BALL  1.4.1
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Classes | Protected Attributes | List of all members
BALL::AmberFF Class Reference

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

Inheritance diagram for BALL::AmberFF:
BALL::ForceField

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 AmberFFoperator= (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 ()
ForceFieldoperator= (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 AtomVectorgetAtoms () const
BALL_INLINE SystemgetSystem ()
BALL_INLINE const SystemgetSystem () const
BALL_INLINE bool getUseSelection () const
BALL_INLINE void disableSelection ()
BALL_INLINE void enableSelection ()
BALL_INLINE bool isSelectionEnabled () const
ForceFieldParametersgetParameters ()
Size countComponents () const
const TimeStampgetUpdateTime () const
const TimeStampgetSetupTime () const
void insertComponent (ForceFieldComponent *force_field_component)
void removeComponent (const ForceFieldComponent *force_field_component)
void removeComponent (const String &name)
ForceFieldComponentgetComponent (const Size index) const
ForceFieldComponentgetComponent (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
Systemsystem_
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.