BALL::SecondaryStructureProcessor Class Reference
[Miscellaneous]

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

#include <BALL/STRUCTURE/secondaryStructureProcessor.h>

Inheritance diagram for BALL::SecondaryStructureProcessor:

[legend]

List of all members.

Public Member Functions
Constructors
	SecondaryStructureProcessor ()
Processor-related methods
virtual Processor::Result	operator() (Composite &composite)
Protected Member Functions
void	compute_ ()
	Compute the secondary structure.
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_

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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.

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Constructor & Destructor Documentation

BALL::SecondaryStructureProcessor::SecondaryStructureProcessor

(

)

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Member Function Documentation

void BALL::SecondaryStructureProcessor::changeAllXToY_	(	char	X,
		char	Y,
		String &	target
	)			[protected]

void BALL::SecondaryStructureProcessor::compute_

(

)

[protected]

Compute the secondary structure.

void BALL::SecondaryStructureProcessor::insertTurn_	(	int	turn,
		int	position
	)			[protected]

virtual Processor::Result BALL::SecondaryStructureProcessor::operator()

(

Composite &

)

[virtual]

operator ()

Reimplemented from BALL::UnaryProcessor< Composite >.

char BALL::SecondaryStructureProcessor::setSecondaryStructureType_	(	SecondaryStructure *	ss,
		char	type
	)			[protected]

bool BALL::SecondaryStructureProcessor::testString2_	(	const String &	s,
		Size	offset
	)			[protected]

bool BALL::SecondaryStructureProcessor::testString3_	(	const String &	s,
		Size	offset,
		char	x
	)			[protected]

bool BALL::SecondaryStructureProcessor::testString_	(	const String &	s,
		Size	offset,
		Size	offset_2
	)			[protected]

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Member Data Documentation

String BALL::SecondaryStructureProcessor::fiveturn_ [protected]

Definition at line 77 of file secondaryStructureProcessor.h.

String BALL::SecondaryStructureProcessor::fourturn_ [protected]

Definition at line 78 of file secondaryStructureProcessor.h.

std::vector<std::vector<Position> > BALL::SecondaryStructureProcessor::HBonds_ [protected]

Definition at line 71 of file secondaryStructureProcessor.h.

std::vector<std::vector<int> > BALL::SecondaryStructureProcessor::posbridges_ [protected]

Definition at line 74 of file secondaryStructureProcessor.h.

String BALL::SecondaryStructureProcessor::sheet_ [protected]

Definition at line 76 of file secondaryStructureProcessor.h.

String BALL::SecondaryStructureProcessor::summary_ [protected]

Definition at line 80 of file secondaryStructureProcessor.h.

String BALL::SecondaryStructureProcessor::threeturn_ [protected]

Definition at line 79 of file secondaryStructureProcessor.h.