BALL::ResidueRotamerSet Class Reference
[Rotamers]

#include <BALL/STRUCTURE/residueRotamerSet.h>

Classes
struct	RotamerProbabilityGreaterThan_
Public Types
Type definitions

typedef std::vector< Rotamer > ::const_iterator	ConstIterator
typedef std::vector< Rotamer > ::const_iterator	const_iterator
typedef std::vector< Rotamer > ::iterator	Iterator
typedef std::vector< Rotamer > ::iterator	iterator
Public Member Functions
Constructors and Destructors

	ResidueRotamerSet ()
	ResidueRotamerSet (const ResidueRotamerSet &rotamer_set)
	ResidueRotamerSet (const Residue &residue, Size number_of_torsions)
virtual	~ResidueRotamerSet ()
External Iteration

Iterator	begin ()
Iterator	end ()
ConstIterator	begin () const
ConstIterator	end () const
Assignment

const ResidueRotamerSet &	operator= (const ResidueRotamerSet &residue_rotamer_set)
	The assignment operator.
Accessors

const String &	getName () const
	Get the name of the ResidueRotamerSet.
bool	isValid () const
	Find out if the class instance is valid.
Size	getNumberOfRotamers () const
	Return the number of rotamers from this residue rotamer set.
Size	getNumberOfTorsions () const
void	setNumberOfTorsions (Size number_of_torsions) throw (Exception::IndexOverflow)
const Rotamer &	operator[] (Position index) const throw (Exception::IndexOverflow)
	Random access operator for single rotamers.
bool	hasTorsionPhi () const
Angle	getTorsionPhi () const
void	setTorsionPhi (const Angle &phi)
bool	hasTorsionPsi () const
Angle	getTorsionPsi () const
void	setTorsionPsi (const Angle &psi)
Rotamer Assignment

bool	setTemplateResidue (const Residue &residue, Size number_of_torsions)
	Set the template residue, name, base coordinates ...
bool	setRotamer (Residue &residue, const Rotamer &rotamer)
Rotamer	getRotamer (const Residue &residue) const
const Rotamer &	getRotamer (Position index) const
void	setName (const String &name)
	Assign a new name.
void	addRotamer (const Rotamer &rotamer)
	Add a rotamer to the current set.
void	deleteRotamer (Iterator loc)
	Delete the Rotamer at the given iterator location.
void	deleteRotamers (Iterator begin, Iterator end)
	Delete the range of rotamers.
void	sort ()
	Sort the rotamers descendingly according to their probability.
Protected Member Functions
void	addMovable_ (std::vector< String > &movable, const Atom &a, const HashSet< String > &assigned_atoms)
void	setTorsionAngle_ (Residue &residue, const std::vector< String > &movable, float torsion)
	Set the torsion angles.
Protected Attributes
bool	valid_
	Indicates whether the instance is valid.
String	name_
	Name of the residue (variant name).
std::vector< Rotamer >	rotamers_
	Array containing all rotamers.
std::vector< String >	movable_atoms_chi1_
	Names of the movable atoms (names) for each of the torsions.
std::vector< String >	movable_atoms_chi2_
std::vector< String >	movable_atoms_chi3_
std::vector< String >	movable_atoms_chi4_
Size	number_of_torsions_
	Number of valid torsions in the side chain.
StringHashMap< Vector3 >	original_coordinates_
	Original coordinates of the template residue.
bool	has_torsion_phi_
	true if this residue rotamer set is backbone dependent
bool	has_torsion_psi_
	true if this residue rotamer set is backbone dependent
Angle	phi_
	The torsion phi.
Angle	psi_
	The torsion psi.

Detailed Description

Residue Rotamer Set.

This class stores all potential rotamers for a given side chain type. By linking a residue rotamer set to a specific side chain, one can iteratively try all contained rotamers for this side chain. The rotamers for a side chain are typically stored in a rotamer library .

The basic functionality is to store the rotamers and to modify residues according to this rotamers.

Definition at line 91 of file residueRotamerSet.h.

