ResidueRotamerSet Class Reference
[Rotamers]

Residue Rotamer Set. More...

#include <residueRotamerSet.h>

List of all members.

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 ()
	Default constructor.
	ResidueRotamerSet (const ResidueRotamerSet &rotamer_set)
	Copy constructor.
	ResidueRotamerSet (const Residue &residue, Size number_of_torsions)
	Detailed constructor.
virtual	~ResidueRotamerSet ()
	Destructor.
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
	Return the number of valid torsions in the side chain.
void	setNumberOfTorsions (Size number_of_torsions) throw (Exception::IndexOverflow)
	Set the number of valid torsions for this side chain.
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)
	Assign a specific rotamer.
Rotamer	getRotamer (const Residue &residue) const
	Calculate the torsion angle of a residue.
const Rotamer &	getRotamer (Position index) const
	Return a reference to a given rotamer by number.
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)
	Determine all movable 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.

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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.

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Constructor & Destructor Documentation

ResidueRotamerSet::ResidueRotamerSet (   )

Default constructor.

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Member Function Documentation

void 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.

Size ResidueRotamerSet::getNumberOfTorsions (   )  const

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

const Rotamer& 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 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.

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

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