BALL 1.5.0
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BALL::SecondaryStructureProcessor Class Reference

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

#include <BALL/STRUCTURE/secondaryStructureProcessor.h>

Inheritance diagram for BALL::SecondaryStructureProcessor:
BALL::UnaryProcessor< Composite > BALL::UnaryFunctor< Composite, Processor::Result >

Public Member Functions

Constructors
 SecondaryStructureProcessor ()
 
- Public Member Functions inherited from BALL::UnaryProcessor< Composite >
 UnaryProcessor ()
 
 UnaryProcessor (const UnaryProcessor &)
 
virtual ~UnaryProcessor ()
 
virtual bool start ()
 
virtual bool finish ()
 

Processor-related methods

std::vector< std::vector< Position > > HBonds_
 
std::vector< std::vector< int > > posbridges_
 
String sheet_
 
String fiveturn_
 
String fourturn_
 
String threeturn_
 
String summary_
 
virtual Processor::Result operator() (Composite &composite)
 
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)
 

Additional Inherited Members

- Public Types inherited from BALL::UnaryFunctor< Composite, Processor::Result >
typedef Processor::Result result_type
 
typedef Composite argument_type
 
typedef Compositeargument_reference
 
typedef const Compositeconst_argument_reference
 
typedef Compositeargument_pointer
 
typedef const Compositeconst_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.

Constructor & Destructor Documentation

◆ SecondaryStructureProcessor()

BALL::SecondaryStructureProcessor::SecondaryStructureProcessor ( )

Member Function Documentation

◆ changeAllXToY_()

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

◆ compute_()

void BALL::SecondaryStructureProcessor::compute_ ( )
protected

Compute the secondary structure.

◆ insertTurn_()

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

◆ operator()()

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

operator ()

Reimplemented from BALL::UnaryProcessor< Composite >.

◆ setSecondaryStructureType_()

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

◆ testString2_()

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

◆ testString3_()

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

◆ testString_()

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

Member Data Documentation

◆ fiveturn_

String BALL::SecondaryStructureProcessor::fiveturn_
protected

Definition at line 77 of file secondaryStructureProcessor.h.

◆ fourturn_

String BALL::SecondaryStructureProcessor::fourturn_
protected

Definition at line 78 of file secondaryStructureProcessor.h.

◆ HBonds_

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

Definition at line 71 of file secondaryStructureProcessor.h.

◆ posbridges_

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

Definition at line 74 of file secondaryStructureProcessor.h.

◆ sheet_

String BALL::SecondaryStructureProcessor::sheet_
protected

Definition at line 76 of file secondaryStructureProcessor.h.

◆ summary_

String BALL::SecondaryStructureProcessor::summary_
protected

Definition at line 80 of file secondaryStructureProcessor.h.

◆ threeturn_

String BALL::SecondaryStructureProcessor::threeturn_
protected

Definition at line 79 of file secondaryStructureProcessor.h.