#include <CartGrid.fwd.hh>

Inheritance diagram for core::grid::CartGrid< T >:

Collaboration diagram for core::grid::CartGrid< T >:

Public Types
typedef numeric::xyzVector< int >	GridPt

Public Member Functions
	CartGrid ()

virtual	~CartGrid ()

void	setBase (core::Real x, core::Real y, core::Real z)

void	setDimensions (int nX, int nY, int nZ, core::Real lX, core::Real lY, core::Real lZ)

void	set_name (std::string const &name)

std::string	get_name () const

int	longestSide () const

bool	equalDimensions (CartGrid< T > const &rhs) const

bool	equalBase (CartGrid< T > const &rhs) const

bool	is_in_grid (core::Real x, core::Real y, core::Real z) const

bool	setupZones ()

void	translate (core::Real x, core::Real y, core::Real z)

bool	setValue (int ix, int iy, int iz, T value)

bool	setValue (core::Real fx, core::Real fy, core::Real fz, T value)

T	getValue (int ix, int iy, int iz) const

T	getValue (core::Real fx, core::Real fy, core::Real fz) const

void	zero ()

void	setFullOccupied (T value)

void	clone (CartGrid< T > &copy) const

void	reset_boundaries ()

void	fluff (utility::pointer::owning_ptr< CartGrid< T > > input, utility::pointer::owning_ptr< CartGrid< T > > original, int amount=6)

void	read (std::string const &filename)

void	write (std::string const &filename) const

bool	isFullyOccupied () const

bool	isEmpty () const

utility::json_spirit::Value	serialize () const

void	deserialize (utility::json_spirit::mObject grid_data)

void	sum (utility::vector0< utility::pointer::owning_ptr< CartGrid< T > > > const &list_grids)

void	expand (int expansion)

void	split (int nsplits, int igrid, core::Real pad, utility::pointer::owning_ptr< CartGrid< T > > grid)

core::Vector	getBase () const

core::Vector	getTop () const

void	getNumberOfPoints (int &x, int &y, int &z) const

GridPt	gridpt (Vector const &coords) const

Vector	coords (GridPt const &gridpt) const

T	getValue (GridPt const &gridpt) const

T	getValue (Vector const &coords) const

T	getMinValue () const

T	getMaxValue () const

void	setValue (GridPt const &gridpt, T value)

void	setValue (Vector const &coords, T value)

void	write_to_BRIX (std::string const &filename)

void	write_to_BRIX (std::ostream &out)

Private Member Functions
void	setTop ()

void	setValue (int index, T value)

T	getValue (int index) const

int	get_index (int ix, int iy, int iz) const

Private Attributes
int	nX_

int	nY_

int	nZ_

core::Real	lX_

core::Real	lY_

core::Real	lZ_

core::Real	bX_

core::Real	bY_

core::Real	bZ_

core::Real	tX_

core::Real	tY_

core::Real	tZ_

std::string	name_

int	npoints_

bool	fullyOccupied_

T *	zones_

Detailed Description

template<typename T>
class core::grid::CartGrid< T >

Definition at line 21 of file CartGrid.fwd.hh.

Member Typedef Documentation

template<typename T>

typedef numeric::xyzVector< int > core::grid::CartGrid< T >::GridPt

Definition at line 45 of file CartGrid.hh.

Constructor & Destructor Documentation

template<typename T>

core::grid::CartGrid< T >::CartGrid ( )

inline

Definition at line 47 of file CartGrid.hh.

template<typename T>

virtual core::grid::CartGrid< T >::~CartGrid ( )

inlinevirtual

Definition at line 60 of file CartGrid.hh.

Member Function Documentation

template<typename T>

void core::grid::CartGrid< T >::clone ( CartGrid< T > & copy) const

inline

Definition at line 260 of file CartGrid.hh.

Referenced by core::grid::CartGrid< core::Real >::reset_boundaries().

template<typename T>

Vector core::grid::CartGrid< T >::coords ( GridPt const & gridpt) const

inline

Definition at line 679 of file CartGrid.hh.

