BALL::IMGDock Class Reference

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

Inheritance diagram for BALL::IMGDock:

Classes
struct	Option
struct	Default

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)

Attributes
int	rec

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)

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

IMGDock() [1/3]

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

IMGDock() [2/3]

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

IMGDock() [3/3]

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

~IMGDock()

BALL::IMGDock::~IMGDock

(

)

Member Function Documentation

dockLigand()

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.

getDefaultOptions()

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

static

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

getEnergy()

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()

getLigand()

const AtomContainer * BALL::IMGDock::getLigand

(

)

getScore()

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)

printFragments()

void BALL::IMGDock::printFragments

(

std::ostream &

out = std::cout

)

prints information about each fragment of the ligand

printResults()

void BALL::IMGDock::printResults

(

std::ostream &

out = std::cout

)

rotateLigandFragment()

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

setup() [1/2]

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.

setup() [2/2]

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

virtual

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

Reimplemented from BALL::DockingAlgorithm.

start()

void BALL::IMGDock::start ( )

virtual

Reimplemented from BALL::DockingAlgorithm.

startDock()

void BALL::IMGDock::startDock

(

bool

verbose = 0

)

steps()

void BALL::IMGDock::steps

(

Size

no = 1

)

update()

void BALL::IMGDock::update

(

)

updates energy and forces between target and ligand

Member Data Documentation

rec

int BALL::IMGDock::rec

Definition at line 127 of file IMGDock.h.