Uses of Class
org.strbio.mol.Polymer

Packages that use Polymer

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 Polymer in org.strbio.mol

Subclasses of Polymer in org.strbio.mol

class	Profile Class to represent a protein with profile information.
class	ProfilePSI Class to represent a profile with position specific information (PSI), such as PSI-BLAST info and JMC's backbone potential.
class	Protein Class to represent a single protein.

Fields in org.strbio.mol declared as Polymer

Polymer	Alignment.fold the fold in the alignment.
Polymer	AlignmentSet.fold The fold being aligned.
Polymer	Alignment.seq the sequence in the alignment.
Polymer	AlignmentSet.seq The sequence being aligned.

Methods in org.strbio.mol that return Polymer

protected Polymer[]	Polymer.autoSplit() splits a polymer into several, if it has a break in the chain.
Polymer	ProfilePSI.copy() Return a copy of yourself.
Polymer	Profile.copy() Return a copy of yourself.
Polymer	Protein.copy() Return a copy of yourself.
Polymer	Polymer.copy() Return a copy of yourself.
Polymer	ProfileSet.newPolymer() Everything in this set should be a Profile (or subclass of it).
Polymer	ProfilePSISet.newPolymer()
Polymer	ProteinSet.newPolymer() Make sure this set contains only Proteins.
Polymer	PolymerSet.newPolymer() Create a new polymer to add to the set... this may be replaced by subclasses which encapsulate specific polymers.
Polymer	ProfileSet.newPolymer(ProteinSet q)
Polymer	PolymerSet.p(int i) short for polymer(i)
Polymer	PolymerSet.polymer(int i) Return the i'th polymer in the set.
Polymer	Polymer.reverseCopy() Return a reversed copy of yourself.
Polymer	PolymerSet.searchByName(java.lang.String name) return a Polymer matching a given name, or null if not in set
Polymer	PolymerSet.searchByNameFuzzy(java.lang.String name) Find a Polymer matching a given name, using fuzzy matching.
Polymer	PolymerSet.searchByNameFuzzy(java.lang.String name, int fuzziness) Find a Polymer matching a given name, using fuzzy matching.
protected Polymer	ProfilePSI.splitCopy()
protected Polymer	Profile.splitCopy() When a Profile is split, sequence names should go to each child.
protected Polymer	Protein.splitCopy()
protected Polymer	Polymer.splitCopy() This should return a copy of all data which should be copied during AutoSplit (not including monomers, monDistance, name).

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

void	PolymerSet.add(Polymer q) add in a single Polymer to this set, without duplicating it.
AlignmentSet	ThreadSet.addStrMatch(Polymer seq, Polymer fold) add a single structural match to the set.
void	Polymer.copyAtoms(Polymer q) copy the atoms from another polymer.
int[]	PolymerSet.findClosest(Polymer q) return the most similar Polymer (by sequence ID) in a set to a given Polymer.
Alignment	Polymer.getGlobalAlignment(Polymer y, AlignmentParameters ap, Alignment nail) This does the above, but without actually storing the alignment as gaps in the polymers.
AlignmentSet	ThreadSet.getStrMatch(Polymer seq, Polymer fold) Get first structural match, if one exists, with a given seq and fold, or null if one doesn't exist.
double	Polymer.globalAlign(Polymer y, AlignmentParameters ap, Alignment nail) a mostly generic global alignment function.
double	Polymer.globalAlign(Polymer y, GapModel gm, ScoreList sl, int[] nail) Deprecated. use AlignmentParameters
double	Polymer.globalCompare(Polymer y, AlignmentParameters ap) a mostly generic global comparison function.
double	Polymer.globalCompare(Polymer y, GapModel gm, ScoreList sl) Deprecated. use AlignmentParameters
static void	Polymer.minareaSuperimpose(Polymer a, Polymer b) Superimpose two polymers using minarea.
void	Polymer.quickAlign(Polymer y) standard needleman-wunch alignment algorithm, with identity matrix, and constant gap penalty of 1.
void	Polymer.quickAlign(Polymer y, double gapI, double gapE) standard needleman-wunch alignment algorithm, with identity matrix and given gap penalties
int	Polymer.quickCompare(Polymer y) standard needleman-wunch comparison algorithm, with identity matrix and a constant gap penalty of 1.
double	Polymer.quickCompare(Polymer y, double gapI, double gapE) standard needleman-wunch comparison algorithm, with identity matrix and given gap penalties.
void	PolymerSet.remove(Polymer q) Remove a polymer from the set.
void	PolymerSet.setPolymerAt(int i, Polymer p) set the i'th polymer in the set.
void	Polymer.stripCommonGaps(Polymer q) strip out all gaps in 2 polymers which occur at the same location.

