Package org.biojava.nbio.structure.secstruc

Class SecStrucState

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

  • 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)