Referenced by protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(), protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(), protocols::qsar::scoring_grid::SingleGrid::get_point_value_list_within_range(), protocols::qsar::scoring_grid::SingleGrid::grid_to_kin(), protocols::ligand_docking::grid_to_kin(), protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(), protocols::qsar::scoring_grid::SingleGrid::set_ring(), protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(), and protocols::ligand_docking::set_sphere().

template<typename T>

void core::grid::CartGrid< T >::deserialize ( utility::json_spirit::mObject grid_data)

inline

Definition at line 492 of file CartGrid.hh.

Referenced by protocols::qsar::scoring_grid::SingleGrid::deserialize().

template<typename T>

bool core::grid::CartGrid< T >::equalBase ( CartGrid< T > const & rhs) const

inline

Definition at line 137 of file CartGrid.hh.

Referenced by core::grid::CartGrid< core::Real >::sum().

template<typename T>

bool core::grid::CartGrid< T >::equalDimensions ( CartGrid< T > const & rhs) const

inline

Definition at line 118 of file CartGrid.hh.

Referenced by core::grid::CartGrid< core::Real >::sum().

template<typename T>

void core::grid::CartGrid< T >::expand ( int expansion)

inline

Definition at line 549 of file CartGrid.hh.

template<typename T>

void core::grid::CartGrid< T >::fluff	(	utility::pointer::owning_ptr< CartGrid< T > >	input,
		utility::pointer::owning_ptr< CartGrid< T > >	original,
		int	amount = `6`
	)

inline

Definition at line 346 of file CartGrid.hh.

template<typename T>

int core::grid::CartGrid< T >::get_index	(	int	ix,
		int	iy,
		int	iz
	)		const

inlineprivate

Definition at line 870 of file CartGrid.hh.

Referenced by core::grid::CartGrid< core::Real >::getValue(), and core::grid::CartGrid< core::Real >::setValue().

template<typename T>

std::string core::grid::CartGrid< T >::get_name ( ) const

inline

Definition at line 105 of file CartGrid.hh.

Referenced by core::grid::CartGrid< core::Real >::serialize(), and core::grid::CartGrid< core::Real >::write().

template<typename T>

core::Vector core::grid::CartGrid< T >::getBase ( ) const

inline

Definition at line 650 of file CartGrid.hh.

template<typename T>

T core::grid::CartGrid< T >::getMaxValue ( ) const

inline

Definition at line 704 of file CartGrid.hh.

Referenced by protocols::qsar::scoring_grid::SingleGrid::get_max_value().

template<typename T>

T core::grid::CartGrid< T >::getMinValue ( ) const

inline

Definition at line 699 of file CartGrid.hh.

Referenced by protocols::qsar::scoring_grid::SingleGrid::get_min_value().

template<typename T>

void core::grid::CartGrid< T >::getNumberOfPoints	(	int &	x,
		int &	y,
		int &	z
	)		const

inline

Definition at line 660 of file CartGrid.hh.

Referenced by protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(), protocols::qsar::scoring_grid::SingleGrid::get_dimensions(), protocols::qsar::scoring_grid::SingleGrid::get_point_value_list_within_range(), protocols::qsar::scoring_grid::SingleGrid::grid_to_kin(), protocols::ligand_docking::grid_to_kin(), protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(), protocols::qsar::scoring_grid::SingleGrid::set_ring(), protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(), and protocols::ligand_docking::set_sphere().

template<typename T>

core::Vector core::grid::CartGrid< T >::getTop ( ) const

inline

Definition at line 655 of file CartGrid.hh.

template<typename T>

T core::grid::CartGrid< T >::getValue	(	int	ix,
		int	iy,
		int	iz
	)		const

inline

Definition at line 221 of file CartGrid.hh.

