BALL::BindingPocketProcessor Class Reference
[Miscellaneous]

#include <BALL/STRUCTURE/bindingPocketProcessor.h>

Inheritance diagram for BALL::BindingPocketProcessor:

List of all members.

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 .
virtual Processor::Result	operator() (Composite &composite)
const vector< std::pair < Vector3, double > > &	getActiveSitePoints () const
const vector< vector < std::pair< Vector3, double > > > &	getLayers () const
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_ &sp)

---

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)

---

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_ &	sp
	)			[friend]

output operator for Sphere

---

Member Data Documentation

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

HashGrid3<Sphere_> BALL::BindingPocketProcessor::BC_grid_ [private]

need for computation of burial count

double BALL::BindingPocketProcessor::BC_threshold_ [private]

threshold for burial count filer

double BALL::BindingPocketProcessor::c_factor_ [private]

std::vector<Sphere_> BALL::BindingPocketProcessor::candidates [private]

store all possible new spheres

HashGrid3<Sphere_> BALL::BindingPocketProcessor::candidates_grid_ [private]

store all possible new spheres

HashGrid3<Sphere_> BALL::BindingPocketProcessor::clayer_grid_ [private]

needed for sphere collision

Position BALL::BindingPocketProcessor::found_new_ [private]

number of newly found spheres

Position BALL::BindingPocketProcessor::layer_ [private]

current layer

HashGrid3<Sphere_> BALL::BindingPocketProcessor::layer_grid_ [private]

store all sphere layers

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

Options BALL::BindingPocketProcessor::options

options for BALLPass

double BALL::BindingPocketProcessor::protein_clash_rad_ [private]

radius for collision with protein atoms

HashGrid3<Sphere_> BALL::BindingPocketProcessor::protein_grid_ [private]

store protein atoms

HashGrid3<Sphere_> BALL::BindingPocketProcessor::pw_grid_ [private]

need for computation of probe weight

bool BALL::BindingPocketProcessor::second_it_ [private]

double BALL::BindingPocketProcessor::second_layer_rad_ [private]

sphere radius for following layers

std::vector<Sphere_> BALL::BindingPocketProcessor::sorted_spheres_ [private]

HashGrid3<Sphere_> BALL::BindingPocketProcessor::sphere_grid_ [private]

store all spheres

double BALL::BindingPocketProcessor::sphere_rad_ [private]

first layer radius