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

Alignment(Polymer s, Polymer f)
make a new alignment with a seq and fold.

Alignment(Polymer s, Polymer f, int[] v)
make a new alignment from two polymers and an integer array.

AlignmentSet(Polymer s, Polymer f)
make a new alignment with given seq, fold.

Polymer(Polymer q)
Copy another Polymer, making copies of all data fields.

Uses of Polymer in org.strbio.mol.lib

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

void	GapModelAdapter.calculateFirstPosition(float[][] mat, int[][] nextX, int[][] nextY, Polymer seq, Polymer fold)
void	GapModelAdapter.dealWithEndPenalties(float[][] mat, Polymer seq, Polymer fold) This fills in the matrix with impossible penalties, if we want to disallow gaps at the ends.
void	ScoreReversePSIBlast.finished(Polymer p)
void	ScorePhiPsi.finished(Polymer p)
void	ScorePSIBlast.finished(Polymer p)
void	ScoreAverageReversePSIBlast.finished(Polymer p)
void	ScoreAveragePSIBlast.finished(Polymer p)
void	ScoreSetup.finished(Polymer p) This function is called when you are done using the function on a polymer.
void	ScoreAlphaTau.finished(Polymer p)
void	ScoreList.finished(Polymer p) Tell scoring functions you're finished with a given protein, for all scoring functions that implement ScoreSetup.
void	ScoreUFSippl90.finished(Polymer s, Polymer f)
void	ScoreSippl90.finished(Polymer s, Polymer f)
void	ScoreSetup2.finished(Polymer seq, Polymer fold) This function is called when you are done using the function on a pair.
void	ScoreAveragePSIBlast.finished(Polymer s, Polymer f)
void	GapDistanceDependent.finished(Polymer seq, Polymer fold) Forget about distance matrix.
void	GapModelAdapter.finished(Polymer seq, Polymer fold) Default is no finish.
void	GapModel.finished(Polymer seq, Polymer fold) Do anything after align/comparison?
void	ScoreList.finished(Polymer seq, Polymer fold) Tell scoring functions you're finished with a given protein pair, for all scoring functions that implement ScoreSetup2.
void	AlignmentParameters.finished(Polymer seq, Polymer fold) Tell objects that we're done doing an alignment on a given seq and fold.
double	GapDistanceDependent.gapCostDeletion(Polymer seq, Polymer fold, int seqi, int seqj, int foldi, int foldj)
double	GapConstant.gapCostDeletion(Polymer seq, Polymer fold, int seqi, int seqj, int foldi, int foldj)
double	GapAffine.gapCostDeletion(Polymer seq, Polymer fold, int seqi, int seqj, int foldi, int foldj)
double	GapModel.gapCostDeletion(Polymer seq, Polymer fold, int seqi, int seqj, int foldi, int foldj) This function should return the gap cost for aligning residues seqi and foldi, then seqj and foldj.
double	GapDistanceDependent.gapCostInsertion(Polymer seq, Polymer fold, int seqi, int seqj, int foldi, int foldj)
double	GapConstant.gapCostInsertion(Polymer seq, Polymer fold, int seqi, int seqj, int foldi, int foldj)
double	GapAffine.gapCostInsertion(Polymer seq, Polymer fold, int seqi, int seqj, int foldi, int foldj)
double	GapModel.gapCostInsertion(Polymer seq, Polymer fold, int seqi, int seqj, int foldi, int foldj) This function should return the gap cost for aligning residues seqi and foldi, then seqj and foldj.
void	GapDistanceDependent.processGlobalMatrix(float[][] mat, int[][] nextX, int[][] nextY, Polymer seq, Polymer fold) This function is optimized for gap penalties which are affine in only 1 direction, and have to be fully looked at in the other direction.
