Class SecStrucCalc

  • public class SecStrucCalc
    extends Object
    Calculate and assign the secondary structure (SS) to the Groups of a Structure object. This object also stores the result of the calculation.

    The rules for SS calculation are the ones defined by DSSP: Kabsch,W. and Sander,C. (1983) Biopolymers 22, 2577-2637. Original DSSP article see at: dssp.pdf. Some parts are also taken from: T.E.Creighton, Proteins - Structure and Molecular Properties, 2nd Edition, Freeman 1994.

    Andreas Prlic, Aleix Lafita, Anthony Bradley
    • Method Detail

      • calculate

        public List<SecStrucStatecalculate​(Structure s,
                                             boolean assign)
                                      throws StructureException
        Predicts the secondary structure of this Structure object, using a DSSP implementation.
        s - Structure to predict the SS
        assign - sets the SS information to the Groups of s
        a List of SS annotation objects
      • printDSSP

        public String printDSSP()
        Generate a DSSP file format ouput String of this SS prediction.
        String in DSSP output file format
      • printHelixSummary

        public String printHelixSummary()
        Generate a summary of this SS prediction with information about the three types of helix turns in different row sequences.

        This is similar to the summary output of Jmol, and useful to visualize the helix patterns.

        String helix summary
      • printFASTA

        public String printFASTA()
        Generate a FASTA sequence with the SS annotation letters in the aminoacid sequence order.
        String in FASTA sequence format