in 2ary structure prediction; this might be either a training or prediction set.
 class TrainingSet
          Class to represent a set of profiles being used in 2ary structure prediction as a training set.