Package pl.poznan.put.structure.formats

Class DefaultDotBracketFromPdb

java.lang.Object
pl.poznan.put.structure.formats.DefaultDotBracketFromPdb
All Implemented Interfaces:
DotBracket, DotBracketFromPdb
Direct Known Subclasses:
ImmutableDefaultDotBracketFromPdb
@Immutable public abstract class DefaultDotBracketFromPdb extends Object implements DotBracketFromPdb
A default implementation of a dot-bracket structure which is mapped to data from 3D coordinates.

  • Constructor Details

    • DefaultDotBracketFromPdb

      public DefaultDotBracketFromPdb()

  • Method Details

    • model

      @Parameter(order=3) public abstract PdbModel model()

    • combineStrands

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

    • originalIndex

      public final int originalIndex(DotBracketSymbol symbol)
      Description copied from interface: DotBracket
      Returns the index of a dot-bracket symbol according to some external source like PDB numbering.
      Specified by:
      originalIndex in interface DotBracket
      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 @Auxiliary public List<Strand> strands()
      Specified by:
      strands in interface DotBracket
      Returns:
      The list of strands.

    • sequence

      @Parameter(order=1) public abstract String sequence()
      Specified by:
      sequence in interface DotBracket
      Returns:
      The sequence of nucleotides.

    • structure

      @Parameter(order=2) public abstract String structure()
      Specified by:
      structure in interface DotBracket
      Returns:
      The sequence of dots and brackets representing paired and unpaired residues.

    • pairs

      @Lazy @Auxiliary public Map<DotBracketSymbol,DotBracketSymbol> pairs()
      Specified by:
      pairs in interface DotBracket

    • identifier

      public final PdbResidueIdentifier identifier(DotBracketSymbol symbol)
      Description copied from interface: DotBracketFromPdb
      Maps the given dot-bracket symbol to its corresponding residue identifier.
      Specified by:
      identifier in interface DotBracketFromPdb
      Parameters:
      symbol - The symbol to look for.
      Returns:
      The PDB residue identifier.

    • symbol

      public final DotBracketSymbol symbol(PdbResidueIdentifier residueIdentifier)
      Description copied from interface: DotBracketFromPdb
      Maps the given residue identifier to its corresponding dot-bracket symbol.
      Specified by:
      symbol in interface DotBracketFromPdb
      Parameters:
      residueIdentifier - The residue identifier to look for.
      Returns:
      The dot-bracket symbol.

    • contains

      public final boolean contains(PdbResidueIdentifier residueIdentifier)
      Description copied from interface: DotBracketFromPdb
      Checks if this structure contains a mapping for the given residue identifier.
      Specified by:
      contains in interface DotBracketFromPdb
      Parameters:
      residueIdentifier - The residue identifier to check.
      Returns:
      True, if there is a mapping for the given residue identifier.

    • combineStrands

      public final List<DotBracketFromPdb> combineStrands(List<ClassifiedBasePair> nonCanonical)
      Description copied from interface: DotBracketFromPdb
      Combines strands which are connected via canonical or non-canonical base pairs.
      Specified by:
      combineStrands in interface DotBracketFromPdb
      Parameters:
      nonCanonical - The list of non-canonical base pairs to take into account.
      Returns:
      The list of dot-bracket structures from the combined strands.

    • residueToSymbol

      @Lazy protected Map<PdbResidueIdentifier,DotBracketSymbol> residueToSymbol()

    • symbolToResidue

      @Lazy protected Map<DotBracketSymbol,PdbResidueIdentifier> symbolToResidue()

    • validate

      @Check protected DefaultDotBracketFromPdb validate()

    • symbols

      public List<DotBracketSymbol> symbols()
      Specified by:
      symbols in interface DotBracket
      Returns:
      The list of dot-bracket symbols.

    • candidatesToCombine

      protected final List<List<Strand>> candidatesToCombine()