BALL::MMFF94StretchBend Class Reference

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

Inheritance diagram for BALL::MMFF94StretchBend:

Classes
struct	StretchBend
struct	Bend
	see MMFFANG.PAR More...
struct	Stretch

Public Member Functions
	MMFF94StretchBend ()
	MMFF94StretchBend (ForceField &force_field)
	MMFF94StretchBend (const MMFF94StretchBend &to_copy)
virtual	~MMFF94StretchBend ()
virtual bool	setup ()
virtual double	updateEnergy ()
	Calculates and returns the component's energy.
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.
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.
double	calculateBendEmpiricalForceConstant (Atom &atom1, Atom &atom2, Atom &atom3, double angle_0) const
	Bend emperical force constant.
double	calculateStretchR0 (const Bond &bond)
	Calculate the radius value per Schomaker-Stevenson Rule.
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 ()
double	updateScore ()
Public Member Functions inherited from BALL::ScoringComponent
	ScoringComponent ()
	ScoringComponent (const ScoringComponent &sc)
	ScoringComponent (ScoringFunction &sf)
void	selectBaseFunction (String function)
virtual	~ScoringComponent ()
virtual void	clear ()
virtual void	setupLigand ()
ScoringFunction *	getScoringFunction () const
void	setScoringFunction (ScoringFunction &sf)
String	getName () const
void	setName (const String &name)
const String &	getTypeName ()
double	getRawScore () const
double	getScaledScore () const
virtual void	update (const vector< std::pair< Atom *, Atom * > > &pair_vector)
virtual void	setLigandIntraMolecular (bool b)
bool	isLigandIntraMolecular ()
bool	isGridable ()
bool	isAtomPairwise ()
void	setCoefficient (const double &coeff)
const double &	getCoefficient ()
void	setNormalizationParameters (double stddev, double mean)
void	getNormalizationParameters (double &stddev, double &mean)
bool	isEnabled ()
void	enable ()
void	disable ()

Additional Inherited Members
Protected Member Functions inherited from BALL::ScoringComponent
double	scaleScore (double score) const
ForceField *	force_field_
double	energy_
Protected Attributes inherited from BALL::ScoringComponent
bool	ligand_intra_molecular_
bool	gridable_
bool	atom_pairwise_
ScoringFunction *	scoring_function_
ScoringBaseFunction *	base_function_
double	score_
double	coefficient_
double	stddev_
double	mean_
bool	enabled_
String	type_name_

Detailed Description

MMFF94 bond stretch component

Definition at line 25 of file MMFF94StretchBend.h.

Constructor & Destructor Documentation

MMFF94StretchBend() [1/3]

BALL::MMFF94StretchBend::MMFF94StretchBend

(

)

Default constructor.

MMFF94StretchBend() [2/3]

BALL::MMFF94StretchBend::MMFF94StretchBend

(

ForceField &

force_field

)

Constructor.

MMFF94StretchBend() [3/3]

BALL::MMFF94StretchBend::MMFF94StretchBend

(

const MMFF94StretchBend &

to_copy

)

Copy constructor

~MMFF94StretchBend()

virtual BALL::MMFF94StretchBend::~MMFF94StretchBend ( )

virtual

Destructor.

Member Function Documentation

calculateBendEmpiricalForceConstant()

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

Bend emperical force constant.

calculateBendEmpiricalReferenceAngle()

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

Bend emperical reference angle.

calculateSBTIJK()

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

calculateStretchConstant()

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

calculateStretchR0()

double BALL::MMFF94StretchBend::calculateStretchR0

(

const Bond &

bond

)

Calculate the radius value per Schomaker-Stevenson Rule.

getBendEnergy()

double BALL::MMFF94StretchBend::getBendEnergy

(

)

const

getBends()

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

inline

Definition at line 149 of file MMFF94StretchBend.h.

getBendType()

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

getStretchBendEnergy()

double BALL::MMFF94StretchBend::getStretchBendEnergy

(

)

const

getStretchBends()

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

inline

Definition at line 155 of file MMFF94StretchBend.h.

getStretchEnergy()

double BALL::MMFF94StretchBend::getStretchEnergy

(

)

const

getStretches()

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

inline

Definition at line 152 of file MMFF94StretchBend.h.

setup()

virtual bool BALL::MMFF94StretchBend::setup ( )

virtual

Setup method.

Exceptions

BALL::Exception::TooManyErrors

Reimplemented from BALL::ForceFieldComponent.

updateBendEnergy()

virtual double BALL::MMFF94StretchBend::updateBendEnergy ( )

virtual

updateBendForces()

virtual void BALL::MMFF94StretchBend::updateBendForces ( )

virtual

updateEnergy()

virtual double BALL::MMFF94StretchBend::updateEnergy ( )

virtual

Calculates and returns the component's energy.

Reimplemented from BALL::ForceFieldComponent.

updateForces()

virtual void BALL::MMFF94StretchBend::updateForces ( )

virtual

Calculates and returns the component's forces.

Reimplemented from BALL::ForceFieldComponent.

updateStretchBendEnergy()

virtual double BALL::MMFF94StretchBend::updateStretchBendEnergy ( )

virtual

updateStretchBendForces()

virtual void BALL::MMFF94StretchBend::updateStretchBendForces ( )

virtual

updateStretchEnergy()

virtual double BALL::MMFF94StretchBend::updateStretchEnergy ( )

virtual

updateStretchForces()

virtual void BALL::MMFF94StretchBend::updateStretchForces ( )

virtual