Uses of Class
pl.poznan.put.structure.formats.BpSeq

Packages that use BpSeq

Package	Description
pl.poznan.put.structure	Package contains classes useful in describing secondary structure (base pairs, helices, etc.)
pl.poznan.put.structure.formats
pl.poznan.put.structure.pseudoknots	Package contains classes that handle pseudoknots in secondary structure.
pl.poznan.put.structure.pseudoknots.dp	A set of dynamic programming solutions to pseudoknot detection.s
pl.poznan.put.structure.pseudoknots.elimination

Uses of BpSeq in pl.poznan.put.structure

Methods in pl.poznan.put.structure that return BpSeq

Modifier and Type	Method	Description
static BpSeq	CanonicalStructureExtractor.bpSeq(ResidueCollection residueCollection)	Extracts the canonical secondary structure from the 3D data and outputs it in BPSEQ format.

Uses of BpSeq in pl.poznan.put.structure.formats

Subclasses of BpSeq in pl.poznan.put.structure.formats

Modifier and Type	Class	Description
final class	ImmutableBpSeq	Immutable implementation of BpSeq.

Methods in pl.poznan.put.structure.formats that return BpSeq

Modifier and Type	Method	Description
static BpSeq	BpSeq.fromBasePairs(List<PdbNamedResidueIdentifier> residues, Collection<? extends ClassifiedBasePair> basePairs)	Creates an instance of BPSEQ from a list of residue identifiers and a list of base pairs.
static BpSeq	BpSeq.fromCt(Ct ct)	Converts RNA secondary structure in CT format to BPSEQ format.
static BpSeq	BpSeq.fromDotBracket(DotBracket db)	Converts RNA secondary structure in dot-bracket format to BPSEQ format.
static BpSeq	BpSeq.fromString(String data)	Parses string into an instance of this class.
final BpSeq	BpSeq.withoutIsolatedPairs()	Finds all isolated base pairs and creates a copy of this instance without them.
final BpSeq	BpSeq.withoutPair(BpSeq.Entry entry)	Creates a copy of this instance, but with the given pair removed.

Methods in pl.poznan.put.structure.formats with parameters of type BpSeq

Modifier and Type	Method	Description
DotBracket	Converter.convert(BpSeq bpSeq)	Converts the secondary structure from BPSEQ to dot-bracket format.
final DotBracket	DefaultConverter.convert(BpSeq bpSeq)	Converts the secondary structure in BPSEQ format to dot-bracket.
static ImmutableBpSeq	ImmutableBpSeq.copyOf(BpSeq instance)	Creates an immutable copy of a BpSeq value.
final ImmutableBpSeq.Builder	ImmutableBpSeq.Builder.from(BpSeq instance)	Fill a builder with attribute values from the provided BpSeq instance.
static Ct	Ct.fromBpSeq(BpSeq bpSeq)	Converts RNA secondary structure in BPSEQ format to CT format.
static Ct	Ct.fromBpSeqAndPdbModel(BpSeq bpSeq, PdbModel model)	Converts RNA secondary structure in BPSEQ format to CT format, taking into account information from 3D coordinates (residue numbering, chain sizes).

Uses of BpSeq in pl.poznan.put.structure.pseudoknots

Methods in pl.poznan.put.structure.pseudoknots that return types with arguments of type BpSeq

Modifier and Type	Method	Description
List<BpSeq>	PseudoknotFinder.findPseudoknots(BpSeq bpSeq)	Finds pseudoknots in BPSEQ data.

Methods in pl.poznan.put.structure.pseudoknots with parameters of type BpSeq

Modifier and Type	Method	Description
static List<Region>	Region.createRegions(BpSeq bpSeq)	Creates a list of regions from a secondary structure in BPSEQ format.
List<BpSeq>	PseudoknotFinder.findPseudoknots(BpSeq bpSeq)	Finds pseudoknots in BPSEQ data.

Uses of BpSeq in pl.poznan.put.structure.pseudoknots.dp

Methods in pl.poznan.put.structure.pseudoknots.dp that return types with arguments of type BpSeq

Modifier and Type	Method	Description
final List<BpSeq>	DynamicProgrammingAll.findPseudoknots(BpSeq bpSeq)

Methods in pl.poznan.put.structure.pseudoknots.dp with parameters of type BpSeq

Modifier and Type	Method	Description
final List<BpSeq>	DynamicProgrammingAll.findPseudoknots(BpSeq bpSeq)

Uses of BpSeq in pl.poznan.put.structure.pseudoknots.elimination

Methods in pl.poznan.put.structure.pseudoknots.elimination that return types with arguments of type BpSeq

Modifier and Type	Method	Description
final List<BpSeq>	AbstractRegionRemover.findPseudoknots(BpSeq bpSeq)	Finds pseudoknots by removing one region at a time until there are any conflicts.

Methods in pl.poznan.put.structure.pseudoknots.elimination with parameters of type BpSeq

Modifier and Type	Method	Description
final List<BpSeq>	AbstractRegionRemover.findPseudoknots(BpSeq bpSeq)	Finds pseudoknots by removing one region at a time until there are any conflicts.