BALL::DockProblem Class Reference

#include <BALL/DOCKING/GENETICDOCK/dockProblem.h>

Public Member Functions
	DockProblem ()
	DockProblem (AtomContainer &sys_lig, BALL::ScoringFunction *sf, EvolutionaryDocking *docker, bool post_dock_optimization)
virtual	~DockProblem ()
virtual void	setup (AtomContainer &sys_lig)
virtual double	calculate ()
void	move ()
bool	redraw ()
AtomContainer *	getLigand ()
void	connectTo (GeneticAlgorithm *opt)

Protected Member Functions
void	restore ()

Protected Attributes
EvolutionaryDocking *	docker_
DoubleParameter	double_parameter_
QuaternionParameter	quaternion_parameter_
AtomContainer *	ligand_
AtomContainer *	draw_ligand_
Vector3	t_origin_
Vector3	t_extension_
Vector3	binding_pocket_center_
BALL::ScoringFunction *	scoring_function_
std::vector< Vector3 >	ligand_positions_
RotateBonds *	rb_
Options	opt_
bool	redraw_
bool	post_dock_optimization_

Detailed Description

Definition at line 35 of file dockProblem.h.

Constructor & Destructor Documentation

BALL::DockProblem::DockProblem

(

)

constructor

BALL::DockProblem::DockProblem	(	AtomContainer &	sys_lig,
		BALL::ScoringFunction *	sf,
		EvolutionaryDocking *	docker,
		bool	post_dock_optimization
	)

constructor

virtual BALL::DockProblem::~DockProblem ( )

virtual

destructor

Member Function Documentation

virtual double BALL::DockProblem::calculate ( )

virtual

calculate fitness score for one individual

void BALL::DockProblem::connectTo

(

GeneticAlgorithm *

opt

)

AtomContainer* BALL::DockProblem::getLigand

(

)

void BALL::DockProblem::move

(

)

move molecule according to vectors double_parameter_ and quaternion_parameter_, which are set by GeneticAlgorithm::calculate()

bool BALL::DockProblem::redraw

(

)

true if best solution has changed

void BALL::DockProblem::restore ( )

protected

set all rotable molecules to original positions

virtual void BALL::DockProblem::setup ( AtomContainer &  sys_lig )

virtual

Member Data Documentation

Vector3 BALL::DockProblem::binding_pocket_center_

protected

Definition at line 89 of file dockProblem.h.

EvolutionaryDocking* BALL::DockProblem::docker_

protected

Definition at line 75 of file dockProblem.h.

DoubleParameter BALL::DockProblem::double_parameter_

protected

Definition at line 77 of file dockProblem.h.

AtomContainer * BALL::DockProblem::draw_ligand_

protected

Definition at line 83 of file dockProblem.h.

AtomContainer* BALL::DockProblem::ligand_

protected

pointer to ligand molecule

Definition at line 83 of file dockProblem.h.

std::vector<Vector3 > BALL::DockProblem::ligand_positions_

protected

Vector to restore the position values of the ligand

Definition at line 97 of file dockProblem.h.

Options BALL::DockProblem::opt_

protected

amber options

Definition at line 111 of file dockProblem.h.

bool BALL::DockProblem::post_dock_optimization_

protected

Definition at line 115 of file dockProblem.h.

QuaternionParameter BALL::DockProblem::quaternion_parameter_

protected

Definition at line 79 of file dockProblem.h.

RotateBonds* BALL::DockProblem::rb_

protected

rotate bonds class

Definition at line 101 of file dockProblem.h.

bool BALL::DockProblem::redraw_

protected

Definition at line 113 of file dockProblem.h.

BALL::ScoringFunction* BALL::DockProblem::scoring_function_

protected

calculate conformation score

Definition at line 93 of file dockProblem.h.

Vector3 BALL::DockProblem::t_extension_

protected

Definition at line 87 of file dockProblem.h.

Vector3 BALL::DockProblem::t_origin_

protected

variables to store position and extentions of ligand and receptor

Definition at line 87 of file dockProblem.h.