#include <BALL/DOCKING/IMGDOCK/IMGDock.h>

Inheritance diagram for BALL::IMGDock:

Classes
struct	Default

struct	Option

Public Member Functions
Constructors&Destructors
	IMGDock (System &receptor, System &ligand, Options &new_options)

	IMGDock (System &receptor, System &ligand)

	IMGDock (System &receptor, System &ligand, string config_file)

	~IMGDock ()

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

	DockingAlgorithm (System &receptor, System &ligand, Options &new_options)

	DockingAlgorithm (System &receptor, System &ligand)

virtual	~DockingAlgorithm ()

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 float	getProgress () 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)

Accessors
void	setup (System &receptor, System &ligand, Options &new_options)

void	setup (System &receptor, System &ligand)

void	start ()

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

double	getEnergy ()

double	getScore ()

void	printFragments (std::ostream &out=std::cout)

void	printResults (std::ostream &out=std::cout)

void	rotateLigandFragment (Size fragment, Size bond, int degree)

void	steps (Size no=1)

void	update ()

void	startDock (bool verbose=0)

const AtomContainer *	getLigand ()

static void	getDefaultOptions (Options &options)

Attributes
int	rec

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 }

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)

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

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

Static Protected Member Functions inherited from BALL::DockingAlgorithm
static void	writeSubcategories_ (Options &category, std::ostream &out)

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_

Detailed Description

Iterative Multi-Greedy Docking

Definition at line 38 of file IMGDock.h.

Constructor & Destructor Documentation

BALL::IMGDock::IMGDock	(	System &	receptor,
		System &	ligand,
		Options &	new_options
	)

BALL::IMGDock::IMGDock	(	System &	receptor,
		System &	ligand
	)

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

BALL::IMGDock::~IMGDock ( )

Member Function Documentation

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

virtual

tries to dock a given ligand and return the obtained energy ( = internal conformation energy of the ligand + binding free energy)

Reimplemented from BALL::DockingAlgorithm.

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

static

stores the default options of this algorithms in the given Option object

double BALL::IMGDock::getEnergy ( )

returns the energy of current conformation of the ligand candidate ( = conformation energy+interaction energy), as calculated by the last call of update()

const AtomContainer* BALL::IMGDock::getLigand ( )

double BALL::IMGDock::getScore ( )

returns the IMGDock score for the current conformation of the ligand candidate as calculated by the last call of update(); i.e. the interaction+conformation energy scaled ...
– with respect to the depth of burial of the ligand candidate into the binding pocket
– and with respect to the number/fraction of ligand atoms that are located within the various reference areas (which are defined by the user)

void BALL::IMGDock::printFragments ( std::ostream & out = std::cout )

prints information about each fragment of the ligand

void BALL::IMGDock::printResults ( std::ostream & out = std::cout )

void BALL::IMGDock::rotateLigandFragment	(	Size	fragment,
		Size	bond,
		int	degree
	)

rotate a ligand fragment around one of its bonds that connects it to another fragment

void BALL::IMGDock::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::IMGDock::setup	(	System &	receptor,
		System &	ligand
	)

virtual

Alternative setup. Assigns systems 1 and two without changing the options for this DockingAlgorithm.

Reimplemented from BALL::DockingAlgorithm.

void BALL::IMGDock::start ( )

virtual

Reimplemented from BALL::DockingAlgorithm.

void BALL::IMGDock::startDock ( bool verbose = 0 )

void BALL::IMGDock::steps ( Size no = 1 )

void BALL::IMGDock::update ( )

updates energy and forces between target and ligand

Member Data Documentation

int BALL::IMGDock::rec

Definition at line 127 of file IMGDock.h.

Classes

Public Member Functions

Accessors

Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation