Class SecStrucState

  • All Implemented Interfaces:
    java.io.Serializable

    public class SecStrucState
    extends SecStrucInfo
    This class extends the basic container for secondary structure annotation, including all the information used in the DSSP algorithm.
    Author:
    Andreas Prlic, Aleix Lafita
    See Also:
    Serialized Form
    • Constructor Detail

      • SecStrucState

        public SecStrucState​(Group g,
                             java.lang.String ass,
                             SecStrucType t)
    • Method Detail

      • isBend

        public boolean isBend()
      • setBend

        public void setBend​(boolean bend)
      • getKappa

        public float getKappa()
      • setKappa

        public void setKappa​(float kappa)
      • getTurn

        public char[] getTurn()
      • setTurn

        public void setTurn​(char c,
                            int t)
        Set the turn column corresponding to 3,4 or 5 helix patterns. If starting > or ending < was set and the opposite is being set, the value will be converted to X. If a number was set, it will be overwritten by the new character.
        Parameters:
        c - character in the column
        t - turn of the helix {3,4,5}
      • getAccept1

        public HBond getAccept1()
      • setAccept1

        public void setAccept1​(HBond accept1)
      • getAccept2

        public HBond getAccept2()
      • setAccept2

        public void setAccept2​(HBond accept2)
      • getDonor1

        public HBond getDonor1()
      • setDonor1

        public void setDonor1​(HBond donor1)
      • getDonor2

        public HBond getDonor2()
      • setDonor2

        public void setDonor2​(HBond donor2)
      • getPhi

        public double getPhi()
      • setPhi

        public void setPhi​(double phi)
      • getPsi

        public double getPsi()
      • setPsi

        public void setPsi​(double psi)
      • getOmega

        public double getOmega()
      • setOmega

        public void setOmega​(double omega)
      • addBridge

        public boolean addBridge​(BetaBridge bridge)
        Adds a Bridge to the residue. Each residue can only store two bridges. If the residue contains already two Bridges, the Bridge will not be added and the method returns false.
        Parameters:
        bridge -
        Returns:
        false if the Bridge was not added, true otherwise
      • setBridge1

        public void setBridge1​(BetaBridge bridge1)
      • setBridge2

        public void setBridge2​(BetaBridge bridge2)
      • printDSSPline

        public java.lang.String printDSSPline​(int index)