Member Typedef Documentation

typedef std::vector<Rotamer>::const_iterator BALL::ResidueRotamerSet::const_iterator

Definition at line 100 of file residueRotamerSet.h.

typedef std::vector<Rotamer>::const_iterator BALL::ResidueRotamerSet::ConstIterator

Definition at line 99 of file residueRotamerSet.h.

typedef std::vector<Rotamer>::iterator BALL::ResidueRotamerSet::iterator

Definition at line 103 of file residueRotamerSet.h.

typedef std::vector<Rotamer>::iterator BALL::ResidueRotamerSet::Iterator

Definition at line 102 of file residueRotamerSet.h.

Constructor & Destructor Documentation

BALL::ResidueRotamerSet::ResidueRotamerSet ( )

Default constructor.

BALL::ResidueRotamerSet::ResidueRotamerSet ( const ResidueRotamerSet & rotamer_set )

Copy constructor

BALL::ResidueRotamerSet::ResidueRotamerSet	(	const Residue &	residue,
		Size	number_of_torsions
	)

Detailed constructor

virtual BALL::ResidueRotamerSet::~ResidueRotamerSet ( ) [virtual]

Destructor

Member Function Documentation

void BALL::ResidueRotamerSet::addMovable_	(	std::vector< String > &	movable,
		const Atom &	a,
		const HashSet< String > &	assigned_atoms
	)			`[protected]`

Determine all movable atoms. This method walks along the bonds starting at a and adds them to the movable vector. Atoms whose names are contained in assigned_atoms are ignored.

void BALL::ResidueRotamerSet::addRotamer ( const Rotamer & rotamer )

Add a rotamer to the current set.

ConstIterator BALL::ResidueRotamerSet::begin ( ) const [inline]

Definition at line 150 of file residueRotamerSet.h.

Iterator BALL::ResidueRotamerSet::begin ( ) [inline]

Definition at line 136 of file residueRotamerSet.h.

void BALL::ResidueRotamerSet::deleteRotamer ( Iterator loc )

Delete the Rotamer at the given iterator location.

void BALL::ResidueRotamerSet::deleteRotamers	(	Iterator	begin,
		Iterator	end
	)

Delete the range of rotamers.

ConstIterator BALL::ResidueRotamerSet::end ( ) const [inline]

Definition at line 157 of file residueRotamerSet.h.

Iterator BALL::ResidueRotamerSet::end ( ) [inline]

Definition at line 143 of file residueRotamerSet.h.

const String& BALL::ResidueRotamerSet::getName ( ) const

Get the name of the ResidueRotamerSet.

Size BALL::ResidueRotamerSet::getNumberOfRotamers ( ) const

Return the number of rotamers from this residue rotamer set.

Size BALL::ResidueRotamerSet::getNumberOfTorsions ( ) const

Return the number of valid torsions in the side chain. The number returned is between zero and four.

const Rotamer& BALL::ResidueRotamerSet::getRotamer ( Position index ) const

Return a reference to a given rotamer by number. The index should be in the range [0, getNumberOfRotamers ()[, however the index is computed modulo the maximum number, so it really doesn't matter.

Rotamer BALL::ResidueRotamerSet::getRotamer ( const Residue & residue ) const

Calculate the torsion angle of a residue. Retrieve the side-chain torsion angles from the residue's current conformation.

Angle BALL::ResidueRotamerSet::getTorsionPhi ( ) const

Angle BALL::ResidueRotamerSet::getTorsionPsi ( ) const

bool BALL::ResidueRotamerSet::hasTorsionPhi ( ) const

bool BALL::ResidueRotamerSet::hasTorsionPsi ( ) const

bool BALL::ResidueRotamerSet::isValid ( ) const

Find out if the class instance is valid.

const ResidueRotamerSet& BALL::ResidueRotamerSet::operator= ( const ResidueRotamerSet & residue_rotamer_set )

The assignment operator.

const Rotamer& BALL::ResidueRotamerSet::operator[] ( Position index ) const throw (Exception::IndexOverflow)