BALL::AtomVector Class Reference
[General Force Field Classes.]

#include <BALL/MOLMEC/COMMON/atomVector.h>

Inheritance diagram for BALL::AtomVector:

Public Types
Type definitions

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

	AtomVector ()
	AtomVector (const Composite &composite, bool selected_only=false)
	AtomVector (const AtomVector &atoms, bool deep=true)
virtual	~AtomVector ()
Assignments

const AtomVector &	operator= (const AtomVector &rhs)
void	set (const AtomVector &atoms)
const AtomVector &	operator= (const Composite &rhs)
void	set (const Composite &composite, bool selected_only=false)
Accessors

Atom *&	operator[] (int i)
	Random access operator.
Atom *const &	operator[] (int i) const
void	savePositions ()
void	resetPositions ()
void	moveTo (const Gradient &direction, double step=1.0)
void	moveTo (const Gradient &direction, double step, Size k)
void	resize (Size new_size)
Iteration

iterator	begin ()
const_iterator	begin () const
iterator	end ()
const_iterator	end () const
Protected Attributes
std::vector< Vector3 >	saved_position_

Detailed Description

Atom vector class. This class is used to store atom pointers.

Definition at line 29 of file atomVector.h.

Member Typedef Documentation

typedef std::vector<Atom*>::const_iterator BALL::AtomVector::ConstIterator

Const iterator type.

Definition at line 46 of file atomVector.h.

typedef std::vector<Atom*>::iterator BALL::AtomVector::Iterator

Iterator type

Definition at line 42 of file atomVector.h.

Constructor & Destructor Documentation

BALL::AtomVector::AtomVector ( )

Default constructor.

BALL::AtomVector::AtomVector	(	const Composite &	composite,
		bool	selected_only = `false`
	)

Construct from a Composite. This method constructs an AtomVector from a given composite using selection or not.

Parameters:

	composite	the composite containing the atoms
	selected_only	store the selected atoms only (if true)

BALL::AtomVector::AtomVector	(	const AtomVector &	atoms,
		bool	deep = `true`
	)

Copy constructor

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

Destructor.

Member Function Documentation

const_iterator BALL::AtomVector::begin ( ) const [inline]

Definition at line 170 of file atomVector.h.

iterator BALL::AtomVector::begin ( ) [inline]

Return an iterator, pointing to the first atom pointer.

Definition at line 169 of file atomVector.h.

const_iterator BALL::AtomVector::end ( ) const [inline]

Definition at line 176 of file atomVector.h.

iterator BALL::AtomVector::end ( ) [inline]

Return an iterator, pointing behind the last atom pointer.

Definition at line 175 of file atomVector.h.

void BALL::AtomVector::moveTo	(	const Gradient &	direction,
		double	step,
		Size	k
	)

Move the first k atoms along a direction vector. The method translates all atoms a long a given direction. The direction vector is multiplied with a step length step. If a saved position exists ( savePositions() ), it is used as a start position (i.e. the final positions are ${{start}} + {step} {{direction}}$). Otherwise, the current atom positions are used. If the gradient's size differs from the number of atoms, nothing is done.

void BALL::AtomVector::moveTo	(	const Gradient &	direction,
		double	step = `1.0`
	)

Move all atoms along a direction vector. The method translates all atoms a long a given direction. The direction vector is multiplied with a step length step. If a saved position exists ( savePositions() ), it is used as a start position (i.e. the final positions are ${{start}} + {step} {{direction}}$). Otherwise, the current atom positions are used. If the gradient's size differs from the number of atoms, nothing is done.

const AtomVector& BALL::AtomVector::operator= ( const Composite & rhs )

Assignment operator for Composites. Calls set() and extracts all atoms, if none of the atoms in composite are selected or the selected atoms only (if any atom is selected in composite.

See also:: Selectable

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

Assignment operator

Atom* const& BALL::AtomVector::operator[] ( int i ) const [inline]

Definition at line 116 of file atomVector.h.

Atom* & BALL::AtomVector::operator[] ( int i ) [inline]

Random access operator.

Definition at line 115 of file atomVector.h.

void BALL::AtomVector::resetPositions ( )

Resets the atom positions to the saved positions. If coordinates weres stored using savePositions() , the atoms coordinates are reset to the saved positions. If no savedPositions exist the coordinates remain unchanged.

void BALL::AtomVector::resize ( Size new_size )

Resize the vector. If the vector is resized to to more elements, than are contained, it is filled with NullPointers.

void BALL::AtomVector::savePositions ( )

Store the current atom positions. AtomVector also contains an array with positions for each atom. moveTo() considers these coordinates as start coordinates.

void BALL::AtomVector::set	(	const Composite &	composite,
		bool	selected_only = `false`
	)

Assign from a composite. This method iterates over the composite tree and extracts all atoms.

Parameters:

selected_only

extract only selected atoms if set to true

void BALL::AtomVector::set ( const AtomVector & atoms )

Assign from another atom vector

Member Data Documentation

std::vector<Vector3> BALL::AtomVector::saved_position_ [protected]

Definition at line 184 of file atomVector.h.

BALL::AtomVector Class Reference [General Force Field Classes.]

Public Types