BALL::ResidueRotamerSet Class Reference

#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. More...
Accessors
const String &	getName () const
	Get the name of the ResidueRotamerSet. More...
bool	isValid () const
	Find out if the class instance is valid. More...
Size	getNumberOfRotamers () const
	Return the number of rotamers from this residue rotamer set. More...
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. More...
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 ... More...
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. More...
void	addRotamer (const Rotamer &rotamer)
	Add a rotamer to the current set. More...
void	deleteRotamer (Iterator loc)
	Delete the Rotamer at the given iterator location. More...
void	deleteRotamers (Iterator begin, Iterator end)
	Delete the range of rotamers. More...
void	sort ()
	Sort the rotamers descendingly according to their probability. More...

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. More...

Protected Attributes
bool	valid_
	Indicates whether the instance is valid. More...
String	name_
	Name of the residue (variant name) More...
std::vector< Rotamer >	rotamers_
	Array containing all rotamers. More...
std::vector< String >	movable_atoms_chi1_
	Names of the movable atoms (names) for each of the torsions. More...
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. More...
StringHashMap< Vector3 >	original_coordinates_
	Original coordinates of the template residue. More...
bool	has_torsion_phi_
	true if this residue rotamer set is backbone dependent More...
bool	has_torsion_psi_
	true if this residue rotamer set is backbone dependent More...
Angle	phi_
	The torsion phi. More...
Angle	psi_
	The torsion psi. More...

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 87 of file residueRotamerSet.h.

Member Typedef Documentation

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

Definition at line 96 of file residueRotamerSet.h.

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

Definition at line 95 of file residueRotamerSet.h.

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

Definition at line 98 of file residueRotamerSet.h.

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

Definition at line 99 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.

Iterator BALL::ResidueRotamerSet::begin ( )

inline

Definition at line 132 of file residueRotamerSet.h.

ConstIterator BALL::ResidueRotamerSet::begin ( ) const

inline

Definition at line 146 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.

Iterator BALL::ResidueRotamerSet::end ( )

inline

Definition at line 139 of file residueRotamerSet.h.

ConstIterator BALL::ResidueRotamerSet::end ( ) const

inline

Definition at line 153 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.

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.

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.

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
	)

Random access operator for single rotamers.

void BALL::ResidueRotamerSet::setName

(

const String &

name

)

Assign a new name.

void BALL::ResidueRotamerSet::setNumberOfTorsions	(	Size	number_of_torsions	)
throw	(	Exception::IndexOverflow
	)

Set the number of valid torsions for this side chain.

Exceptions

Exception::IndexOverflow

if the number of torsions is above four.

bool BALL::ResidueRotamerSet::setRotamer	(	Residue &	residue,
		const Rotamer &	rotamer
	)

Assign a specific rotamer. Set the side-chain torsions of residue to the values specified by rotamer.

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

Set the template residue, name, base coordinates ...

void BALL::ResidueRotamerSet::setTorsionAngle_ ( Residue &  residue, const std::vector< String > &  movable, float  torsion  )

protected

Set the torsion angles.

void BALL::ResidueRotamerSet::setTorsionPhi

(

const Angle &

phi

)

void BALL::ResidueRotamerSet::setTorsionPsi

(

const Angle &

psi

)

void BALL::ResidueRotamerSet::sort

(

)

Sort the rotamers descendingly according to their probability.

Member Data Documentation

bool BALL::ResidueRotamerSet::has_torsion_phi_

protected

true if this residue rotamer set is backbone dependent

Definition at line 295 of file residueRotamerSet.h.

bool BALL::ResidueRotamerSet::has_torsion_psi_

protected

true if this residue rotamer set is backbone dependent

Definition at line 298 of file residueRotamerSet.h.

std::vector<String> BALL::ResidueRotamerSet::movable_atoms_chi1_

protected

Names of the movable atoms (names) for each of the torsions.

Definition at line 283 of file residueRotamerSet.h.

std::vector<String> BALL::ResidueRotamerSet::movable_atoms_chi2_

protected

Definition at line 284 of file residueRotamerSet.h.

std::vector<String> BALL::ResidueRotamerSet::movable_atoms_chi3_

protected

Definition at line 285 of file residueRotamerSet.h.

std::vector<String> BALL::ResidueRotamerSet::movable_atoms_chi4_

protected

Definition at line 286 of file residueRotamerSet.h.

String BALL::ResidueRotamerSet::name_

protected

Name of the residue (variant name)

Definition at line 277 of file residueRotamerSet.h.

Size BALL::ResidueRotamerSet::number_of_torsions_

protected

Number of valid torsions in the side chain.

Definition at line 289 of file residueRotamerSet.h.

StringHashMap<Vector3> BALL::ResidueRotamerSet::original_coordinates_

protected

Original coordinates of the template residue.

Definition at line 292 of file residueRotamerSet.h.

Angle BALL::ResidueRotamerSet::phi_

protected

The torsion phi.

Definition at line 301 of file residueRotamerSet.h.

Angle BALL::ResidueRotamerSet::psi_

protected

The torsion psi.

Definition at line 304 of file residueRotamerSet.h.

std::vector<Rotamer> BALL::ResidueRotamerSet::rotamers_

protected

Array containing all rotamers.

Definition at line 280 of file residueRotamerSet.h.

bool BALL::ResidueRotamerSet::valid_

protected

Indicates whether the instance is valid.

Definition at line 274 of file residueRotamerSet.h.