Class SecStrucCalc


  • public class SecStrucCalc
    extends java.lang.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.

    Author:
    Andreas Prlic, Aleix Lafita
    • Field Summary

      Fields 
      Modifier and Type Field Description
      static double CA_MIN_DIST
      min distance of two CA atoms if H-bonds are allowed to form
      static double HBONDHIGHENERGY
      higher limit for H-bond energy
      static int HBONDLOWENERGY
      Minimal H-bond energy in cal/mol
      static double MAX_PEPTIDE_BOND_LENGTH
      max distance CA atoms in peptide bond (backbone discontinuity)
      static double MINDIST
      min distance between two residues
      static double Q
      constant for electrostatic energy
    • Constructor Summary

      Constructors 
      Constructor Description
      SecStrucCalc()  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      java.util.List<SecStrucState> calculate​(Structure s, boolean assign)
      Predicts the secondary structure of this Structure object, using a DSSP implementation.
      boolean equals​(java.lang.Object o)  
      java.lang.String printDSSP()
      Generate a DSSP file format ouput String of this SS prediction.
      java.lang.String printFASTA()
      Generate a FASTA sequence with the SS annotation letters in the aminoacid sequence order.
      java.lang.String printHelixSummary()
      Generate a summary of this SS prediction with information about the three types of helix turns in different row sequences.
      java.lang.String toString()  
      • Methods inherited from class java.lang.Object

        clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
    • Field Detail

      • MINDIST

        public static final double MINDIST
        min distance between two residues
        See Also:
        Constant Field Values
      • CA_MIN_DIST

        public static final double CA_MIN_DIST
        min distance of two CA atoms if H-bonds are allowed to form
        See Also:
        Constant Field Values
      • MAX_PEPTIDE_BOND_LENGTH

        public static final double MAX_PEPTIDE_BOND_LENGTH
        max distance CA atoms in peptide bond (backbone discontinuity)
        See Also:
        Constant Field Values
      • HBONDLOWENERGY

        public static final int HBONDLOWENERGY
        Minimal H-bond energy in cal/mol
        See Also:
        Constant Field Values
      • HBONDHIGHENERGY

        public static final double HBONDHIGHENERGY
        higher limit for H-bond energy
        See Also:
        Constant Field Values
      • Q

        public static final double Q
        constant for electrostatic energy
              f  *  q1 *   q2  *  scale
         Q = -332 * 0.42 * 0.20 * 1000.0
        
        q1 and q2 are partial charges which are placed on the C,O (+q1,-q1) and N,H (-q2,+q2)
        See Also:
        Constant Field Values
    • Constructor Detail

      • SecStrucCalc

        public SecStrucCalc()
    • Method Detail

      • calculate

        public java.util.List<SecStrucState> calculate​(Structure s,
                                                       boolean assign)
                                                throws StructureException
        Predicts the secondary structure of this Structure object, using a DSSP implementation.
        Parameters:
        s - Structure to predict the SS
        assign - sets the SS information to the Groups of s
        Returns:
        a List of SS annotation objects
        Throws:
        StructureException
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
      • printDSSP

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

        public java.lang.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.

        Returns:
        String helix summary
      • printFASTA

        public java.lang.String printFASTA()
        Generate a FASTA sequence with the SS annotation letters in the aminoacid sequence order.
        Returns:
        String in FASTA sequence format
      • equals

        public boolean equals​(java.lang.Object o)
        Overrides:
        equals in class java.lang.Object