BALL::BindingPocketProcessor Class Reference
[Miscellaneous]

#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 .
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_ &)

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]`