Referenced by protocols::qsar::scoring_grid::SingleGrid::atom_score(), protocols::qsar::scoring_grid::SingleGrid::get_point(), protocols::qsar::scoring_grid::SingleGrid::get_point_value_list_within_range(), core::grid::CartGrid< core::Real >::getValue(), protocols::ligand_docking::grid_score(), protocols::ligand_docking::grid_score_atr_rep(), protocols::qsar::scoring_grid::SingleGrid::grid_to_kin(), protocols::ligand_docking::grid_to_kin(), core::grid::CartGrid< core::Real >::reset_boundaries(), protocols::qsar::scoring_grid::SingleGrid::score(), protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(), protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(), core::grid::CartGrid< core::Real >::split(), core::grid::CartGrid< core::Real >::sum(), core::grid::CartGrid< core::Real >::write(), and core::grid::CartGrid< core::Real >::write_to_BRIX().

template<typename T>

T core::grid::CartGrid< T >::getValue	(	core::Real	fx,
		core::Real	fy,
		core::Real	fz
	)		const

inline

Definition at line 227 of file CartGrid.hh.

template<typename T>

T core::grid::CartGrid< T >::getValue ( GridPt const & gridpt) const

inline

Definition at line 689 of file CartGrid.hh.

template<typename T>

T core::grid::CartGrid< T >::getValue ( Vector const & coords) const

inline

Definition at line 694 of file CartGrid.hh.

template<typename T>

T core::grid::CartGrid< T >::getValue ( int index) const

inlineprivate

Definition at line 859 of file CartGrid.hh.

template<typename T>

GridPt core::grid::CartGrid< T >::gridpt ( Vector const & coords) const

inline

Definition at line 667 of file CartGrid.hh.

Referenced by protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(), protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(), protocols::qsar::scoring_grid::SingleGrid::set_ring(), protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(), protocols::ligand_docking::set_sphere(), and core::grid::CartGrid< core::Real >::write_to_BRIX().

template<typename T>

bool core::grid::CartGrid< T >::is_in_grid	(	core::Real	x,
		core::Real	y,
		core::Real	z
	)		const

inline

Definition at line 145 of file CartGrid.hh.

template<typename T>

bool core::grid::CartGrid< T >::isEmpty ( ) const

inline

Definition at line 464 of file CartGrid.hh.

template<typename T>

bool core::grid::CartGrid< T >::isFullyOccupied ( ) const

inline

Definition at line 460 of file CartGrid.hh.

template<typename T>

int core::grid::CartGrid< T >::longestSide ( ) const

inline

Definition at line 110 of file CartGrid.hh.

template<typename T>

void core::grid::CartGrid< T >::read ( std::string const & filename)

inline

Definition at line 376 of file CartGrid.hh.

template<typename T>

void core::grid::CartGrid< T >::reset_boundaries ( )

inline

Definition at line 287 of file CartGrid.hh.

template<typename T>

utility::json_spirit::Value core::grid::CartGrid< T >::serialize ( ) const

inline

Definition at line 473 of file CartGrid.hh.

Referenced by protocols::qsar::scoring_grid::SingleGrid::serialize().

template<typename T>

void core::grid::CartGrid< T >::set_name ( std::string const & name)

inline

Definition at line 100 of file CartGrid.hh.

Referenced by core::grid::CartGrid< core::Real >::deserialize(), and core::grid::CartGrid< core::Real >::read().

template<typename T>

void core::grid::CartGrid< T >::setBase	(	core::Real	x,
		core::Real	y,
		core::Real	z
	)

inline

Definition at line 78 of file CartGrid.hh.

Referenced by core::grid::CartGrid< core::Real >::deserialize(), protocols::qsar::scoring_grid::SingleGrid::initialize(), protocols::ligand_docking::make_atr_rep_grid(), protocols::ligand_docking::make_atr_rep_grid_without_ligands(), and core::grid::CartGrid< core::Real >::read().

template<typename T>

void core::grid::CartGrid< T >::setDimensions	(	int	nX,
		int	nY,
		int	nZ,
		core::Real	lX,
		core::Real	lY,
		core::Real	lZ
	)

inline

Definition at line 87 of file CartGrid.hh.

Referenced by core::grid::CartGrid< core::Real >::deserialize(), protocols::qsar::scoring_grid::SingleGrid::initialize(), and core::grid::CartGrid< core::Real >::read().

template<typename T>

void core::grid::CartGrid< T >::setFullOccupied ( T value)

inline

Definition at line 251 of file CartGrid.hh.

