Package pl.poznan.put.structure.formats

Interface Summary

Interface	Description
Converter	A converter from BPSEQ to dot-bracket.
DotBracket	An RNA structure encoded in dot-bracket format.
DotBracketFromPdb	A dot-bracket structure with correspondence to a 3D structure.
Strand	A continuous segment of residues.

Class Summary

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.
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.
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.
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.