org.biojava.nbio.structure.secstruc

Class SecStruc

java.lang.Object

org.biojava.nbio.structure.secstruc.SecStruc

public class SecStruc
extends Object

Assign secondary structure to a Structure object. tries to use the rules as defined by DSSP Kabsch,W. and Sander,C. (1983) Biopolymers 22, 2577-2637. original DSSP article see at : dssp.pdf some bits also taken from T.E.Creighton Proteins - Structure and Molecular Properties 2nd Edition, Freeman 1994

Field Summary

Fields

Modifier and Type	Field and Description
static int	CA_MIN_DIST the minimal distance of two CA atoms if H-bonds are allowed to form.
static double	HBONDHIGHENERGY higher limit for H-bond energy
static int	HBONDLOWENERGY Minimal H-bond energy in cal / mol
static double	MINDIST the minimal distance between two residues
static double	Q constant for electrostatic energy

Constructor Summary

Constructors

Constructor and Description
SecStruc()

Method Summary

Methods

Modifier and Type	Method and Description
void	assign(Structure s) assigns the secondary structure to the groups in this Structure object and set the results in the group properties.
double	calculateHBondEnergy(SecStrucGroup one, SecStrucGroup two) calculate HBond energy of two groups in cal/mol ...
SecStrucGroup[]	getGroups()
static BigDecimal	getPreciseDistance(Atom a, Atom b) calculate distance between two atoms.
static void	main(String[] args)
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

MINDIST

public static double MINDIST

the minimal distance between two residues

CA_MIN_DIST

public static int CA_MIN_DIST

the minimal distance of two CA atoms if H-bonds are allowed to form.

HBONDLOWENERGY

public static int HBONDLOWENERGY

Minimal H-bond energy in cal / mol

HBONDHIGHENERGY

public static double HBONDHIGHENERGY

higher limit for H-bond energy

Q

public static 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)

Constructor Detail

SecStruc

public SecStruc()

Method Detail

main

public static void main(String[] args)

assign

public void assign(Structure s)
            throws StructureException

assigns the secondary structure to the groups in this Structure object and set the results in the group properties.

Parameters:

s -

Throws:

StructureException

toString

public String toString()

Overrides:

toString in class Object

calculateHBondEnergy

public double calculateHBondEnergy(SecStrucGroup one,
                          SecStrucGroup two)
                            throws StructureException

calculate HBond energy of two groups in cal/mol ... see Creighton page 147 f Jeffrey, George A., An introduction to hydrogen bonding, Oxford University Press, 1997. categorizes hbonds with donor-acceptor distances of 2.2-2.5 å as "strong, mostly covalent", 2.5-3.2 å as "moderate, mostly electrostatic", 3.2-4.0 å as "weak, electrostatic". Energies are given as 40-14, 15-4, and <4 kcal/mol respectively.

Throws:

StructureException

getPreciseDistance

public static BigDecimal getPreciseDistance(Atom a,
                            Atom b)
                                     throws StructureException

calculate distance between two atoms.

Parameters:

a - an Atom object

b - an Atom object

Returns:

a double

Throws:

StructureException - ...

getGroups

public SecStrucGroup[] getGroups()