#include <BALL/STRUCTURE/bindingPocketProcessor.h>

Inheritance diagram for BALL::BindingPocketProcessor:

Classes
struct	Default

struct	Option

class	Sphere_

class	SphereComparator_

Public Member Functions
	BindingPocketProcessor ()

	BindingPocketProcessor (Options &new_options)

	BindingPocketProcessor (const BindingPocketProcessor &pp)

virtual	~BindingPocketProcessor ()

const BindingPocketProcessor &	operator= (const BindingPocketProcessor &pp)

virtual bool	finish ()
	Finish . More...

virtual Processor::Result	operator() (Composite &composite)

const vector< std::pair < Vector3, double > > &	getActiveSitePoints () const

const vector< vector < std::pair< Vector3, double > > > &	getLayers () const

Public Member Functions inherited from BALL::UnaryProcessor< Composite >
	UnaryProcessor ()

	UnaryProcessor (const UnaryProcessor &)

virtual	~UnaryProcessor ()

virtual bool	start ()

Public Attributes
Options	options

Private Member Functions
double	radius_ (const String &element)

void	trySphere__ (HashGridBox3< Sphere_ >::DataIterator data_it, HashGridBox3< Sphere_ >::DataIterator data_it2, HashGridBox3< Sphere_ >::DataIterator data_it3)

void	addSphere_s_ ()

Vector3	calculateT_ (HashGridBox3< Sphere_ >::DataIterator data_it, HashGridBox3< Sphere_ >::DataIterator data_it2)

void	testFirst_ (HashGrid3< Sphere_ > &hg, HashGridBox3< Sphere_ >::DataIterator data_it, Position x, Position y, Position z)

void	testSecond_ (HashGrid3< Sphere_ > &hg, HashGridBox3< Sphere_ >::DataIterator data_it, HashGridBox3< Sphere_ >::DataIterator data_it2, Position x, Position y, Position z, Position step)

bool	testSphereClash_ (Vector3 &v)

bool	testProteinClash_ (Vector3 &v)

bool	testBC_ (Sphere_ &sp)

void	weedCandidates_ ()

bool	parse_ ()

Private Attributes
Position	layer_

HashGrid3< Sphere_ >	sphere_grid_

HashGrid3< Sphere_ >	protein_grid_

HashGrid3< Sphere_ >	layer_grid_

HashGrid3< Sphere_ >	clayer_grid_

HashGrid3< Sphere_ >	BC_grid_

HashGrid3< Sphere_ >	pw_grid_

HashGrid3< Sphere_ >	candidates_grid_

std::vector< Sphere_ >	sorted_spheres_

double	sphere_rad_

double	second_layer_rad_

double	protein_clash_rad_

double	BC_threshold_

Position	found_new_

double	c_factor_

std::vector< Sphere_ >	candidates

std::vector< std::pair < Vector3, double > >	asps_

std::vector< std::vector < std::pair< Vector3, double > > >	layers_

bool	second_it_

Friends
std::ostream &	operator<< (std::ostream &os, const BindingPocketProcessor::Sphere_ &)

Additional Inherited Members
Public Types inherited from BALL::UnaryFunctor< Composite, Processor::Result >
typedef Processor::Result	result_type

typedef Composite	argument_type

typedef Composite &	argument_reference

typedef const Composite &	const_argument_reference

typedef Composite *	argument_pointer

typedef const Composite *	const_argument_pointer

Detailed Description

This processor searches for binding pockets in a given atom container. The pockets are detected with the PASS method (Fast Feature Selection Using Fractal Dimension (2000) Caetano Traina, Jr., Agma Traina, et al)

Definition at line 40 of file bindingPocketProcessor.h.

Constructor & Destructor Documentation

BALL::BindingPocketProcessor::BindingPocketProcessor ( )

standard constructor

BALL::BindingPocketProcessor::BindingPocketProcessor ( Options & new_options )

constructor with options

BALL::BindingPocketProcessor::BindingPocketProcessor ( const BindingPocketProcessor & pp )

copy constructor

virtual BALL::BindingPocketProcessor::~BindingPocketProcessor ( )

virtual

destructor

Member Function Documentation

void BALL::BindingPocketProcessor::addSphere_s_ ( )

private

compute sphere layers

Vector3 BALL::BindingPocketProcessor::calculateT_	(	HashGridBox3< Sphere_ >::DataIterator	data_it,
		HashGridBox3< Sphere_ >::DataIterator	data_it2
	)

private

geometric computation

virtual bool BALL::BindingPocketProcessor::finish ( )

virtual

Finish .