Referenced by protocols::qsar::scoring_grid::SingleGrid::fill_with_value().

template<typename T>

void core::grid::CartGrid< T >::setTop ( )

inlineprivate

Definition at line 842 of file CartGrid.hh.

Referenced by core::grid::CartGrid< core::Real >::setBase(), core::grid::CartGrid< core::Real >::setDimensions(), and core::grid::CartGrid< core::Real >::translate().

template<typename T>

bool core::grid::CartGrid< T >::setupZones ( )

inline

Definition at line 163 of file CartGrid.hh.

Referenced by core::grid::CartGrid< core::Real >::deserialize(), core::grid::CartGrid< core::Real >::expand(), protocols::qsar::scoring_grid::SingleGrid::initialize(), core::grid::CartGrid< core::Real >::read(), and core::grid::CartGrid< core::Real >::reset_boundaries().

template<typename T>

bool core::grid::CartGrid< T >::setValue	(	int	ix,
		int	iy,
		int	iz,
		T	value
	)

inline

Definition at line 186 of file CartGrid.hh.

Referenced by protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(), core::grid::CartGrid< core::Real >::fluff(), core::grid::CartGrid< core::Real >::read(), core::grid::CartGrid< core::Real >::reset_boundaries(), protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(), protocols::qsar::scoring_grid::SingleGrid::set_point(), protocols::qsar::scoring_grid::SingleGrid::set_ring(), protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(), protocols::ligand_docking::set_sphere(), core::grid::CartGrid< core::Real >::setValue(), and core::grid::CartGrid< core::Real >::sum().

template<typename T>

bool core::grid::CartGrid< T >::setValue	(	core::Real	fx,
		core::Real	fy,
		core::Real	fz,
		T	value
	)

inline

Definition at line 200 of file CartGrid.hh.

template<typename T>

void core::grid::CartGrid< T >::setValue	(	GridPt const &	gridpt,
		T	value
	)

inline

Definition at line 709 of file CartGrid.hh.

template<typename T>

void core::grid::CartGrid< T >::setValue	(	Vector const &	coords,
		T	value
	)

inline

Definition at line 714 of file CartGrid.hh.

template<typename T>

void core::grid::CartGrid< T >::setValue	(	int	index,
		T	value
	)

inlineprivate

Definition at line 849 of file CartGrid.hh.

template<typename T>

void core::grid::CartGrid< T >::split	(	int	nsplits,
		int	igrid,
		core::Real	pad,
		utility::pointer::owning_ptr< CartGrid< T > >	grid
	)

inline

Definition at line 561 of file CartGrid.hh.

template<typename T>

void core::grid::CartGrid< T >::sum ( utility::vector0< utility::pointer::owning_ptr< CartGrid< T > > > const & list_grids)

inline

Definition at line 527 of file CartGrid.hh.

template<typename T>

void core::grid::CartGrid< T >::translate	(	core::Real	x,
		core::Real	y,
		core::Real	z
	)

inline

Definition at line 178 of file CartGrid.hh.

template<typename T>

void core::grid::CartGrid< T >::write ( std::string const & filename) const

inline

Definition at line 440 of file CartGrid.hh.

template<typename T>

void core::grid::CartGrid< T >::write_to_BRIX ( std::string const & filename)

inline

This format was choosen because it's space-efficient for small integer values (such as are typically stored in grids) and PyMOL can read it. Typical extension is .brix or .omap

Definition at line 722 of file CartGrid.hh.

Referenced by protocols::qsar::scoring_grid::SingleGrid::dump_BRIX(), and core::grid::CartGrid< core::Real >::write_to_BRIX().

template<typename T>

void core::grid::CartGrid< T >::write_to_BRIX ( std::ostream & out)

inline

Definition at line 729 of file CartGrid.hh.

template<typename T>

void core::grid::CartGrid< T >::zero ( )

inline

Definition at line 243 of file CartGrid.hh.

Referenced by protocols::qsar::scoring_grid::SingleGrid::initialize(), and core::grid::CartGrid< core::Real >::sum().