#include <BALL/MOLMEC/MMFF94/MMFF94.h>

Inheritance diagram for BALL::MMFF94:

Classes
struct	Default

struct	Option

Public Member Functions
Constructors and Destructor
	MMFF94 ()

	MMFF94 (System &system)

	MMFF94 (System &system, const Options &options)

	MMFF94 (const MMFF94 &force_field)

virtual	~MMFF94 ()

Assignment
const MMFF94 &	operator= (const MMFF94 &force_field)

virtual void	clear ()

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

Accessors specific to the MMFF94 force field
double	getStretchEnergy () const

double	getBendEnergy () const

double	getStretchBendEnergy () const

double	getTorsionEnergy () const

double	getNonbondedEnergy () const

double	getESEnergy () const

double	getVdWEnergy () const

double	getPlaneEnergy () const

bool	hasInitializedParameters () const

Size	getUpdateFrequency () const

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

const vector< Bond * >	getBonds () const

const vector< HashSet< Atom * > > &	getRings () const

const vector< HashSet< Atom * > > &	getAromaticRings () const

bool	isInOneAromaticRing (const Bond &bond) const

bool	assignMMFF94BondType (Bond &bond) const

const vector< MMFF94AtomType > &	getAtomTypes () const

const MMFF94StretchParameters &	getStretchParameters () const

const MMFF94AtomTypeEquivalences &	getEquivalences () const

bool	areInOneRing (vector< Atom * > v, Size ring_size=0) const

bool	areInOneAromaticRing (const vector< Atom * > &v, Size ring_size=0) const

bool	checkAtomType (Atom &atom)

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 Member Functions
void	insertComponents_ ()

void	transformAromaticBonds_ ()

void	collectBonds_ ()

void	assignBondTypes_ ()

void	collectRings_ ()

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

void	sortSelectedAtomVector_ ()

virtual void	performRequiredUpdates_ ()

Protected Attributes
String	folder_

MMFF94AtomTypes	atom_types_

MMFF94StretchParameters	bond_parameters_

MMFF94AtomTypeEquivalences	equivalences_

MMFF94ESParameters	es_parameters_

vector< HashSet< Atom * > >	rings_

vector< HashSet< Atom * > >	aromatic_rings_

bool	parameters_initialized_

vector< Bond * >	bonds_

MMFF94AtomTyper	atom_typer_

MMFF94ChargeProcessor	charge_processor_

Kekuliser	kekuliser_

HashSet< Bond * >	aromatic_bonds_

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

Detailed Description

MMFF94 force field class.

Definition at line 49 of file MMFF94.h.

Constructor & Destructor Documentation

BALL::MMFF94::MMFF94 ( )

Default constructor.

BALL::MMFF94::MMFF94 ( System & system )

Constructor.

BALL::MMFF94::MMFF94	(	System &	system,
		const Options &	options
	)

Constructor.

BALL::MMFF94::MMFF94 ( const MMFF94 & force_field )

Copy constructor

virtual BALL::MMFF94::~MMFF94 ( )

virtual

Destructor.

Member Function Documentation

bool BALL::MMFF94::areInOneAromaticRing	(	const vector< Atom * > &	v,
		Size	ring_size = `0`
	)		const

bool BALL::MMFF94::areInOneRing	(	vector< Atom * >	v,
		Size	ring_size = `0`
	)		const

void BALL::MMFF94::assignBondTypes_ ( )

protected

bool BALL::MMFF94::assignMMFF94BondType ( Bond & bond ) const

bool BALL::MMFF94::checkAtomType ( Atom & atom )

Check wheter the atoms type is valid. If not, add it to unassigned atoms.

virtual void BALL::MMFF94::clear ( )

virtual

Clear method

Reimplemented from BALL::ForceField.

void BALL::MMFF94::collectBonds_ ( )

protected

void BALL::MMFF94::collectRings_ ( )

protected

const vector<HashSet<Atom*> >& BALL::MMFF94::getAromaticRings ( ) const

inline

Definition at line 275 of file MMFF94.h.

const vector<MMFF94AtomType>& BALL::MMFF94::getAtomTypes ( ) const

inline

Definition at line 284 of file MMFF94.h.

double BALL::MMFF94::getBendEnergy ( ) const

Return the angle bend contribution to the total energy

const vector<Bond*> BALL::MMFF94::getBonds ( ) const

inline

Definition at line 269 of file MMFF94.h.

const MMFF94AtomTypeEquivalences& BALL::MMFF94::getEquivalences ( ) const

inline

Definition at line 290 of file MMFF94.h.

double BALL::MMFF94::getESEnergy ( ) const

Return the electrostatic contribution to the total energy.

double BALL::MMFF94::getNonbondedEnergy ( ) const

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

double BALL::MMFF94::getPlaneEnergy ( ) const

virtual String BALL::MMFF94::getResults ( ) const

virtual

Get the current results in String form.

Reimplemented from BALL::ForceField.

const vector<HashSet<Atom*> >& BALL::MMFF94::getRings ( ) const

inline

Definition at line 272 of file MMFF94.h.

double BALL::MMFF94::getStretchBendEnergy ( ) const

double BALL::MMFF94::getStretchEnergy ( ) const

Return the bond stretch contribution to the total energy

const MMFF94StretchParameters& BALL::MMFF94::getStretchParameters ( ) const

inline

Definition at line 287 of file MMFF94.h.

double BALL::MMFF94::getTorsionEnergy ( ) const

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

Size BALL::MMFF94::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::MMFF94::getVdWEnergy ( ) const

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

bool BALL::MMFF94::hasInitializedParameters ( ) const

Return true, if the parameters have already been initialized

void BALL::MMFF94::insertComponents_ ( )

protected

bool BALL::MMFF94::isInOneAromaticRing ( const Bond & bond ) const

const MMFF94& BALL::MMFF94::operator= ( const MMFF94 & force_field )

Assignment operator

virtual bool BALL::MMFF94::specificSetup ( ) throw (Exception::TooManyErrors)

virtual

Force field specific setup

Reimplemented from BALL::ForceField.

void BALL::MMFF94::transformAromaticBonds_ ( )

protected

Member Data Documentation

HashSet<Bond*> BALL::MMFF94::aromatic_bonds_

protected

Definition at line 326 of file MMFF94.h.

vector<HashSet<Atom*> > BALL::MMFF94::aromatic_rings_

protected

Definition at line 320 of file MMFF94.h.

MMFF94AtomTyper BALL::MMFF94::atom_typer_

protected

Definition at line 323 of file MMFF94.h.

MMFF94AtomTypes BALL::MMFF94::atom_types_

protected

Definition at line 315 of file MMFF94.h.

MMFF94StretchParameters BALL::MMFF94::bond_parameters_

protected

Definition at line 316 of file MMFF94.h.

vector<Bond*> BALL::MMFF94::bonds_

protected

Definition at line 322 of file MMFF94.h.

MMFF94ChargeProcessor BALL::MMFF94::charge_processor_

protected

Definition at line 324 of file MMFF94.h.

MMFF94AtomTypeEquivalences BALL::MMFF94::equivalences_

protected

Definition at line 317 of file MMFF94.h.

MMFF94ESParameters BALL::MMFF94::es_parameters_

protected

Definition at line 318 of file MMFF94.h.

String BALL::MMFF94::folder_

protected

Definition at line 314 of file MMFF94.h.

Kekuliser BALL::MMFF94::kekuliser_

protected

Definition at line 325 of file MMFF94.h.

bool BALL::MMFF94::parameters_initialized_

protected

Definition at line 321 of file MMFF94.h.

vector<HashSet<Atom*> > BALL::MMFF94::rings_

protected

Definition at line 319 of file MMFF94.h.

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation