AtomVector Class Reference
[General Force Field Classes.]

Atom vector class. More...

#include <atomVector.h>

List of all members.

Public Types
Type definitions
typedef std::vector< Atom * >::iterator	Iterator
	Iterator type.
typedef std::vector< Atom * >::const_iterator	ConstIterator
	Const iterator type.
Public Member Functions
Constructors and Destructors
	AtomVector ()
	Default constructor.
	AtomVector (const Composite &composite, bool selected_only=false)
	Construct from a Composite.
	AtomVector (const AtomVector &atoms, bool deep=true)
	Copy constructor.
virtual	~AtomVector ()
	Destructor.
Assignments
const AtomVector &	operator= (const AtomVector &rhs)
	Assignment operator.
void	set (const AtomVector &atoms)
	Assign from another atom vector.
const AtomVector &	operator= (const Composite &rhs)
	Assignment operator for Composites.
void	set (const Composite &composite, bool selected_only=false)
	Assign from a composite.
Accessors
Atom *&	operator[] (int i)
	Random access operator.
Atom *const &	operator[] (int i) const
void	savePositions ()
	Store the current atom positions.
void	resetPositions ()
	Resets the atom positions to the saved positions.
void	moveTo (const Gradient &direction, double step=1.0)
	Move all atoms along a direction vector.
void	moveTo (const Gradient &direction, double step, Size k)
	Move the first k atoms along a direction vector.
void	resize (Size new_size)
	Resize the vector.
Iteration
iterator	begin ()
	Return an iterator, pointing to the first atom pointer.
const_iterator	begin () const
iterator	end ()
	Return an iterator, pointing behind the last atom pointer.
const_iterator	end () const
Protected Attributes
std::vector< Vector3 >	saved_position_

---

Detailed Description

Atom vector class.

This class is used to store atom pointers.

---

Member Typedef Documentation

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

Const iterator type.

---

Constructor & Destructor Documentation

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)

---

Member Function Documentation

iterator AtomVector::begin (   )

Return an iterator, pointing to the first atom pointer.

iterator AtomVector::end (   )

Return an iterator, pointing behind the last atom pointer.

void 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 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& 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

void 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 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 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 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