BALL::RotamerLibrary Class Reference
[Rotamers]

Rotamer Library Class. More...

#include <rotamerLibrary.h>

List of all members.

Public Member Functions
Constructors and Destructors
	RotamerLibrary ()
	Default constructor.
	RotamerLibrary (const String &filename, const FragmentDB &fragment_db)
	Detailed constructor, provided for convenience.
	RotamerLibrary (const FragmentDB &fragment_db)
	Detailed constructor.
	RotamerLibrary (const RotamerLibrary &library)
	Copy constructor.
virtual	~RotamerLibrary ()
	Destructor.
Assignment
RotamerLibrary &	operator= (const RotamerLibrary &rhs)
	Assignment operator.
Accessors
ResidueRotamerSet *	getRotamerSet (const String &name)
	Return the residue set of the residue name.
ResidueRotamerSet *	getRotamerSet (const String &name, float phi, float psi)
	Return the residue set of the given name and torsions.
ResidueRotamerSet *	getRotamerSet (const Residue &residue)
	Return the residue set of the given residue.
Size	getNumberOfRotamers () const
	Return total number of rotamers.
Size	getNumberOfRotamers (const String &name) const
	Return the number of rotamers of the residue with the name.
Size	getNumberOfRotamerSets () const
	returns the number of rotamer sets
void	addRotamer (const String &name, const Rotamer &rotamer, Size number_of_torsions, Index phi, Index psi)
	adds rotamer with specific phi/psi backbone torsion
void	addRotamer (const String &name, const Rotamer &rotamer, Size number_of_torsions)
	adds a rotamer with name
bool	isBackboneDependent () const
	returns true if the rotamers are backbone dependent
void	setBackboneDependent (bool dependent)
	sets whether the rotamers are backbone dependent or not
bool	hasRotamers (const String &name) const
	returns true if the library contains rotamers with this name
bool	validate ()
	method to test the validity of this library, typically called after the building (see SCWRLLibraryFile)
void	sort ()
	method to sort the Rotamers of each ResidueRotamerSet descendingly according to the probability
void	clear ()
	Clear rotamer library.
Static Public Attributes
String constants
static const String	DEFAULT_LIBRARY
	Rotamer library used when calling the default constructor.
static const String	DEFAULT_FRAGMENT_DB
	Fragment DB used when calling the default constructor.
Protected Attributes
HashMap< Index, HashMap< Index, HashMap< String, ResidueRotamerSet > > >	bb_dep_sets_
	Contains the available variants (phi, psi, name, rotamer set) in case of bb dep.
HashMap< String, ResidueRotamerSet >	bb_indep_sets_
	Contains the available variants (name, rotamer set) in case of bb indep.
Size	step_width_
	discretization step width of the torsion angles
FragmentDB	fragment_db_
	fragment db used in this class
bool	backbone_dependent_
	flag which is true when the library has backbone dependent rotamers
Index	getNearestBackboneTorsion_ (double angle) const

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Detailed Description

Rotamer Library Class.

A rotamer library contains a list of possible rotamers for each of the 18 amino acid side chains (GLY and ALA do not have rotamers).

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Constructor & Destructor Documentation

BALL::RotamerLibrary::RotamerLibrary

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Default constructor.

Uses rotamer library RotamerLibrary::DEFAULT_LIBRARY and fragment db RotamerLibrary::DEFAULT_FRAGMENT_DB.

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Member Function Documentation

void BALL::RotamerLibrary::clear

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Clear rotamer library.

Removes all rotamers and sets library to backbone independent.