Package pl.poznan.put.structure.formats
package pl.poznan.put.structure.formats
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ClassDescriptionRNA secondary structure in BPSEQ format.An entry of a BPSEQ data.A dot-bracket encoded structure made from combining one or more strands.A dot-bracket encoded structure made from combining one or more strands.A converter from BPSEQ to dot-bracket.An RNA secondary structure encoded in CT (connect) format.A single entry in the CT formatted structure.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.A default implementation of a dot-bracket.A default implementation of a dot-bracket structure which is mapped to data from 3D coordinates.A default implementation of a strand.An RNA structure encoded in dot-bracket format.A dot-bracket structure with correspondence to a 3D structure.Immutable implementation of
BpSeq.Builds instances of typeImmutableBpSeq.Immutable implementation ofCombinedStrand.Builds instances of typeImmutableCombinedStrand.Immutable implementation ofCombinedStrandFromPdb.Builds instances of typeImmutableCombinedStrandFromPdb.Immutable implementation ofCt.Builds instances of typeImmutableCt.Immutable implementation ofDefaultConverter.Builds instances of typeImmutableDefaultConverter.Immutable implementation ofDefaultDotBracket.Builds instances of typeImmutableDefaultDotBracket.Immutable implementation ofDefaultDotBracketFromPdb.Builds instances of typeImmutableDefaultDotBracketFromPdb.Immutable implementation ofDefaultStrand.Builds instances of typeImmutableDefaultStrand.Immutable implementation ofBpSeq.Entry.Builds instances of typeImmutableEntry.Immutable implementation ofCt.ExtendedEntry.Builds instances of typeImmutableExtendedEntry.Immutable implementation ofMultiLineDotBracket.Builds instances of typeImmutableMultiLineDotBracket.Immutable implementation ofStrandView.Builds instances of typeImmutableStrandView.Immutable implementation ofTerminalMissing.Builds instances of typeImmutableTerminalMissing.An extended secondary structure, which contains also non-canonical base pairs.A continuous segment of residues.A strand which is defined as a fragment of a dot-bracket structure.A colecction of missing dot-bracket symbols at 5' or 3' end.