BALL::EvolutionaryDocking Class Reference

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

Inheritance diagram for BALL::EvolutionaryDocking:

Classes
struct	Default
struct	Option

Public Member Functions
	EvolutionaryDocking (System &system1, System &system2, Options &new_options)
	EvolutionaryDocking (System &receptor, System &ligand, string config_file)
	~EvolutionaryDocking ()
virtual void	setup (System &ligand, BALL::ScoringFunction *sf, Options &new_options)
virtual void	setup (System &ligand, BALL::ScoringFunction *sf)
void	setup (System &receptor, System &ligand, Options &new_options)
void	start ()
double	dockLigand (AtomContainer &ligand, bool verbose=0)
float	getProgress () const
bool	redraw ()
Vector3 &	getReferenceLigandCenter ()
Public Member Functions inherited from BALL::DockingAlgorithm
	DockingAlgorithm ()
	DockingAlgorithm (System &receptor, System &ligand, Options &new_options)
	DockingAlgorithm (System &receptor, System &ligand)
virtual	~DockingAlgorithm ()
virtual void	setup (System &receptor, System &ligand)
ScoringFunction *	getScoringFunction ()
void	setScoringFunction (ScoringFunction *scoring)
void	processMultiMoleculeFile (string input_filename, string output_filename, double score_cutoff, vector< double > *min_atoms_in_ref_areas=0, String toolinfo="", String timestamp="")
void	setLigand (AtomContainer *ligand)
const AtomContainer *	getLigand ()
const AtomContainer *	getReferenceLigand ()
const String &	getName ()
virtual void	pause ()
virtual void	proceed ()
virtual void	abort ()
virtual void	finish ()
virtual void	reset ()
virtual bool	hasFinished () const
virtual bool	wasAborted () const
virtual bool	wasPaused () const
virtual ConformationSet	getConformationSet (Index total_conformations=0)
double	calculateRMSD (const AtomContainer &S1, const AtomContainer &S2, int *no_matched_atoms=NULL)
const AtomContainer *	getVisualizationPose ()
void	setVisualizationPose (const double &score)
double	getVisualizationPoseScore ()
DISPLAYMODE	getDisplayMode ()
void	setDisplayMode (DISPLAYMODE display_mode)
void	setMaxFps (int no)

Static Public Member Functions
static void	getDefaultOptions (Options &options)
Static Public Member Functions inherited from BALL::DockingAlgorithm
static void	readOptionFile (String filename, Options &output_options, list< Constraint * > &output_constraints, const AtomContainer *ref_ligand=0)
static void	writeOptionFile (String filename, Options &input_options, list< Constraint * > &input_constraints)
static Matrix4x4	mapCompounds (const AtomContainer &S1, const AtomContainer &S2, Size &no_matched_heavy_atoms, double &rmsd, double upper_bound, double lower_bound, double tolerance)

Protected Member Functions
void	destroy_ ()
void	applyBestConformation ()
Protected Member Functions inherited from BALL::DockingAlgorithm
void	mapLigandOntoReferenceLigand ()

Protected Attributes
GeneticAlgorithm *	ga_
DockProblem *	dp_
Vector3	reference_center_
Protected Attributes inherited from BALL::DockingAlgorithm
System *	system1_
System *	system2_
bool	pause_
bool	abort_
bool	finished_
AtomContainer *	reference_ligand_
String	name_
AtomContainer *	receptor_
AtomContainer *	ligand_
ScoringFunction *	scoring_function_
String	parameter_filename_
String	scoring_type_
DISPLAYMODE	display_mode_
AtomContainer	visualization_pose_
double	visualization_pose_score_
double	min_sec_between_visualizations_
Timer	visualization_timer_

Additional Inherited Members
Public Types inherited from BALL::DockingAlgorithm
enum	DISPLAYMODE { NO_DISPLAY = 0, BEST_INTERMEDIATE_POSES = 1, ALL_INTERMEDIATE_POSES = 2, NO_INTERMEDIATE_POSES = 3 }
Public Attributes inherited from BALL::DockingAlgorithm
Options	options
bool	new_pose_to_be_visualized
Static Public Attributes inherited from BALL::DockingAlgorithm
static const String	OPTION_FILE_PARAMETER_NAME
Static Protected Member Functions inherited from BALL::DockingAlgorithm
static void	writeSubcategories_ (Options &category, std::ostream &out)

Detailed Description

class EvolutionaryDocking This class is derived from class DockingAlgorithm. small ligand docking algorithm via a genetic Algorithm.

Definition at line 35 of file evolutionaryDocking.h.

Constructor & Destructor Documentation

BALL::EvolutionaryDocking::EvolutionaryDocking	(	System &	system1,
		System &	system2,
		Options &	new_options
	)

BALL::EvolutionaryDocking::EvolutionaryDocking	(	System &	receptor,
		System &	ligand,
		string	config_file
	)

BALL::EvolutionaryDocking::~EvolutionaryDocking

(

)

destructor

Member Function Documentation

void BALL::EvolutionaryDocking::applyBestConformation ( )

protected

void BALL::EvolutionaryDocking::destroy_ ( )

protected

Free all allocated memory and destroys the options and results

double BALL::EvolutionaryDocking::dockLigand ( AtomContainer &  ligand, bool  verbose = 0  )

virtual

docks the given ligand and returns the score for the best conformation

Reimplemented from BALL::DockingAlgorithm.

static void BALL::EvolutionaryDocking::getDefaultOptions ( Options &  options )

static

return ranked conformations.stores the default options of this algorithms in the given Option object

float BALL::EvolutionaryDocking::getProgress ( ) const

virtual

return the overall docking progress as a percentage

Reimplemented from BALL::DockingAlgorithm.

Vector3& BALL::EvolutionaryDocking::getReferenceLigandCenter

(

)

bool BALL::EvolutionaryDocking::redraw

(

)

true if new ligand position has to be drawn

virtual void BALL::EvolutionaryDocking::setup ( System &  ligand, BALL::ScoringFunction *  sf, Options &  new_options  )

virtual

The setup routines.

virtual void BALL::EvolutionaryDocking::setup ( System &  ligand, BALL::ScoringFunction *  sf  )

virtual

void BALL::EvolutionaryDocking::setup ( System &  receptor, System &  ligand, Options &  new_options  )

virtual

OperationsFull setup. Assigns systems 1 and two and the options for this DockingAlgorithm.

Reimplemented from BALL::DockingAlgorithm.

void BALL::EvolutionaryDocking::start ( )

virtual

Start the main loop of the algorithm.

Reimplemented from BALL::DockingAlgorithm.

Member Data Documentation

DockProblem* BALL::EvolutionaryDocking::dp_

protected

mapping class for docking

Definition at line 130 of file evolutionaryDocking.h.

GeneticAlgorithm* BALL::EvolutionaryDocking::ga_

protected

optimization method

Definition at line 126 of file evolutionaryDocking.h.

Vector3 BALL::EvolutionaryDocking::reference_center_

protected

the geometrical center of the reference ligand

Definition at line 133 of file evolutionaryDocking.h.