Package pl.poznan.put.structure.formats

Class Ct

java.lang.Object
pl.poznan.put.structure.formats.Ct
All Implemented Interfaces:
Serializable
Direct Known Subclasses:
ImmutableCt
@Immutable public abstract class Ct extends Object implements Serializable
An RNA secondary structure encoded in CT (connect) format.
See Also:

  • Constructor Details

    • Ct

      public Ct()

  • Method Details

    • fromString

      public static Ct fromString(String data)
      Parses string into an instance of this class.
      Parameters:
      data - The string with CT data.
      Returns:
      An instance of this class with parsed data.

    • fromBpSeq

      public static Ct fromBpSeq(BpSeq bpSeq)
      Converts RNA secondary structure in BPSEQ format to CT format.
      Parameters:
      bpSeq - The data in BPSEQ format.
      Returns:
      An instance of this class with converted data.

    • fromBpSeqAndPdbModel

      public static Ct fromBpSeqAndPdbModel(BpSeq bpSeq, PdbModel model)
      Converts RNA secondary structure in BPSEQ format to CT format, taking into account information from 3D coordinates (residue numbering, chain sizes).
      Parameters:
      bpSeq - The data in BPSEQ format.
      model - The 3D data.
      Returns:
      An instance of this class with converted data.

    • fromDotBracket

      public static Ct fromDotBracket(DotBracket dotBracket)
      Converts RNA secondary structure in dot-bracket format to CT format.
      Parameters:
      dotBracket - The data in dot-bracket format.
      Returns:
      An instance of this class with converted data.

    • entries

      @Parameter(order=1) @NaturalOrder public abstract SortedSet<Ct.ExtendedEntry> entries()
      Returns:
      The list of CT entries.

    • strandCount

      public final int strandCount()
      Returns:
      The number of strands.

    • withoutPair

      public final Ct withoutPair(Ct.ExtendedEntry entry)
      Creates a copy of this instance, but with the given pair removed.
      Parameters:
      entry - The pair to remove.
      Returns:
      A copy of this instance without the given pair.

    • withoutIsolatedPairs

      public final Ct withoutIsolatedPairs()
      Finds all isolated base pairs and creates a copy of this instance without them.
      Returns:
      A copy of this instance, but with all isolated base pairs removed.

    • toString

      public final String toString()
      Overrides:
      toString in class Object

    • validate

      @Check protected Ct validate()