org.biojava.bio.structure.secstruc
Class SecStruc

java.lang.Object
  extended by org.biojava.bio.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
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
SecStruc()
           
 
Method Summary
 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 ...
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 - ...