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.