BALL::GeometricFit Class Reference

#include <BALL/DOCKING/geometricFit.h>

Inheritance diagram for BALL::GeometricFit:

Classes
struct	Default
struct	Option
class	Peak_
class	RotationAngles_

Public Types
enum	ProteinIndex { PROTEIN_A = 1, PROTEIN_B = 2 }
enum	SurfaceType { CONNOLLY = 1, VAN_DER_WAALS = 2, FTDOCK = 3 }
Public Types inherited from BALL::DockingAlgorithm
enum	DISPLAYMODE { NO_DISPLAY = 0, BEST_INTERMEDIATE_POSES = 1, ALL_INTERMEDIATE_POSES = 2, NO_INTERMEDIATE_POSES = 3 }

Public Member Functions
	GeometricFit ()
	GeometricFit (System &system1, System &system2)
	GeometricFit (Options &new_options)
	GeometricFit (System &system1, System &system2, Options &new_options)
	GeometricFit (const GeometricFit &geo_fit)
	~GeometricFit ()
virtual void	setup (System &system1, System &system2, Options &new_options)
virtual void	setup (System &system1, System &system2)
void	start ()
float	getProgress () const
bool	hasFinished () const
Vector3	getTranslation (Index con_num) const
Vector3	getOrientation (Index con_num) const
ConformationSet	getConformationSet (Index total_number=0)
Public Member Functions inherited from BALL::DockingAlgorithm
	DockingAlgorithm ()
	DockingAlgorithm (System &receptor, System &ligand, Options &new_options)
	DockingAlgorithm (System &receptor, System &ligand)
virtual	~DockingAlgorithm ()
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	pause ()
virtual void	proceed ()
virtual void	abort ()
virtual void	finish ()
virtual void	reset ()
virtual bool	wasAborted () const
virtual bool	wasPaused () const
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)

Public Attributes
Options	options
Public Attributes inherited from BALL::DockingAlgorithm
Options	options
bool	new_pose_to_be_visualized

Protected Member Functions
void	destroy_ ()
void	findInsidePoints_ (System &system, ProteinIndex pro_idx)
void	findConnollySurfacePoints_ (System &system, ProteinIndex pro_idx)
void	findVanDerWaalsSurfacePoints_ (System &system, ProteinIndex pro_idx)
void	findFTDockInsidePoints_ (System &system, ProteinIndex pro_idx)
void	findFTDockSurfacePoints_ (System &system, ProteinIndex pro_idx)
Vector3	getMassCenter_ (System &system)
float	getRadius_ (System &system)
void	doPreTranslation_ (ProteinIndex pro_idx)
void	initGridSizes_ ()
int	optimizeGridSize_ (int raw_size)
void	initFFTGrid_ (ProteinIndex pro_idx)
void	makeFFTGrid_ (ProteinIndex pro_idx)
void	getGlobalPeak_ (Peak_ *peak_list)
void	changeProteinOrientation_ (System &system, Vector3 euler_ang)
void	calcConjugate_ (ProteinIndex pro_idx)
void	FFTGridMulti_ ()
Vector3	getTranslation_ (const Vector3 &mat_pos)
Vector3	getSeparation_ (const Vector3 &mat_pos)
Protected Member Functions inherited from BALL::DockingAlgorithm
void	mapLigandOntoReferenceLigand ()

Protected Attributes
FFT3D *	FFT_grid_a_
FFT3D *	FFT_grid_b_
float	radius_a_
float	radius_b_
Vector3	FFT_grid_lower_index_
Vector3	FFT_grid_upper_index_
Vector3	FFT_grid_lower_coord_
Vector3	FFT_grid_upper_coord_
Vector3	FFT_grid_size_index_
Vector3	pre_translation_a_
Vector3	pre_translation_b_
Vector3	FFT_grid_origin_
int	current_round_
int	total_round_
std::multiset< Peak_ >	peak_set_
System	system_backup_a_
System	system_backup_b_
vector< Vector3 >	translations_
vector< Vector3 >	orientations_
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
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)
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

GeometricFit This class is derived from class DockingAlgorithm. Protein docking algorithm via geometric fit invented by Katchalski-Katzir, et al. (1992) is implemented in this class.

Definition at line 36 of file geometricFit.h.

Member Enumeration Documentation

enum BALL::GeometricFit::ProteinIndex

Enumerator
PROTEIN_A
PROTEIN_B

Definition at line 258 of file geometricFit.h.

enum BALL::GeometricFit::SurfaceType

Enumerator
CONNOLLY
VAN_DER_WAALS
FTDOCK

Definition at line 261 of file geometricFit.h.

Constructor & Destructor Documentation

BALL::GeometricFit::GeometricFit

(

)

Default constructor Creates an empty GeometricFit object

BALL::GeometricFit::GeometricFit	(	System &	system1,
		System &	system2
	)

Constructor. Creates an instance of Geometric Fit and calls setup(system1, system2). The options used are the default options.

BALL::GeometricFit::GeometricFit

(

Options &

new_options

)

Constructor. Creates an instance of Geometric Fit and assigns the given options to the Geometric Fit object's options.

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

Constructor. Creates an instance of FDPB and calls setup(system1, system2, new_options)

BALL::GeometricFit::GeometricFit

(

const GeometricFit &

geo_fit

)

Copy Constructor.

