org.biojava.nbio.structure.secstruc

Class SecStrucCalc

java.lang.Object

org.biojava.nbio.structure.secstruc.SecStrucCalc

public class SecStrucCalc
extends Object

Calculate and assign the secondary structure (SS) to the Groups of a Structure object. This object also stores the result of the calculation.

The rules for SS calculation are the ones defined by DSSP: Kabsch,W. and Sander,C. (1983) Biopolymers 22, 2577-2637. Original DSSP article see at: dssp.pdf. Some parts are also taken from: T.E.Creighton, Proteins - Structure and Molecular Properties, 2nd Edition, Freeman 1994.

Author:

Andreas Prlic, Aleix Lafita

Field Summary

Fields

Modifier and Type	Field and Description
static double	CA_MIN_DIST min 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	MAX_PEPTIDE_BOND_LENGTH max distance CA atoms in peptide bond (backbone discontinuity)
static double	MINDIST min distance between two residues
static double	Q constant for electrostatic energy

Constructor Summary

Constructors

Constructor and Description
SecStrucCalc()

Method Summary

Modifier and Type	Method and Description
List<SecStrucState>	calculate(Structure s, boolean assign) Predicts the secondary structure of this Structure object, using a DSSP implementation.
boolean	equals(Object o)
String	printDSSP() Generate a DSSP file format ouput String of this SS prediction.
String	printFASTA() Generate a FASTA sequence with the SS annotation letters in the aminoacid sequence order.
String	printHelixSummary() Generate a summary of this SS prediction with information about the three types of helix turns in different row sequences.
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

MINDIST

public static final double MINDIST

min distance between two residues

See Also:

Constant Field Values

CA_MIN_DIST

public static final double CA_MIN_DIST

min distance of two CA atoms if H-bonds are allowed to form

See Also:

Constant Field Values

MAX_PEPTIDE_BOND_LENGTH

public static final double MAX_PEPTIDE_BOND_LENGTH

max distance CA atoms in peptide bond (backbone discontinuity)

See Also:

Constant Field Values

HBONDLOWENERGY

public static final int HBONDLOWENERGY

Minimal H-bond energy in cal/mol

See Also:

Constant Field Values

HBONDHIGHENERGY

public static final double HBONDHIGHENERGY

higher limit for H-bond energy

See Also:

Constant Field Values

Q

public static final 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)

See Also:

Constant Field Values

Constructor Detail

SecStrucCalc

public SecStrucCalc()

Method Detail

calculate

public List<SecStrucState> calculate(Structure s,
                                     boolean assign)
                              throws StructureException

Predicts the secondary structure of this Structure object, using a DSSP implementation.

Parameters:

s - Structure to predict the SS

assign - sets the SS information to the Groups of s

Returns:

a List of SS annotation objects

Throws:

StructureException

toString

public String toString()

Overrides:

toString in class Object

printDSSP

public String printDSSP()

Generate a DSSP file format ouput String of this SS prediction.

Returns:

String in DSSP output file format

printHelixSummary

public String printHelixSummary()

Generate a summary of this SS prediction with information about the three types of helix turns in different row sequences.

This is similar to the summary output of Jmol, and useful to visualize the helix patterns.

Returns:

String helix summary

printFASTA

public String printFASTA()

Generate a FASTA sequence with the SS annotation letters in the aminoacid sequence order.

Returns:

String in FASTA sequence format

equals

public boolean equals(Object o)

Overrides:

equals in class Object