BALL::RotamerLibrary Class Reference
[Rotamers]

Rotamer Library Class. More...

#include <BALL/STRUCTURE/rotamerLibrary.h>

List of all members.

Public Member Functions
Constructors and Destructors
	RotamerLibrary ()
	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 ()
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

---

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
	)

adds a rotamer with name

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::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 String &

name

)

const

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

Size BALL::RotamerLibrary::getNumberOfRotamers

(

)

const

Return total number of rotamers.

Size BALL::RotamerLibrary::getNumberOfRotamerSets

(

)

const

returns the number of rotamer sets

ResidueRotamerSet* BALL::RotamerLibrary::getRotamerSet

(

const Residue &

residue

)

Return the residue set of the given residue.

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 String &

name

)

Return the residue set of the residue name.

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)

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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.