BALL::DockingAlgorithm Class Reference

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

Inheritance diagram for BALL::DockingAlgorithm:

Public Types
enum	DISPLAYMODE { NO_DISPLAY = 0, BEST_INTERMEDIATE_POSES = 1, ALL_INTERMEDIATE_POSES = 2, NO_INTERMEDIATE_POSES = 3 }

Public Member Functions
	DockingAlgorithm ()
	DockingAlgorithm (System &receptor, System &ligand, Options &new_options)
	DockingAlgorithm (System &receptor, System &ligand)
virtual	~DockingAlgorithm ()
virtual void	setup (System &receptor, System &ligand, Options &new_options)
virtual void	setup (System &receptor, System &ligand)
virtual double	dockLigand (AtomContainer &ligand, bool verbose=0)
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	start ()
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)

Static Public Member Functions
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
Options	options
bool	new_pose_to_be_visualized

Static Public Attributes
static const String	OPTION_FILE_PARAMETER_NAME

Protected Member Functions
void	mapLigandOntoReferenceLigand ()

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

Protected Attributes
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

Interface class for docking algorithms.

Definition at line 45 of file dockingAlgorithm.h.

Member Enumeration Documentation

enum BALL::DockingAlgorithm::DISPLAYMODE

Enumerator
NO_DISPLAY
BEST_INTERMEDIATE_POSES
ALL_INTERMEDIATE_POSES
NO_INTERMEDIATE_POSES

Definition at line 49 of file dockingAlgorithm.h.

Constructor & Destructor Documentation

BALL::DockingAlgorithm::DockingAlgorithm

(

)

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

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

virtual BALL::DockingAlgorithm::~DockingAlgorithm ( )

virtual

Member Function Documentation

virtual void BALL::DockingAlgorithm::abort ( )

virtual

double BALL::DockingAlgorithm::calculateRMSD	(	const AtomContainer &	S1,
		const AtomContainer &	S2,
		int *	no_matched_atoms = NULL
	)

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

virtual

dock the given ligand and return its score

Reimplemented in BALL::EvolutionaryDocking, and BALL::IMGDock.

virtual void BALL::DockingAlgorithm::finish ( )

virtual

virtual ConformationSet BALL::DockingAlgorithm::getConformationSet ( Index  total_conformations = 0 )

virtual

Return total_conformations putative complexes, ordered according to their rank. If total_conformations == 0, the option TOP_N is used

Reimplemented in BALL::GeometricFit.

DISPLAYMODE BALL::DockingAlgorithm::getDisplayMode

(

)

const AtomContainer* BALL::DockingAlgorithm::getLigand

(

)

const String& BALL::DockingAlgorithm::getName

(

)

get the name of this docking algorithm

virtual float BALL::DockingAlgorithm::getProgress ( ) const

virtual

Reimplemented in BALL::GeometricFit, and BALL::EvolutionaryDocking.

const AtomContainer* BALL::DockingAlgorithm::getReferenceLigand

(

)

ScoringFunction* BALL::DockingAlgorithm::getScoringFunction

(

)

return the ScoringFunction that is used by this DockingAlgorithm

const AtomContainer* BALL::DockingAlgorithm::getVisualizationPose

(

)

double BALL::DockingAlgorithm::getVisualizationPoseScore

(

)

virtual bool BALL::DockingAlgorithm::hasFinished ( ) const

virtual

Reimplemented in BALL::GeometricFit.

static Matrix4x4 BALL::DockingAlgorithm::mapCompounds ( const AtomContainer &  S1, const AtomContainer &  S2, Size &  no_matched_heavy_atoms, double &  rmsd, double  upper_bound, double  lower_bound, double  tolerance  )

static

void BALL::DockingAlgorithm::mapLigandOntoReferenceLigand ( )

protected

virtual void BALL::DockingAlgorithm::pause ( )

virtual

virtual void BALL::DockingAlgorithm::proceed ( )

virtual

void BALL::DockingAlgorithm::processMultiMoleculeFile	(	string	input_filename,
		string	output_filename,
		double	score_cutoff,
		vector< double > *	min_atoms_in_ref_areas = 0,
		String	toolinfo = "",
		String	timestamp = ""
	)

static void BALL::DockingAlgorithm::readOptionFile ( String  filename, Options &  output_options, list< Constraint * > &  output_constraints, const AtomContainer *  ref_ligand = 0  )

static

virtual void BALL::DockingAlgorithm::reset ( )

virtual

resets Algorithm before new dock-run, e.g. sets finished_ to false

void BALL::DockingAlgorithm::setDisplayMode

(

DISPLAYMODE

display_mode

)

void BALL::DockingAlgorithm::setLigand

(

AtomContainer *

ligand

)

void BALL::DockingAlgorithm::setMaxFps

(

int

no

)

Set the maximal number of frames per second for the visualization output. This affects only the number of poses that are written for visualization NOT the actual speed of the docking algorithm itself.

void BALL::DockingAlgorithm::setScoringFunction ( ScoringFunction *  scoring )

inline

Definition at line 94 of file dockingAlgorithm.h.