Reimplemented from BALL::UnaryProcessor< Composite >.

const vector<std::pair<Vector3,double> >& BALL::BindingPocketProcessor::getActiveSitePoints ( ) const

Returns the position and burial counts of the calculated actice site points

const vector<vector<std::pair<Vector3,double> > >& BALL::BindingPocketProcessor::getLayers ( ) const

Returns a vector of vectors, each containing one layer with position and probe weight of its spheres

virtual Processor::Result BALL::BindingPocketProcessor::operator() ( Composite & )

virtual

operator ()

Reimplemented from BALL::UnaryProcessor< Composite >.

const BindingPocketProcessor& BALL::BindingPocketProcessor::operator= ( const BindingPocketProcessor & pp )

assignment operator

bool BALL::BindingPocketProcessor::parse_ ( )

private

read parameter file

double BALL::BindingPocketProcessor::radius_ ( const String & element )

private

Determine the radius of an element

Parameters

element the full name of the element for which a radius should be looked up. Example: "Oxygen"

Exceptions

IllegalArgument if an unknown element has been passed

Returns: The radius of the specified element

bool BALL::BindingPocketProcessor::testBC_ ( Sphere_ & sp )

private

test for burial count

void BALL::BindingPocketProcessor::testFirst_	(	HashGrid3< Sphere_ > &	hg,
		HashGridBox3< Sphere_ >::DataIterator	data_it,
		Position	x,
		Position	y,
		Position	z
	)

private

test if three spheres produce two offspring spheres

bool BALL::BindingPocketProcessor::testProteinClash_ ( Vector3 & v )

private

test clash with protein atoms

void BALL::BindingPocketProcessor::testSecond_	(	HashGrid3< Sphere_ > &	hg,
		HashGridBox3< Sphere_ >::DataIterator	data_it,
		HashGridBox3< Sphere_ >::DataIterator	data_it2,
		Position	x,
		Position	y,
		Position	z,
		Position	step
	)

private

bool BALL::BindingPocketProcessor::testSphereClash_ ( Vector3 & v )

private

test clash with all existing spheres

void BALL::BindingPocketProcessor::trySphere__	(	HashGridBox3< Sphere_ >::DataIterator	data_it,
		HashGridBox3< Sphere_ >::DataIterator	data_it2,
		HashGridBox3< Sphere_ >::DataIterator	data_it3
	)

private

calculates two spheres if possible

void BALL::BindingPocketProcessor::weedCandidates_ ( )

private

remove redundant spheres

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	os,
		const BindingPocketProcessor::Sphere_ &
	)

friend

output operator for Sphere TODO: implement!

Definition at line 225 of file bindingPocketProcessor.h.

Member Data Documentation

std::vector<std::pair<Vector3,double> > BALL::BindingPocketProcessor::asps_

private

Definition at line 283 of file bindingPocketProcessor.h.

HashGrid3<Sphere_> BALL::BindingPocketProcessor::BC_grid_

private

need for computation of burial count

Definition at line 245 of file bindingPocketProcessor.h.

double BALL::BindingPocketProcessor::BC_threshold_

private

threshold for burial count filer

Definition at line 271 of file bindingPocketProcessor.h.

double BALL::BindingPocketProcessor::c_factor_

private

Definition at line 277 of file bindingPocketProcessor.h.

std::vector<Sphere_> BALL::BindingPocketProcessor::candidates

private

store all possible new spheres

Definition at line 281 of file bindingPocketProcessor.h.

HashGrid3<Sphere_> BALL::BindingPocketProcessor::candidates_grid_

private

store all possible new spheres

Definition at line 253 of file bindingPocketProcessor.h.

HashGrid3<Sphere_> BALL::BindingPocketProcessor::clayer_grid_

private

needed for sphere collision

Definition at line 241 of file bindingPocketProcessor.h.

Position BALL::BindingPocketProcessor::found_new_

private

number of newly found spheres

Definition at line 275 of file bindingPocketProcessor.h.

Position BALL::BindingPocketProcessor::layer_

private

current layer

Definition at line 220 of file bindingPocketProcessor.h.

HashGrid3<Sphere_> BALL::BindingPocketProcessor::layer_grid_

private

store all sphere layers

Definition at line 237 of file bindingPocketProcessor.h.

std::vector<std::vector<std::pair<Vector3,double> > > BALL::BindingPocketProcessor::layers_

private

Definition at line 285 of file bindingPocketProcessor.h.

Options BALL::BindingPocketProcessor::options

options for BALLPass

Definition at line 151 of file bindingPocketProcessor.h.

double BALL::BindingPocketProcessor::protein_clash_rad_

private

radius for collision with protein atoms

Definition at line 267 of file bindingPocketProcessor.h.

HashGrid3<Sphere_> BALL::BindingPocketProcessor::protein_grid_

private

store protein atoms

Definition at line 233 of file bindingPocketProcessor.h.

HashGrid3<Sphere_> BALL::BindingPocketProcessor::pw_grid_

private

need for computation of probe weight

Definition at line 249 of file bindingPocketProcessor.h.

bool BALL::BindingPocketProcessor::second_it_

private

Definition at line 340 of file bindingPocketProcessor.h.

double BALL::BindingPocketProcessor::second_layer_rad_

private

sphere radius for following layers

Definition at line 263 of file bindingPocketProcessor.h.

std::vector<Sphere_> BALL::BindingPocketProcessor::sorted_spheres_

private

Definition at line 255 of file bindingPocketProcessor.h.

HashGrid3<Sphere_> BALL::BindingPocketProcessor::sphere_grid_

private

store all spheres

Definition at line 225 of file bindingPocketProcessor.h.

double BALL::BindingPocketProcessor::sphere_rad_

private

first layer radius

Definition at line 259 of file bindingPocketProcessor.h.

Classes

Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation