#include <BALL/MOLMEC/MMFF94/MMFF94StretchBend.h>

Inheritance diagram for BALL::MMFF94StretchBend:

Classes
struct	Bend
	see MMFFANG.PAR More...

struct	Stretch

struct	StretchBend

Public Member Functions
	MMFF94StretchBend ()

	MMFF94StretchBend (ForceField &force_field)

	MMFF94StretchBend (const MMFF94StretchBend &to_copy)

virtual	~MMFF94StretchBend ()

virtual bool	setup () throw (Exception::TooManyErrors)

virtual double	updateEnergy ()
	Calculates and returns the component's energy. More...

virtual double	updateBendEnergy ()

virtual double	updateStretchEnergy ()

virtual double	updateStretchBendEnergy ()

double	getStretchEnergy () const

double	getBendEnergy () const

double	getStretchBendEnergy () const

virtual void	updateForces ()
	Calculates and returns the component's forces. More...

virtual void	updateBendForces ()

virtual void	updateStretchForces ()

virtual void	updateStretchBendForces ()

const vector< Bend > &	getBends () const

const vector< Stretch > &	getStretches () const

const vector< StretchBend > &	getStretchBends () const

Index	calculateSBTIJK (Position angle_type, bool bond_type1, bool bond_type2)

Position	getBendType (const Bond &bond1, const Bond &bond2, Atom &atom1, Atom &atom2, Atom &atom3) const

double	calculateBendEmpiricalReferenceAngle (Atom &atom1, Atom &atom2, Atom &atom3) const
	Bend emperical reference angle. More...

double	calculateBendEmpiricalForceConstant (Atom &atom1, Atom &atom2, Atom &atom3, double angle_0) const
	Bend emperical force constant. More...

double	calculateStretchR0 (const Bond &bond)
	Calculate the radius value per Schomaker-Stevenson Rule. More...

double	calculateStretchConstant (const Bond &bond, double r0)

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

	ForceFieldComponent (ForceField &force_field)

	ForceFieldComponent (const ForceFieldComponent &force_field_component)

virtual	~ForceFieldComponent ()

ForceField *	getForceField () const

void	setForceField (ForceField &force_field)

void	setName (const String &name)

String	getName () const

bool	isEnabled () const

void	setEnabled (bool state)

virtual double	getEnergy () const

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

Private Member Functions
void	AddDV3_ (Vector3 &f3, const TVector3< double > d3)

void	calculateDeltas_ ()

bool	setupBends_ ()

bool	setupStretches_ ()

bool	setupStretchBends_ ()

void	errorOccured_ (const String &string, const Atom &a1, const Atom &a2, const Atom &a3)

Private Attributes
vector< Bend >	bends_

vector< Stretch >	stretches_

vector< StretchBend >	stretch_bends_

const MMFF94StretchParameters *	stretch_parameters_

MMFF94BendParameters	bend_parameters_

MMFF94StretchBendParameters	sb_parameters_

double	stretch_energy_

double	bend_energy_

double	stretch_bend_energy_

MMFF94 *	mmff94_

bool	stretch_enabled_

bool	bend_enabled_

bool	stretchbend_enabled_

Static Private Attributes
static double	bend_z_ []

static double	bend_c_ []

static String	bend_elements_ []

Additional Inherited Members
Protected Attributes inherited from BALL::ForceFieldComponent
ForceField *	force_field_

double	energy_

Detailed Description

MMFF94 bond stretch component

Definition at line 25 of file MMFF94StretchBend.h.

Constructor & Destructor Documentation

BALL::MMFF94StretchBend::MMFF94StretchBend ( )

Default constructor.

BALL::MMFF94StretchBend::MMFF94StretchBend ( ForceField & force_field )

Constructor.

BALL::MMFF94StretchBend::MMFF94StretchBend ( const MMFF94StretchBend & to_copy )

Copy constructor

virtual BALL::MMFF94StretchBend::~MMFF94StretchBend ( )

virtual

Destructor.

Member Function Documentation

void BALL::MMFF94StretchBend::AddDV3_	(	Vector3 &	f3,
		const TVector3< double >	d3
	)

inlineprivate

double BALL::MMFF94StretchBend::calculateBendEmpiricalForceConstant	(	Atom &	atom1,
		Atom &	atom2,
		Atom &	atom3,
		double	angle_0
	)		const

Bend emperical force constant.

double BALL::MMFF94StretchBend::calculateBendEmpiricalReferenceAngle	(	Atom &	atom1,
		Atom &	atom2,
		Atom &	atom3
	)		const

Bend emperical reference angle.

void BALL::MMFF94StretchBend::calculateDeltas_ ( )

private

Index BALL::MMFF94StretchBend::calculateSBTIJK	(	Position	angle_type,
		bool	bond_type1,
		bool	bond_type2
	)

double BALL::MMFF94StretchBend::calculateStretchConstant	(	const Bond &	bond,
		double	r0
	)

double BALL::MMFF94StretchBend::calculateStretchR0 ( const Bond & bond )

Calculate the radius value per Schomaker-Stevenson Rule.

void BALL::MMFF94StretchBend::errorOccured_	(	const String &	string,
		const Atom &	a1,
		const Atom &	a2,
		const Atom &	a3
	)

private

double BALL::MMFF94StretchBend::getBendEnergy ( ) const

const vector<Bend>& BALL::MMFF94StretchBend::getBends ( ) const

inline

Definition at line 138 of file MMFF94StretchBend.h.

Position BALL::MMFF94StretchBend::getBendType	(	const Bond &	bond1,
		const Bond &	bond2,
		Atom &	atom1,
		Atom &	atom2,
		Atom &	atom3
	)		const

double BALL::MMFF94StretchBend::getStretchBendEnergy ( ) const

const vector<StretchBend>& BALL::MMFF94StretchBend::getStretchBends ( ) const

inline

Definition at line 144 of file MMFF94StretchBend.h.

double BALL::MMFF94StretchBend::getStretchEnergy ( ) const

const vector<Stretch>& BALL::MMFF94StretchBend::getStretches ( ) const

inline

Definition at line 141 of file MMFF94StretchBend.h.

virtual bool BALL::MMFF94StretchBend::setup ( ) throw (Exception::TooManyErrors)

virtual

Setup method.

Reimplemented from BALL::ForceFieldComponent.

bool BALL::MMFF94StretchBend::setupBends_ ( )

private

bool BALL::MMFF94StretchBend::setupStretchBends_ ( )

private

bool BALL::MMFF94StretchBend::setupStretches_ ( )

private

virtual double BALL::MMFF94StretchBend::updateBendEnergy ( )

virtual

virtual void BALL::MMFF94StretchBend::updateBendForces ( )

virtual

virtual double BALL::MMFF94StretchBend::updateEnergy ( )

virtual

Calculates and returns the component's energy.

Reimplemented from BALL::ForceFieldComponent.

virtual void BALL::MMFF94StretchBend::updateForces ( )

virtual

Calculates and returns the component's forces.

Reimplemented from BALL::ForceFieldComponent.

virtual double BALL::MMFF94StretchBend::updateStretchBendEnergy ( )

virtual

virtual void BALL::MMFF94StretchBend::updateStretchBendForces ( )

virtual

virtual double BALL::MMFF94StretchBend::updateStretchEnergy ( )

virtual

virtual void BALL::MMFF94StretchBend::updateStretchForces ( )

virtual

Member Data Documentation

double BALL::MMFF94StretchBend::bend_c_[]

staticprivate

Definition at line 187 of file MMFF94StretchBend.h.

String BALL::MMFF94StretchBend::bend_elements_[]

staticprivate

Definition at line 188 of file MMFF94StretchBend.h.

bool BALL::MMFF94StretchBend::bend_enabled_

private

Definition at line 195 of file MMFF94StretchBend.h.

double BALL::MMFF94StretchBend::bend_energy_

private

Definition at line 191 of file MMFF94StretchBend.h.

MMFF94BendParameters BALL::MMFF94StretchBend::bend_parameters_

private

Definition at line 183 of file MMFF94StretchBend.h.

double BALL::MMFF94StretchBend::bend_z_[]

staticprivate

Definition at line 186 of file MMFF94StretchBend.h.

vector<Bend> BALL::MMFF94StretchBend::bends_

private

Definition at line 178 of file MMFF94StretchBend.h.

MMFF94* BALL::MMFF94StretchBend::mmff94_

private

Definition at line 194 of file MMFF94StretchBend.h.

MMFF94StretchBendParameters BALL::MMFF94StretchBend::sb_parameters_

private

Definition at line 184 of file MMFF94StretchBend.h.

double BALL::MMFF94StretchBend::stretch_bend_energy_

private

Definition at line 192 of file MMFF94StretchBend.h.

vector<StretchBend> BALL::MMFF94StretchBend::stretch_bends_

private

Definition at line 180 of file MMFF94StretchBend.h.

bool BALL::MMFF94StretchBend::stretch_enabled_

private

Definition at line 195 of file MMFF94StretchBend.h.

double BALL::MMFF94StretchBend::stretch_energy_

private

Definition at line 190 of file MMFF94StretchBend.h.

const MMFF94StretchParameters* BALL::MMFF94StretchBend::stretch_parameters_

private

Definition at line 182 of file MMFF94StretchBend.h.

bool BALL::MMFF94StretchBend::stretchbend_enabled_

private

Definition at line 195 of file MMFF94StretchBend.h.

vector<Stretch> BALL::MMFF94StretchBend::stretches_

private

Definition at line 179 of file MMFF94StretchBend.h.

Classes

Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation