BALL::GeometricFit Class Reference
[Docking of molecular structures]

#include <BALL/STRUCTURE/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 Member Functions
	GeometricFit ()
	GeometricFit (System &system1, System &system2)
	GeometricFit (Options &new_options)
	GeometricFit (System &system1, System &system2, Options &new_options)
	~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 Attributes
Options	options
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 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_

Detailed Description

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

Member Enumeration Documentation

enum BALL::GeometricFit::ProteinIndex

Enumerator:

PROTEIN_A
PROTEIN_B

enum BALL::GeometricFit::SurfaceType

Enumerator:

CONNOLLY
VAN_DER_WAALS
FTDOCK

Constructor & Destructor Documentation

BALL::GeometricFit::GeometricFit ( )

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 ( )

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.