BALL::GeometricFit::~GeometricFit

(

)

Member Function Documentation

void BALL::GeometricFit::calcConjugate_ ( ProteinIndex  pro_idx )

protected

void BALL::GeometricFit::changeProteinOrientation_ ( System &  system, Vector3  euler_ang  )

protected

void BALL::GeometricFit::destroy_ ( )

protected

void BALL::GeometricFit::doPreTranslation_ ( ProteinIndex  pro_idx )

protected

void BALL::GeometricFit::FFTGridMulti_ ( )

protected

void BALL::GeometricFit::findConnollySurfacePoints_ ( System &  system, ProteinIndex  pro_idx  )

protected

void BALL::GeometricFit::findFTDockInsidePoints_ ( System &  system, ProteinIndex  pro_idx  )

protected

void BALL::GeometricFit::findFTDockSurfacePoints_ ( System &  system, ProteinIndex  pro_idx  )

protected

void BALL::GeometricFit::findInsidePoints_ ( System &  system, ProteinIndex  pro_idx  )

protected

void BALL::GeometricFit::findVanDerWaalsSurfacePoints_ ( System &  system, ProteinIndex  pro_idx  )

protected

ConformationSet BALL::GeometricFit::getConformationSet ( Index  total_number = 0 )

virtual

Return the ranked conformations.

Reimplemented from BALL::DockingAlgorithm.

void BALL::GeometricFit::getGlobalPeak_ ( Peak_ *  peak_list )

protected

Vector3 BALL::GeometricFit::getMassCenter_ ( System &  system )

protected

Compute the center of mass of system

Vector3 BALL::GeometricFit::getOrientation

(

Index

con_num

)

const

Return the orientation corresponding to conformation con_num.

float BALL::GeometricFit::getProgress ( ) const

virtual

Reimplemented from BALL::DockingAlgorithm.

float BALL::GeometricFit::getRadius_ ( System &  system )

protected

Compute the radius of the circumsphere of all atoms in system.

Vector3 BALL::GeometricFit::getSeparation_ ( const Vector3 &  mat_pos )

protected

Vector3 BALL::GeometricFit::getTranslation

(

Index

con_num

)

const

Return the translation corresponding to conformation con_num.

Vector3 BALL::GeometricFit::getTranslation_ ( const Vector3 &  mat_pos )

protected

bool BALL::GeometricFit::hasFinished ( ) const

virtual

Reimplemented from BALL::DockingAlgorithm.

void BALL::GeometricFit::initFFTGrid_ ( ProteinIndex  pro_idx )

protected

Initialize the grid.

void BALL::GeometricFit::initGridSizes_ ( )

protected

void BALL::GeometricFit::makeFFTGrid_ ( ProteinIndex  pro_idx )

protected

int BALL::GeometricFit::optimizeGridSize_ ( int  raw_size )

protected

Optimize grid size for the FFTW. Certain combinations of certain powers are optimal for the fft algorithm, and this function tries to determine the smallest optimal combination large enough to accomodate the original data.

virtual void BALL::GeometricFit::setup ( System &  system1, System &  system2, Options &  new_options  )

virtual

The setup routines.

Reimplemented from BALL::DockingAlgorithm.

virtual void BALL::GeometricFit::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::GeometricFit::start ( )

virtual

Start the main loop of the algorithm.

Reimplemented from BALL::DockingAlgorithm.

Member Data Documentation

int BALL::GeometricFit::current_round_

protected

Definition at line 428 of file geometricFit.h.

FFT3D* BALL::GeometricFit::FFT_grid_a_

protected

Definition at line 405 of file geometricFit.h.

FFT3D* BALL::GeometricFit::FFT_grid_b_

protected

Definition at line 408 of file geometricFit.h.

Vector3 BALL::GeometricFit::FFT_grid_lower_coord_

protected

Definition at line 415 of file geometricFit.h.

Vector3 BALL::GeometricFit::FFT_grid_lower_index_

protected

Definition at line 413 of file geometricFit.h.

Vector3 BALL::GeometricFit::FFT_grid_origin_

protected

Definition at line 425 of file geometricFit.h.

Vector3 BALL::GeometricFit::FFT_grid_size_index_

protected

Definition at line 418 of file geometricFit.h.

Vector3 BALL::GeometricFit::FFT_grid_upper_coord_

protected

Definition at line 416 of file geometricFit.h.

Vector3 BALL::GeometricFit::FFT_grid_upper_index_

protected

Definition at line 414 of file geometricFit.h.

Options BALL::GeometricFit::options

The options for the algorithm.

Definition at line 334 of file geometricFit.h.

vector<Vector3> BALL::GeometricFit::orientations_

protected

Definition at line 442 of file geometricFit.h.

std::multiset<Peak_> BALL::GeometricFit::peak_set_

protected

Definition at line 434 of file geometricFit.h.

Vector3 BALL::GeometricFit::pre_translation_a_

protected

Definition at line 422 of file geometricFit.h.

Vector3 BALL::GeometricFit::pre_translation_b_

protected

Definition at line 423 of file geometricFit.h.

float BALL::GeometricFit::radius_a_

protected

Definition at line 410 of file geometricFit.h.

float BALL::GeometricFit::radius_b_

protected

Definition at line 411 of file geometricFit.h.

System BALL::GeometricFit::system_backup_a_

protected

Definition at line 437 of file geometricFit.h.

System BALL::GeometricFit::system_backup_b_

protected

Definition at line 438 of file geometricFit.h.

int BALL::GeometricFit::total_round_

protected

Definition at line 431 of file geometricFit.h.

vector<Vector3> BALL::GeometricFit::translations_

protected

Definition at line 441 of file geometricFit.h.