Package org.biojava.nbio.structure.secstruc

Class SecStrucCalc

java.lang.Object
org.biojava.nbio.structure.secstruc.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.

Author:
Andreas Prlic, Aleix Lafita

  • Field Summary

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

  • Constructor Summary

    Constructors
    Constructor
    Description
    SecStrucCalc()
     

  • Method Summary

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

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

  • Field Details

    • MINDIST

      public static final double MINDIST
      min distance between two residues
      See Also:

    • 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:

    • MAX_PEPTIDE_BOND_LENGTH

      public static final double MAX_PEPTIDE_BOND_LENGTH
      max distance CA atoms in peptide bond (backbone discontinuity)
      See Also:

    • HBONDLOWENERGY

      public static final int HBONDLOWENERGY
      Minimal H-bond energy in cal/mol
      See Also:

    • HBONDHIGHENERGY

      public static final double HBONDHIGHENERGY
      higher limit for H-bond energy
      See Also:

    • 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:

  • Constructor Details

    • SecStrucCalc

      public SecStrucCalc()

  • Method Details

    • calculate

      public 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 String toString()
      Overrides:
      toString in class Object

    • printDSSP

      public String printDSSP()
      Generate a DSSP file format ouput String of this SS prediction.
      Returns:
      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.

      Returns:
      String helix summary

    • printFASTA

      public 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(Object o)
      Overrides:
      equals in class Object