Uses of Class
org.strbio.mol.ProteinSet

Packages that use ProteinSet

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.
org.strbio.raf	These classes are related to the RAF file format used by the ASTRAL database.

Uses of ProteinSet in org.strbio.local

Methods in org.strbio.local that return ProteinSet

ProteinSet

BlastPAdapter.blastProteinSet(Printf outfile) Returns a set of proteins in response to a blast query.

Methods in org.strbio.local with parameters of type ProteinSet

java.lang.String

ClustalW.runOnProteinSet(ProteinSet p) return a string containing the raw output (aln file) from running clustalw on a protein set

Uses of ProteinSet in org.strbio.mol

Subclasses of ProteinSet 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.

Methods in org.strbio.mol that return ProteinSet

static ProteinSet	ProteinSet.findDSSP(java.lang.String name, Printf outfile) find and load proteins from a DSSP file (do DSSP on PDB file)
static ProteinSet	ProteinSet.findPDB(java.lang.String name, Printf outfile) find and load proteins from a PDB file.
ProteinSet	Protein.fixDistanceGaps() Filter out distance gaps (inter-CA > 4 A or < 3.6 A), returning a new set of proteins consisting of this protein broken into fragments everywhere there is a problem.
ProteinSet	Protein.getDSSPResults(Printf outfile) runs DSSP on a protein, returning a ProteinSet containing results from DSSP.

Methods in org.strbio.mol with parameters of type ProteinSet

protected Protein	Protein.findDSSPResult(ProteinSet q, Printf outfile) returns the appropriate protein from a set of DSSP results, aligned to this one.
Polymer	ProfileSet.newPolymer(ProteinSet q)

Constructors in org.strbio.mol with parameters of type ProteinSet

Profile(ProteinSet q)
Make a Profile from a ProteinSet, copying all data.

ProfilePSI(ProteinSet q)
Create from a set of proteins.

ProteinSet(ProteinSet y)
Copy another protein set, but not the proteins (only the pointers to them).

Uses of ProteinSet in org.strbio.mol.lib

Subclasses of ProteinSet 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.

Methods in org.strbio.mol.lib that return ProteinSet

ProteinSet	BlastAdapter.blastProteinSet(Printf outfile) Returns a set of proteins in response to a blast query.
ProteinSet	Blast.blastProteinSet(Printf outfile) Returns a set of proteins in response to a blast query.

Methods in org.strbio.mol.lib with parameters of type ProteinSet

void	Pred2ary.predict(ProteinSet ps, Printf outfile) Predicts on a given set of proteins.
void	SSPredictor.predict(ProteinSet p, Printf outfile) Predicts on a given set of proteins.
ThreadResults[]	JMCThreadMethod2.thread(ProteinSet ps, Printf outfile) Thread a given protein set, returning an array of ThreadResults objects.
ThreadResults[]	JMCThreadMethod.thread(ProteinSet ps, Printf outfile) Thread a given protein set, returning an array of ThreadResults objects.
ThreadResults[]	ThreadMethod.thread(ProteinSet ps, Printf outfile) Thread a given protein set, returning an array of ThreadResults objects.

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

Subclasses of ProteinSet 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.

Methods in org.strbio.mol.lib.pred2ary with parameters of type ProteinSet

Polymer

PCPSet.newPolymer(ProteinSet q)

Constructors in org.strbio.mol.lib.pred2ary with parameters of type ProteinSet

PredClassProfile(ProteinSet q)

Uses of ProteinSet in org.strbio.raf

Methods in org.strbio.raf that return ProteinSet

static ProteinSet	RAFProtein.readAtom(java.lang.String filename, Printf outfile)
static ProteinSet	RAFProtein.readSeqres(java.lang.String filename, Printf outfile)