Package pl.poznan.put.structure.formats

Interface DotBracket

All Known Subinterfaces:
DotBracketFromPdb, Strand
All Known Implementing Classes:
AbstractCombinedStrand, CombinedStrand, CombinedStrandFromPdb, DefaultDotBracket, DefaultDotBracketFromPdb, DefaultStrand, ImmutableCombinedStrand, ImmutableCombinedStrandFromPdb, ImmutableDefaultDotBracket, ImmutableDefaultDotBracketFromPdb, ImmutableDefaultStrand, ImmutableStrandView, StrandView
public interface DotBracket
An RNA structure encoded in dot-bracket format.

  • Method Details

    • symbols

      List<DotBracketSymbol> symbols()
      Returns:
      The list of dot-bracket symbols.

    • combineStrands

      List<DotBracket> combineStrands()
      Combines strands which share a base pair into a new dot-bracket instance and returns a list of those.
      Returns:
      The list of dot-bracket instances, each containing strands which only pair with each other.

    • isolatedSymbols

      default Set<DotBracketSymbol> isolatedSymbols()
      Returns:
      A set of isolated symbols, i.e., those which are pairing but are surrounded by unpaired residues.

    • isIsolated

      default boolean isIsolated(DotBracketSymbol symbol)
      Checks if a symbol is isolated, i.e., if it is a pairing symbol and both it and its pair are surrounded by unpaired residues.
      Parameters:
      symbol - A dot-bracket symbol to check.
      Returns:
      True if the symbol is isolated.

    • originalIndex

      default int originalIndex(DotBracketSymbol symbol)
      Returns the index of a dot-bracket symbol according to some external source like PDB numbering.
      Parameters:
      symbol - Dot-bracket symbol for which the original index is sought.
      Returns:
      An index which reflects the numbering in real structure (e.g. PDB).

    • strands

      default List<Strand> strands()
      Returns:
      The list of strands.

    • sequence

      default String sequence()
      Returns:
      The sequence of nucleotides.

    • structure

      default String structure()
      Returns:
      The sequence of dots and brackets representing paired and unpaired residues.

    • pairs

      default Map<DotBracketSymbol,DotBracketSymbol> pairs()

    • toStringWithStrands

      default String toStringWithStrands()
      Returns:
      A string representation of this dot-bracket, where every strand is written out separately.

    • length

      default int length()
      Returns:
      The number of nucleotides in this structure.

    • containsMissing

      default boolean containsMissing()
      Returns:
      True, if at least one symbol represents a missing residue.

    • missingTerminal

      default List<TerminalMissing> missingTerminal()
      Returns:
      The list of missing symbols at 5' and 3' ends of all strands.

    • missingInternal

      default List<DotBracketSymbol> missingInternal()
      Returns:
      The list of missing symbols which are not at 5' or 3' ends of any strand.

    • pseudoknotOrder

      default int pseudoknotOrder()
      Returns:
      The pseudoknot order of this structure.

    • findStrand

      default Strand findStrand(DotBracketSymbol symbol)
      Finds a strand which contains the given symbol.
      Parameters:
      symbol - The symbol to look for.
      Returns:
      The strand containing the symbol.

    • sequence

      default String sequence(boolean separateStrands)
      Creates a string representation of nucleotide sequence, where strands may be separated with ampersand &amp; or not.
      Parameters:
      separateStrands - If true, the result will contain ampersand between strands.
      Returns:
      The string representation of nucleotide sequence.

    • structure

      default String structure(boolean separateStrands)
      Creates a string of dots and brackets which represents base pairing, where strands may be separated with ampersand &amp; or not.
      Parameters:
      separateStrands - If true, the result will contain ampersand between strands.
      Returns:
      The string representation of this structure.