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

virtual

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

Reimplemented in BALL::GeometricFit, BALL::EvolutionaryDocking, and BALL::IMGDock.

virtual void BALL::DockingAlgorithm::setup ( System &  receptor, System &  ligand  )

virtual

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

Reimplemented in BALL::GeometricFit, and BALL::IMGDock.

void BALL::DockingAlgorithm::setVisualizationPose

(

const double &

score

)

virtual void BALL::DockingAlgorithm::start ( )

virtual

Reimplemented in BALL::GeometricFit, BALL::EvolutionaryDocking, and BALL::IMGDock.

virtual bool BALL::DockingAlgorithm::wasAborted ( ) const

inlinevirtual

Definition at line 133 of file dockingAlgorithm.h.

virtual bool BALL::DockingAlgorithm::wasPaused ( ) const

inlinevirtual

Definition at line 137 of file dockingAlgorithm.h.

static void BALL::DockingAlgorithm::writeOptionFile ( String  filename, Options &  input_options, list< Constraint * > &  input_constraints  )

static

static void BALL::DockingAlgorithm::writeSubcategories_ ( Options &  category, std::ostream &  out  )

staticprotected

Member Data Documentation

bool BALL::DockingAlgorithm::abort_

protected

Definition at line 179 of file dockingAlgorithm.h.

DISPLAYMODE BALL::DockingAlgorithm::display_mode_

protected

Definition at line 200 of file dockingAlgorithm.h.

bool BALL::DockingAlgorithm::finished_

protected

Definition at line 180 of file dockingAlgorithm.h.

AtomContainer* BALL::DockingAlgorithm::ligand_

protected

Definition at line 189 of file dockingAlgorithm.h.

double BALL::DockingAlgorithm::min_sec_between_visualizations_

protected

Definition at line 207 of file dockingAlgorithm.h.

String BALL::DockingAlgorithm::name_

protected

the name of the docking algorithm

Definition at line 185 of file dockingAlgorithm.h.

bool BALL::DockingAlgorithm::new_pose_to_be_visualized

Definition at line 162 of file dockingAlgorithm.h.

const String BALL::DockingAlgorithm::OPTION_FILE_PARAMETER_NAME

static

Definition at line 154 of file dockingAlgorithm.h.

Options BALL::DockingAlgorithm::options

Attributes

Definition at line 67 of file dockingAlgorithm.h.

String BALL::DockingAlgorithm::parameter_filename_

protected

Definition at line 195 of file dockingAlgorithm.h.

bool BALL::DockingAlgorithm::pause_

protected

Definition at line 178 of file dockingAlgorithm.h.

AtomContainer* BALL::DockingAlgorithm::receptor_

protected

Definition at line 187 of file dockingAlgorithm.h.

AtomContainer* BALL::DockingAlgorithm::reference_ligand_

protected

Definition at line 182 of file dockingAlgorithm.h.

ScoringFunction* BALL::DockingAlgorithm::scoring_function_

protected

Definition at line 193 of file dockingAlgorithm.h.

String BALL::DockingAlgorithm::scoring_type_

protected

name of the ScoringFunction to be used

Definition at line 198 of file dockingAlgorithm.h.

System* BALL::DockingAlgorithm::system1_

protected

Definition at line 175 of file dockingAlgorithm.h.

System* BALL::DockingAlgorithm::system2_

protected

Definition at line 176 of file dockingAlgorithm.h.

AtomContainer BALL::DockingAlgorithm::visualization_pose_

protected

copy of a intermediate pose that is to be visualized.

Definition at line 203 of file dockingAlgorithm.h.

double BALL::DockingAlgorithm::visualization_pose_score_

protected

Definition at line 205 of file dockingAlgorithm.h.

Timer BALL::DockingAlgorithm::visualization_timer_

protected

Definition at line 208 of file dockingAlgorithm.h.