BALL::ReferenceArea Class Reference

#include <BALL/DOCKING/COMMON/constraints.h>

Inheritance diagram for BALL::ReferenceArea:

Public Member Functions
	ReferenceArea ()
	~ReferenceArea ()
	ReferenceArea (Vector3 &p1, Vector3 &p2, Vector3 &p3, Vector3 &p4, bool atom_fraction, double atoms, double penalty)
	ReferenceArea (Vector3 &p1, Vector3 &p2, int y_expansion, int z_expansion, bool atom_fraction, double atoms, double penalty)
	ReferenceArea (const AtomContainer *sys, bool atom_fraction, double atoms, double penalty)
	ReferenceArea (list< const AtomContainer * > &container_list, const list< String > &interaction_types, double desired_interaction_score, double penalt)
double	calculateScore (AtomContainer *mol)
double	getContainedAtoms ()
System *	createBoundaryMolecule ()
void	enlarge (double angstroem)
void	setNumberDesiredAtoms (double d)
void	setName (String name)
void	setScoringFunction (ScoringFunction *sf)
Public Member Functions inherited from BALL::Constraint
	Constraint ()
virtual	~Constraint ()
String	getName ()
String	getType ()

Friends
class	BALL::DockingAlgorithm
class	BALL::VIEW::DockRLDialog

Additional Inherited Members
Protected Attributes inherited from BALL::Constraint
String	name_
String	type_
double	penalty_
ScoringFunction *	scoring_function_

Detailed Description

ReferenceAreas are cuboids specified by the user for the examined target structure. A given number of ligand atoms or a given fraction of the ligand atoms should be located within these areas, so that docking is optimized in this way.

Definition at line 71 of file constraints.h.

Constructor & Destructor Documentation

BALL::ReferenceArea::ReferenceArea

(

)

BALL::ReferenceArea::~ReferenceArea

(

)

BALL::ReferenceArea::ReferenceArea	(	Vector3 &	p1,
		Vector3 &	p2,
		Vector3 &	p3,
		Vector3 &	p4,
		bool	atom_fraction,
		double	atoms,
		double	penalty
	)

Constructor. Creates a ReferenceArea from 4 given points, that describe a cuboid.
Of those four given points, p1 should be located on the same edge as p2, p3 on the same egde as p2 and p4 on the same edge as p3.

BALL::ReferenceArea::ReferenceArea	(	Vector3 &	p1,
		Vector3 &	p2,
		int	y_expansion,
		int	z_expansion,
		bool	atom_fraction,
		double	atoms,
		double	penalty
	)

Constructor. Creates a ReferenceArea from 2 points that describe one side of the cuboid and the the desired expansion of the cubiod along the x- and y-axes of a right handed coordinate system (after transformation)

BALL::ReferenceArea::ReferenceArea	(	const AtomContainer *	sys,
		bool	atom_fraction,
		double	atoms,
		double	penalty
	)

Constructor that creates a ReferenceArea describing the area occupied by a given AtomContainer

BALL::ReferenceArea::ReferenceArea	(	list< const AtomContainer * > &	container_list,
		const list< String > &	interaction_types,
		double	desired_interaction_score,
		double	penalt
	)

Member Function Documentation

double BALL::ReferenceArea::calculateScore ( AtomContainer *  mol )

virtual

calculates a penalty for the given AtomContainer

Implements BALL::Constraint.

System* BALL::ReferenceArea::createBoundaryMolecule

(

)

Creates a molecule with four atoms located on the bonders of the cube that this ReferenceArea describes.
This can be used for visualization purposes.

Returns

the created System if this ReferenceArea contains a valid ref-area description; else NULL is returned.

void BALL::ReferenceArea::enlarge

(

double

angstroem

)

Enlarge this ReferenceArea by the given amount in all directions

double BALL::ReferenceArea::getContainedAtoms

(

)

returns the number of atoms located within this ReferenceAreas as calculated by the last call of getScore() (respectively ScoringFunction::updateScore() )

void BALL::ReferenceArea::setName ( String  name )

virtual

Set a name for this ReferenceArea. This way, the score summary printed by the ScoringFunction can be analyzed more easily

Reimplemented from BALL::Constraint.

void BALL::ReferenceArea::setNumberDesiredAtoms

(

double

d

)

Sets the number resp. fraction of atoms of a ligand that should be contained in this ReferenceArea

void BALL::ReferenceArea::setScoringFunction ( ScoringFunction *  sf )

virtual

Reimplemented from BALL::Constraint.

Friends And Related Function Documentation

friend class BALL::DockingAlgorithm

friend

Definition at line 137 of file constraints.h.

friend class BALL::VIEW::DockRLDialog

friend

Definition at line 138 of file constraints.h.