BALL::AmberFF Class Reference

#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.
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.
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.