GeometricFit Class Reference
[Docking of molecular structures]

GeometricFit This class is derived from class DockingAlgorithm. More...

#include <geometricFit.h>

Inheritance diagram for GeometricFit:

List of all members.

Public Types
enum	ProteinIndex { PROTEIN_A = 1, PROTEIN_B = 2 }
enum	SurfaceType { CONNOLLY = 1, VAN_DER_WAALS = 2, FTDOCK = 3 }
Public Member Functions
	GeometricFit (System &system1, System &system2) throw ()
	Constructor.
	GeometricFit (Options &new_options) throw ()
	Constructor.
	GeometricFit (System &system1, System &system2, Options &new_options) throw ()
	Constructor.
virtual void	setup (System &system1, System &system2, Options &new_options) throw ()
	The setup routines.
virtual void	setup (System &system1, System &system2) throw ()
	Alternative setup.
void	start () throw ()
	Start the main loop of the algorithm.
float	getProgress () const throw ()
bool	hasFinished () const throw ()
Vector3	getTranslation (Index con_num) const throw ()
	Return the translation corresponding to conformation con_num.
Vector3	getOrientation (Index con_num) const throw ()
	Return the orientation corresponding to conformation con_num.
ConformationSet	getConformationSet (Index total_number=0) throw ()
	Return the ranked conformations.
Public Attributes
Options	options
	The options for the algorithm.
Protected Member Functions
void	destroy_ () throw ()
void	findInsidePoints_ (System &system, ProteinIndex pro_idx) throw ()
void	findConnollySurfacePoints_ (System &system, ProteinIndex pro_idx) throw ()
void	findVanDerWaalsSurfacePoints_ (System &system, ProteinIndex pro_idx) throw ()
void	findFTDockInsidePoints_ (System &system, ProteinIndex pro_idx) throw ()
void	findFTDockSurfacePoints_ (System &system, ProteinIndex pro_idx) throw ()
Vector3	getMassCenter_ (System &system) throw ()
	Compute the center of mass of system.
float	getRadius_ (System &system) throw ()
	Compute the radius of the circumsphere of all atoms in system.
void	doPreTranslation_ (ProteinIndex pro_idx) throw ()
void	initGridSizes_ () throw ()
int	optimizeGridSize_ (int raw_size) throw ()
	Optimize grid size for the FFTW.
void	initFFTGrid_ (ProteinIndex pro_idx) throw ()
	Initialize the grid.
void	makeFFTGrid_ (ProteinIndex pro_idx) throw ()
void	getGlobalPeak_ (Peak_ *peak_list) throw ()
void	changeProteinOrientation_ (System &system, Vector3 euler_ang) throw ()
void	calcConjugate_ (ProteinIndex pro_idx) throw ()
void	FFTGridMulti_ () throw ()
Vector3	getTranslation_ (const Vector3 &mat_pos) throw ()
Vector3	getSeparation_ (const Vector3 &mat_pos) throw ()
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_

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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.

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Constructor & Destructor Documentation

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

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

GeometricFit::GeometricFit (  Options &  new_options  )  throw ()

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

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

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

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Member Function Documentation

ConformationSet GeometricFit::getConformationSet (  Index  total_number = 0  )  throw () [virtual]

Return the ranked conformations. Reimplemented from DockingAlgorithm.

Vector3 GeometricFit::getOrientation (  Index  con_num  )  const throw ()

Return the orientation corresponding to conformation con_num.

float GeometricFit::getRadius_ (  System &  system  )  throw () [protected]

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

Vector3 GeometricFit::getTranslation (  Index  con_num  )  const throw ()

Return the translation corresponding to conformation con_num.

void GeometricFit::initFFTGrid_ (  ProteinIndex  pro_idx  )  throw () [protected]

Initialize the grid.

int GeometricFit::optimizeGridSize_ (  int  raw_size  )  throw () [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 GeometricFit::setup (  System &  system1, System &  system2 )  throw () [virtual]

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

virtual void GeometricFit::setup (  System &  system1, System &  system2, Options &  new_options )  throw () [virtual]

The setup routines. Reimplemented from DockingAlgorithm.

void GeometricFit::start (   )  throw () [virtual]

Start the main loop of the algorithm. Reimplemented from DockingAlgorithm.

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Member Data Documentation

Options GeometricFit::options

The options for the algorithm. Reimplemented from DockingAlgorithm.