Uses of Package
pl.poznan.put.structure.formats

Packages that use pl.poznan.put.structure.formats

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

Classes in pl.poznan.put.structure.formats used by pl.poznan.put.structure

Class	Description
BpSeq	RNA secondary structure in BPSEQ format.

Classes in pl.poznan.put.structure.formats used by pl.poznan.put.structure.formats

Class	Description
AbstractCombinedStrand
BpSeq	RNA secondary structure in BPSEQ format.
BpSeq.Entry	An entry of a BPSEQ data.
CombinedStrand	A dot-bracket encoded structure made from combining one or more strands.
CombinedStrandFromPdb	A dot-bracket encoded structure made from combining one or more strands.
Converter	A converter from BPSEQ to dot-bracket.
Ct	An RNA secondary structure encoded in CT (connect) format.
Ct.ExtendedEntry	A single entry in the CT formatted structure.
DefaultConverter	A default converter from BPSEQ to dot-bracket which iteratively (1) finds non-pseudoknots and assigns the current lowest level, then (2) increases level and (3) treats pseudoknots as the next input to (1) until there are base pairs without level assigned.
DefaultDotBracket	A default implementation of a dot-bracket.
DefaultDotBracketFromPdb	A default implementation of a dot-bracket structure which is mapped to data from 3D coordinates.
DefaultStrand	A default implementation of a strand.
DotBracket	An RNA structure encoded in dot-bracket format.
DotBracketFromPdb	A dot-bracket structure with correspondence to a 3D structure.
ImmutableBpSeq	Immutable implementation of BpSeq.
ImmutableBpSeq.Builder	Builds instances of type ImmutableBpSeq.
ImmutableCombinedStrand	Immutable implementation of CombinedStrand.
ImmutableCombinedStrand.Builder	Builds instances of type ImmutableCombinedStrand.
ImmutableCombinedStrandFromPdb	Immutable implementation of CombinedStrandFromPdb.
ImmutableCombinedStrandFromPdb.Builder	Builds instances of type ImmutableCombinedStrandFromPdb.
ImmutableCt	Immutable implementation of Ct.
ImmutableCt.Builder	Builds instances of type ImmutableCt.
ImmutableDefaultConverter	Immutable implementation of DefaultConverter.
ImmutableDefaultConverter.Builder	Builds instances of type ImmutableDefaultConverter.
ImmutableDefaultDotBracket	Immutable implementation of DefaultDotBracket.
ImmutableDefaultDotBracket.Builder	Builds instances of type ImmutableDefaultDotBracket.
ImmutableDefaultDotBracketFromPdb	Immutable implementation of DefaultDotBracketFromPdb.
ImmutableDefaultDotBracketFromPdb.Builder	Builds instances of type ImmutableDefaultDotBracketFromPdb.
ImmutableDefaultStrand	Immutable implementation of DefaultStrand.
ImmutableDefaultStrand.Builder	Builds instances of type ImmutableDefaultStrand.
ImmutableEntry	Immutable implementation of BpSeq.Entry.
ImmutableEntry.Builder	Builds instances of type ImmutableEntry.
ImmutableExtendedEntry	Immutable implementation of Ct.ExtendedEntry.
ImmutableExtendedEntry.Builder	Builds instances of type ImmutableExtendedEntry.
ImmutableMultiLineDotBracket	Immutable implementation of MultiLineDotBracket.
ImmutableMultiLineDotBracket.Builder	Builds instances of type ImmutableMultiLineDotBracket.
ImmutableStrandView	Immutable implementation of StrandView.
ImmutableStrandView.Builder	Builds instances of type ImmutableStrandView.
ImmutableTerminalMissing	Immutable implementation of TerminalMissing.
ImmutableTerminalMissing.Builder	Builds instances of type ImmutableTerminalMissing.
MultiLineDotBracket	An extended secondary structure, which contains also non-canonical base pairs.
Strand	A continuous segment of residues.
StrandView	A strand which is defined as a fragment of a dot-bracket structure.
TerminalMissing	A colecction of missing dot-bracket symbols at 5' or 3' end.

Classes in pl.poznan.put.structure.formats used by pl.poznan.put.structure.pseudoknots

Class	Description
BpSeq	RNA secondary structure in BPSEQ format.
BpSeq.Entry	An entry of a BPSEQ data.

Classes in pl.poznan.put.structure.formats used by pl.poznan.put.structure.pseudoknots.dp

Class	Description
BpSeq	RNA secondary structure in BPSEQ format.

Classes in pl.poznan.put.structure.formats used by pl.poznan.put.structure.pseudoknots.elimination

Class	Description
BpSeq	RNA secondary structure in BPSEQ format.