Package org.biojava.nbio.structure.secstruc

Class SecStrucState

java.lang.Object
org.biojava.nbio.structure.secstruc.SecStrucInfo
org.biojava.nbio.structure.secstruc.SecStrucState
All Implemented Interfaces:
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:

  • Constructor Details

  • Method Details

    • 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)

    • getBridge1

      public BetaBridge getBridge1()

    • getBridge2

      public BetaBridge getBridge2()

    • 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 String printDSSPline(int index)