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

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

Classes
struct	Default
	Default values. More...
struct	Option
Public Types
Type definitions

typedef std::pair< Size, Size >	AtomIndexPair
typedef std::vector < AtomIndexPair >	AtomIndexArray
Public Member Functions
Constructors and Destructors

	PeriodicBoundary ()
	PeriodicBoundary (const ForceField &force_field)
	PeriodicBoundary (const PeriodicBoundary &periodic_boundary)
virtual	~PeriodicBoundary ()
Assignment

PeriodicBoundary &	operator= (const PeriodicBoundary &periodic_boundary)
virtual void	clear ()
Setup Methods

bool	setup ()
Size	generateMoleculesVector ()
Accessors

void	enable ()
	Enable periodic boundary conditions.
void	disable ()
	Disable periodic boundary conditions.
SimpleBox3	getBox () const
void	setBox (const SimpleBox3 &box)
Size	addSolvent (const String &filename)
Size	removeSolvent ()
Predicates

bool	isEnabled () const
Periodic boundary methods

void	updateMolecules ()
Public Attributes
Variables

Options *	options
Private Attributes
ForceField *	force_field_
bool	enabled_
SimpleBox3	box_
AtomIndexArray	molecules_

Detailed Description

Periodic boundary class for force field simulations. Molecular Mechanics: class representing periodic boundary conditions.

Definition at line 34 of file periodicBoundary.h.

Member Typedef Documentation

typedef std::vector<AtomIndexPair> BALL::PeriodicBoundary::AtomIndexArray

Definition at line 48 of file periodicBoundary.h.

typedef std::pair<Size, Size> BALL::PeriodicBoundary::AtomIndexPair

Definition at line 45 of file periodicBoundary.h.

Constructor & Destructor Documentation

BALL::PeriodicBoundary::PeriodicBoundary ( )

Default constructor.

BALL::PeriodicBoundary::PeriodicBoundary ( const ForceField & force_field )

Constructor.

BALL::PeriodicBoundary::PeriodicBoundary ( const PeriodicBoundary & periodic_boundary )

Copy constructor

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

Destructor.

Member Function Documentation

Size BALL::PeriodicBoundary::addSolvent ( const String & filename )

Fill the defined box with a solvent. This method fills the defined box with solvent molecules. If no box is defined, no solvent is added. The neccessary solvent box template is either taken from the options (solvent_file) or a default is assumed.

: This method replicates the solvent box starting at the box origin in all three dimensions and removes all solvent molecules that are within solvent_distance of a solute molecule or outside the periodic box.

: To ensure periodicity, our SimpleBox instance might be resized to an integral multiple of the spacing of the periodic solvent box. The method returns the number of inserted solvent molecules. All solvent molecules are marked as such by setting their property Molecule::PROPERTY__PERIODIC_BOX_SOLVENT .

See also:: removeSolvent

virtual void BALL::PeriodicBoundary::clear ( ) [virtual]

Clear method

void BALL::PeriodicBoundary::disable ( )

Disable periodic boundary conditions.

void BALL::PeriodicBoundary::enable ( )

Enable periodic boundary conditions.

Size BALL::PeriodicBoundary::generateMoleculesVector ( )

Generate the vector of molecules of the system

SimpleBox3 BALL::PeriodicBoundary::getBox ( ) const

Retrieve the box dimensions.

bool BALL::PeriodicBoundary::isEnabled ( ) const

Returns true if the periodic boundary is enabled

See also:: enable; disable

PeriodicBoundary& BALL::PeriodicBoundary::operator= ( const PeriodicBoundary & periodic_boundary )

Assignment operator.

Size BALL::PeriodicBoundary::removeSolvent ( )

Removes all solvent molecules This method removes all molecules that have the property Molecule::PROPERTY__PERIODIC_BOX_SOLVENT set from the force field's system. The number of removed solvent molecules is returned.