Secondary structure extraction from 3D structure. More...

#include <BALL/STRUCTURE/secondaryStructureProcessor.h>

Inheritance diagram for BALL::SecondaryStructureProcessor:

Public Member Functions
Constructors
	SecondaryStructureProcessor ()

Processor-related methods
virtual Processor::Result	operator() (Composite &composite)

Public Member Functions inherited from BALL::UnaryProcessor< Composite >
	UnaryProcessor ()

	UnaryProcessor (const UnaryProcessor &)

virtual	~UnaryProcessor ()

virtual bool	start ()

virtual bool	finish ()

Protected Member Functions
void	compute_ ()
	Compute the secondary structure. More...

char	setSecondaryStructureType_ (SecondaryStructure *ss, char type)

bool	testString_ (const String &s, Size offset, Size offset_2)

bool	testString2_ (const String &s, Size offset)

bool	testString3_ (const String &s, Size offset, char x)

void	insertTurn_ (int turn, int position)

void	changeAllXToY_ (char X, char Y, String &target)

Protected Attributes
std::vector< std::vector < Position > >	HBonds_

std::vector< std::vector< int > >	posbridges_

String	sheet_

String	fiveturn_

String	fourturn_

String	threeturn_

String	summary_

Additional Inherited Members
Public Types inherited from BALL::UnaryFunctor< Composite, Processor::Result >
typedef Processor::Result	result_type

typedef Composite	argument_type

typedef Composite &	argument_reference

typedef const Composite &	const_argument_reference

typedef Composite *	argument_pointer

typedef const Composite *	const_argument_pointer

Detailed Description

Secondary structure extraction from 3D structure.

Secondary Structure Processor.

This class implements the DSSP algorithm described in "Kabsch W & Sander C (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637."

When applied to a protein, it removes the instances of SecondaryStructure from the protein, predicts the secondary structure elements based (mostly) on H-bond patterns and backbone torsions and reinserts the appropriate secondary structure elements at the predicted positions.

Definition at line 38 of file secondaryStructureProcessor.h.