Rotamer Library Class. More...

#include <BALL/STRUCTURE/rotamerLibrary.h>

Public Member Functions
Constructors and Destructors
	RotamerLibrary ()

	RotamerLibrary (const String &filename, const FragmentDB &fragment_db)
	Detailed constructor, provided for convenience. More...

	RotamerLibrary (const FragmentDB &fragment_db)
	Detailed constructor. More...

	RotamerLibrary (const RotamerLibrary &library)
	Copy constructor. More...

virtual	~RotamerLibrary ()
	Destructor. More...

Assignment
RotamerLibrary &	operator= (const RotamerLibrary &rhs)
	Assignment operator. More...

Accessors
ResidueRotamerSet *	getRotamerSet (const String &name)
	Return the residue set of the residue name. More...

ResidueRotamerSet *	getRotamerSet (const String &name, float phi, float psi)
	Return the residue set of the given name and torsions. More...

ResidueRotamerSet *	getRotamerSet (const Residue &residue)
	Return the residue set of the given residue. More...

Size	getNumberOfRotamers () const
	Return total number of rotamers. More...

Size	getNumberOfRotamers (const String &name) const
	Return the number of rotamers of the residue with the name. More...

Size	getNumberOfRotamerSets () const
	returns the number of rotamer sets More...

void	addRotamer (const String &name, const Rotamer &rotamer, Size number_of_torsions, Index phi, Index psi)
	adds rotamer with specific phi/psi backbone torsion More...

void	addRotamer (const String &name, const Rotamer &rotamer, Size number_of_torsions)
	adds a rotamer with name More...

bool	isBackboneDependent () const
	returns true if the rotamers are backbone dependent More...

void	setBackboneDependent (bool dependent)
	sets whether the rotamers are backbone dependent or not More...

bool	hasRotamers (const String &name) const
	returns true if the library contains rotamers with this name More...

bool	validate ()
	method to test the validity of this library, typically called after the building (see SCWRLLibraryFile) More...

void	sort ()
	method to sort the Rotamers of each ResidueRotamerSet descendingly according to the probability More...

void	clear ()

Static Public Attributes
String constants
static const String	DEFAULT_LIBRARY
	Rotamer library used when calling the default constructor. More...

static const String	DEFAULT_FRAGMENT_DB
	Fragment DB used when calling the default constructor. More...

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. More...

HashMap< String, ResidueRotamerSet >	bb_indep_sets_
	Contains the available variants (name, rotamer set) in case of bb indep. More...

Size	step_width_
	discretization step width of the torsion angles More...

FragmentDB	fragment_db_
	fragment db used in this class More...

bool	backbone_dependent_
	flag which is true when the library has backbone dependent rotamers More...

Index	getNearestBackboneTorsion_ (double angle) const

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).

Definition at line 33 of file rotamerLibrary.h.

Constructor & Destructor Documentation

BALL::RotamerLibrary::RotamerLibrary ( )

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

BALL::RotamerLibrary::RotamerLibrary	(	const String &	filename,
		const FragmentDB &	fragment_db
	)

Detailed constructor, provided for convenience.

BALL::RotamerLibrary::RotamerLibrary ( const FragmentDB & fragment_db )

Detailed constructor.

BALL::RotamerLibrary::RotamerLibrary ( const RotamerLibrary & library )

Copy constructor.

virtual BALL::RotamerLibrary::~RotamerLibrary ( )

virtual

Destructor.

Member Function Documentation

void BALL::RotamerLibrary::addRotamer	(	const String &	name,
		const Rotamer &	rotamer,
		Size	number_of_torsions,
		Index	phi,
		Index	psi
	)

adds rotamer with specific phi/psi backbone torsion

void BALL::RotamerLibrary::addRotamer	(	const String &	name,
		const Rotamer &	rotamer,
		Size	number_of_torsions
	)

adds a rotamer with name

void BALL::RotamerLibrary::clear ( )

Clear rotamer library. Removes all rotamers and sets library to backbone independent.

Index BALL::RotamerLibrary::getNearestBackboneTorsion_ ( double angle ) const

protected

Size BALL::RotamerLibrary::getNumberOfRotamers ( ) const

Return total number of rotamers.

Size BALL::RotamerLibrary::getNumberOfRotamers ( const String & name ) const

Return the number of rotamers of the residue with the name.

Size BALL::RotamerLibrary::getNumberOfRotamerSets ( ) const

returns the number of rotamer sets

ResidueRotamerSet* BALL::RotamerLibrary::getRotamerSet ( const String & name )

Return the residue set of the residue name.

ResidueRotamerSet* BALL::RotamerLibrary::getRotamerSet	(	const String &	name,
		float	phi,
		float	psi
	)

Return the residue set of the given name and torsions.

ResidueRotamerSet* BALL::RotamerLibrary::getRotamerSet ( const Residue & residue )

Return the residue set of the given residue.

bool BALL::RotamerLibrary::hasRotamers ( const String & name ) const

returns true if the library contains rotamers with this name

bool BALL::RotamerLibrary::isBackboneDependent ( ) const

returns true if the rotamers are backbone dependent

RotamerLibrary& BALL::RotamerLibrary::operator= ( const RotamerLibrary & rhs )

Assignment operator.

void BALL::RotamerLibrary::setBackboneDependent ( bool dependent )

sets whether the rotamers are backbone dependent or not

void BALL::RotamerLibrary::sort ( )

method to sort the Rotamers of each ResidueRotamerSet descendingly according to the probability

bool BALL::RotamerLibrary::validate ( )

method to test the validity of this library, typically called after the building (see SCWRLLibraryFile)

Member Data Documentation

bool BALL::RotamerLibrary::backbone_dependent_

protected

flag which is true when the library has backbone dependent rotamers

Definition at line 149 of file rotamerLibrary.h.

HashMap<Index, HashMap<Index, HashMap<String, ResidueRotamerSet> > > BALL::RotamerLibrary::bb_dep_sets_

protected

Contains the available variants (phi, psi, name, rotamer set) in case of bb dep.

Definition at line 134 of file rotamerLibrary.h.

HashMap<String, ResidueRotamerSet> BALL::RotamerLibrary::bb_indep_sets_

protected

Contains the available variants (name, rotamer set) in case of bb indep.

Definition at line 137 of file rotamerLibrary.h.

const String BALL::RotamerLibrary::DEFAULT_FRAGMENT_DB

static

Fragment DB used when calling the default constructor.

Definition at line 47 of file rotamerLibrary.h.

const String BALL::RotamerLibrary::DEFAULT_LIBRARY

static

Rotamer library used when calling the default constructor.

Definition at line 44 of file rotamerLibrary.h.

FragmentDB BALL::RotamerLibrary::fragment_db_

protected

fragment db used in this class

Definition at line 146 of file rotamerLibrary.h.

Size BALL::RotamerLibrary::step_width_

protected

discretization step width of the torsion angles

Definition at line 143 of file rotamerLibrary.h.

Public Member Functions

Static Public Attributes

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation