#include <BALL/MOLMEC/AMBER/amber.h>

Inheritance diagram for BALL::AmberFF:

Classes
struct	Default

struct	Option

Public Member Functions
Constructors and Destructor
	AmberFF ()

	AmberFF (System &system)

	AmberFF (System &system, const Options &options)

	AmberFF (const AmberFF &force_field)

virtual	~AmberFF ()

Assignment
const AmberFF &	operator= (const AmberFF &force_field)

virtual void	clear ()

Setup Methods
virtual bool	specificSetup () throw (Exception::TooManyErrors)

Accessors specific to the AMBER force field
double	getStretchEnergy () const

double	getBendEnergy () const

double	getTorsionEnergy () const

double	getNonbondedEnergy () const

double	getESEnergy () const

double	getVdWEnergy () const

bool	hasInitializedParameters () const

Size	getUpdateFrequency () const

virtual String	getResults () const
	Get the current results in String form. More...

Public Member Functions inherited from BALL::ForceField
	ForceField ()

	ForceField (System &system)

	ForceField (System &system, const Options &options)

	ForceField (const ForceField &force_field)

virtual	~ForceField ()

ForceField &	operator= (const ForceField &force_field)

bool	isValid () const

bool	setup (System &system)

bool	setup (System &system, const Options &options)

void	setMaximumNumberOfErrors (Size nr)

Size	getMaximumNumberOfErrors () const

HashSet< const Atom * > &	getUnassignedAtoms ()
	Get the atoms, for which the force field setup failed. More...

void	setName (const String &name)

String	getName () const

Size	getNumberOfAtoms () const

Size	getNumberOfMovableAtoms () const

BALL_INLINE const AtomVector &	getAtoms () const

BALL_INLINE System *	getSystem ()

BALL_INLINE const System *	getSystem () const

BALL_INLINE bool	getUseSelection () const

BALL_INLINE void	disableSelection ()

BALL_INLINE void	enableSelection ()

BALL_INLINE bool	isSelectionEnabled () const

ForceFieldParameters &	getParameters ()

Size	countComponents () const

const TimeStamp &	getUpdateTime () const

const TimeStamp &	getSetupTime () const

void	insertComponent (ForceFieldComponent *force_field_component)

void	removeComponent (const ForceFieldComponent *force_field_component)

void	removeComponent (const String &name)

ForceFieldComponent *	getComponent (const Size index) const

ForceFieldComponent *	getComponent (const String &name) const

double	getEnergy () const

double	updateEnergy ()

void	updateForces ()

double	getRMSGradient () const

virtual void	update () throw (Exception::TooManyErrors)

std::ostream &	error () throw (Exception::TooManyErrors)

Protected Attributes
String	filename_

bool	parameters_initialized_

Protected Attributes inherited from BALL::ForceField
System *	system_

AtomVector	atoms_

ForceFieldParameters	parameters_

bool	valid_

String	name_

double	energy_

vector< ForceFieldComponent * >	components_

Size	number_of_movable_atoms_

bool	use_selection_

bool	selection_enabled_

TimeStamp	update_time_stamp_

TimeStamp	setup_time_stamp_

HashSet< const Atom * >	unassigned_atoms_

Size	max_number_of_errors_

Size	number_of_errors_

Additional Inherited Members
Public Types inherited from BALL::ForceField
typedef std::vector< std::pair < Atom , Atom > >	PairVector

Public Attributes inherited from BALL::ForceField
Options	options

PeriodicBoundary	periodic_boundary

Protected Member Functions inherited from BALL::ForceField
void	collectAtoms_ (const System &system)

void	sortSelectedAtomVector_ ()

virtual void	performRequiredUpdates_ ()

Detailed Description

AMBER force field class.

Definition at line 31 of file amber.h.

Constructor & Destructor Documentation

BALL::AmberFF::AmberFF ( )

Default constructor.

BALL::AmberFF::AmberFF ( System & system )

Constructor.

BALL::AmberFF::AmberFF	(	System &	system,
		const Options &	options
	)

Constructor.

BALL::AmberFF::AmberFF ( const AmberFF & force_field )

Copy constructor

virtual BALL::AmberFF::~AmberFF ( )

virtual

Destructor.

Member Function Documentation

virtual void BALL::AmberFF::clear ( )

virtual

Clear method

Reimplemented from BALL::ForceField.

double BALL::AmberFF::getBendEnergy ( ) const

Return the angle bend contribution to the total energy

double BALL::AmberFF::getESEnergy ( ) const

Return the electrostatic contribution to the total energy.

double BALL::AmberFF::getNonbondedEnergy ( ) const

Return the nonbonded contribution to the total energy. This energy comprises Van der Waals energy, hydrogen bond energy, and elesctrostatic energy.

virtual String BALL::AmberFF::getResults ( ) const

virtual

Get the current results in String form.

Reimplemented from BALL::ForceField.

double BALL::AmberFF::getStretchEnergy ( ) const

Return the bond stretch contribution to the total energy

double BALL::AmberFF::getTorsionEnergy ( ) const

Return the torsion contribution to the total energy. This energy comprises proper and improper torsions.

Size BALL::AmberFF::getUpdateFrequency ( ) const

virtual

Return the recommended number of iterations between updates. This method return 20 as a default value.

Reimplemented from BALL::ForceField.

double BALL::AmberFF::getVdWEnergy ( ) const

Return the Van der Waals and hydrogen bond contribution to the total energy.

bool BALL::AmberFF::hasInitializedParameters ( ) const

Return true, if the parameters have already been initialized

const AmberFF& BALL::AmberFF::operator= ( const AmberFF & force_field )

Assignment operator

virtual bool BALL::AmberFF::specificSetup ( ) throw (Exception::TooManyErrors)

virtual

Force field specific setup

Reimplemented from BALL::ForceField.

Member Data Documentation

String BALL::AmberFF::filename_

protected

Definition at line 267 of file amber.h.

bool BALL::AmberFF::parameters_initialized_

protected

Definition at line 269 of file amber.h.

Classes

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation