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:

Serialized Form

Field Summary

Fields inherited from class org.biojava.nbio.structure.secstruc.SecStrucInfo

assignment, BIOJAVA_ASSIGNMENT, DSSP_ASSIGNMENT, parent, PDB_AUTHOR_ASSIGNMENT, type

Constructor Summary

Constructors

Constructor	Description
SecStrucState(Group g, String ass, SecStrucType t)

Method Summary

Modifier and Type	Method	Description
boolean	addBridge(BetaBridge bridge)	Adds a Bridge to the residue.
HBond	getAccept1()
HBond	getAccept2()
BetaBridge	getBridge1()
BetaBridge	getBridge2()
HBond	getDonor1()
HBond	getDonor2()
float	getKappa()
double	getOmega()
double	getPhi()
double	getPsi()
char[]	getTurn()
boolean	isBend()
String	printDSSPline(int index)
void	setAccept1(HBond accept1)
void	setAccept2(HBond accept2)
void	setBend(boolean bend)
void	setBridge1(BetaBridge bridge1)
void	setBridge2(BetaBridge bridge2)
void	setDonor1(HBond donor1)
void	setDonor2(HBond donor2)
void	setKappa(float kappa)
void	setOmega(double omega)
void	setPhi(double phi)
void	setPsi(double psi)
void	setTurn(char c, int t)	Set the turn column corresponding to 3,4 or 5 helix patterns.

Methods inherited from class org.biojava.nbio.structure.secstruc.SecStrucInfo

equals, getAssignment, getGroup, getType, hashCode, setType, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

SecStrucState

public SecStrucState(Group g,
                     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)

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)