SecondaryStructureProcessor Class Reference
[Miscellaneous]

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

#include <secondaryStructureProcessor.h>

Inheritance diagram for SecondaryStructureProcessor:

List of all members.

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

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.