void	GapModelAdapter.processGlobalMatrix(float[][] mat, int[][] nextX, int[][] nextY, Polymer seq, Polymer fold) This function will handle any gap model, but very slowly.
void	GapConstant.processGlobalMatrix(float[][] mat, int[][] nextX, int[][] nextY, Polymer seq, Polymer fold) This function is optimized for constant gap penalties.
void	GapAffine.processGlobalMatrix(float[][] mat, int[][] nextX, int[][] nextY, Polymer seq, Polymer fold) This function is optimized for affine gap penalties.
void	GapModel.processGlobalMatrix(float[][] mat, int[][] nextX, int[][] nextY, Polymer seq, Polymer fold) This function is given a sequence and fold being aligned in a global alignment, and a S+1 x F+1 matrix containing the scores for aligning each monomer in the sequence to each monomer in the fold.
void	ScoreReversePSIBlast.setup(Polymer p)
void	ScorePhiPsi.setup(Polymer p)
void	ScorePSIBlast.setup(Polymer p)
void	ScoreAverageReversePSIBlast.setup(Polymer p)
void	ScoreAveragePSIBlast.setup(Polymer p)
void	ScoreSetup.setup(Polymer p) This function is to set up the scoring function for use on a polymer.
void	ScoreAlphaTau.setup(Polymer p)
void	ScoreList.setup(Polymer p) Set up scoring functions for a given protein, for all scoring functions that implement ScoreSetup.
void	ScoreUFSippl90.setup(Polymer s, Polymer f)
void	ScoreSippl90.setup(Polymer s, Polymer f)
void	ScoreSetup2.setup(Polymer seq, Polymer fold) This function is to set up the scoring function for use on a pair.
void	ScoreAveragePSIBlast.setup(Polymer s, Polymer f)
void	OptimalAAParametersFR.setup(Polymer seq, Polymer fold) kludge to set up precalculated phi/psi angles in the fold
void	OptimalAAParameters.setup(Polymer seq, Polymer fold) kludge to set up precalculated phi/psi angles in the fold
void	GapDistanceDependent.setup(Polymer seq, Polymer fold) Calculate distance matrix.
void	GapModelAdapter.setup(Polymer seq, Polymer fold) Default is no setup.
void	GapModel.setup(Polymer seq, Polymer fold) Perform any last minute setup before align/comparison.
void	ScoreList.setup(Polymer seq, Polymer fold) Set up scoring functions for a given protein pair, for all scoring functions that implement ScoreSetup2.
void	AlignmentParameters.setup(Polymer seq, Polymer fold) Set up everything for doing an alignment on a given seq and fold.

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

Subclasses of Polymer in org.strbio.mol.lib.pred2ary

class

PredClassProfile Class to represent a single protein, with class routines and lots of stats.

Methods in org.strbio.mol.lib.pred2ary that return Polymer

Polymer	PCPSet.newPolymer()
Polymer	PCPSet.newPolymer(ProteinSet q)
protected Polymer	PredClassProfile.splitCopy()

Uses of Polymer in org.strbio.raf

Subclasses of Polymer in org.strbio.raf

class

RAFProtein Modified version of org.strbio.mol.Protein... part of this might might be ported back to Protein.

Methods in org.strbio.raf with parameters of type Polymer

double	GapRAF.gapCostDeletion(Polymer seq, Polymer fold, int seqi, int seqj, int foldi, int foldj)
double	GapRAF.gapCostInsertion(Polymer seq, Polymer fold, int seqi, int seqj, int foldi, int foldj)
void	GapRAF.processGlobalMatrix(float[][] mat, int[][] nextX, int[][] nextY, Polymer seq, Polymer fold) This function is optimized for gap penalties which are affine in only 1 direction, and have to be fully looked at in the other direction.