protocols::qsar::scoring_grid::SingleGrid Class Reference

#include <SingleGrid.hh>

Inheritance diagram for protocols::qsar::scoring_grid::SingleGrid:

Collaboration diagram for protocols::qsar::scoring_grid::SingleGrid:

Public Member Functions
	SingleGrid (std::string type)
virtual	~SingleGrid ()
virtual void	initialize (core::Vector const &center, core::Real width, core::Real resolution)
	initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms). More...
virtual void	set_chain (char chain)
	set the chain around which to calculate the grid More...
char	get_chain ()
	get the chain around which the grid is calculated More...
virtual void	refresh (core::pose::Pose const &pose, core::Vector const &center, core::Size const &ligand_chain_id_to_exclude)=0
	populate the grid with values based on a passed pose More...
virtual void	refresh (core::pose::Pose const &pose, core::Vector const &center, utility::vector1< core::Size > ligand_chain_ids_to_exclude)=0
	populate the grid with values based on a passed pose More...
virtual void	refresh (core::pose::Pose const &pose, core::Vector const &center)=0
	populate the grid with values based on a passed pose More...
virtual void	parse_my_tag (utility::tag::TagPtr const tag)=0
	setup a grid based on RosettaScripts input More...
virtual utility::json_spirit::Value	serialize ()
	serialize the SingleGrid to a json_spirit object More...
virtual void	deserialize (utility::json_spirit::mObject data)
	deserialize a json_spirit object to a SingleGrid More...
core::grid::CartGrid < core::Real > const &	get_grid ()
	return a constant reference to the grid More...
void	set_type (std::string type)
	set the grid type More...
virtual std::string	get_type ()
	return the grids type More...
void	set_center (core::Vector center)
	set the center of the grid More...
core::Vector	get_center ()
	get the center of the grid More...
core::Real	get_min_value () const
	get the max score value in the grid More...
core::Real	get_max_value () const
	get the minimum score value in the grid More...
core::Real	get_point (core::Real x, core::Real y, core::Real z)
	get the value of a single point in the grid based on pdb coordinates More...
core::Real	get_point (core::Vector coords)
	get the value of a single point in the grid based on pdb coordinates More...
numeric::xyzVector< core::Size >	get_dimensions ()
	get dimensions of the grid More...
core::Vector	get_pdb_coords (int x, int y, int z)
	get the pdb coordinates based on grid point coordinates More...
core::Vector	get_pdb_coords (core::grid::CartGrid< core::Real >::GridPt gridpt)
	get the pdb coordinates based on grid point coordinates More...
virtual core::Real	score (core::conformation::Residue const &residue, core::Real const max_score, qsarMapOP qsar_map)
	return the current score of a residue using the current grid More...
virtual core::Real	atom_score (core::conformation::Residue const &residue, core::Size atomno, qsarMapOP qsar_map)
	return the current score of an atom using the current grid More...
void	grid_to_kin (utility::io::ozstream &out, core::Real min_val, core::Real max_val, core::Size stride)
virtual bool	is_in_grid (core::conformation::Residue const &residue)
	check to see if residue is in grid More...
std::list< std::pair < core::Vector, core::Real > >	get_point_value_list_within_range (core::Real lower_bound, core::Real upper_bound, core::Size stride)
virtual void	dump_BRIX (std::string const &prefix)
	output a BRIX formatted grid. This really does not work well but is being left for legacy purposes More...
void	set_sphere (core::Vector const &coords, core::Real radius, core::Real value)
void	set_ring (core::Vector const &coords, core::Real inner_radius, core::Real outer_radius, core::Real value)
void	diffuse_ring (core::Vector const &coords, core::Real radius, core::Real width, core::Real magnitude)
void	set_distance_sphere (core::Vector const &coords, core::Real cutoff)
void	set_point (core::Vector const &coords, core::Real value)
void	set_distance_sphere_for_atom (core::Real const &atom_shell, core::Vector const &coords, core::Real cutoff)
void	set_score_sphere_for_atom (numeric::interpolation::spline::InterpolatorOP lj_spline, core::Vector const &coords, core::Real cutoff)
void	fill_with_value (core::Real)
	the entire grid with some value More...
Public Member Functions inherited from protocols::qsar::scoring_grid::GridBase
	GridBase ()
virtual	~GridBase ()

Private Attributes
core::grid::CartGrid< core::Real >	grid_
std::string	type_
core::Vector	center_
char	chain_

Constructor & Destructor Documentation

protocols::qsar::scoring_grid::SingleGrid::SingleGrid

(

std::string

type)

protocols::qsar::scoring_grid::SingleGrid::~SingleGrid ( )

virtual

Member Function Documentation

core::Real protocols::qsar::scoring_grid::SingleGrid::atom_score ( core::conformation::Residue const &  residue, core::Size  atomno, qsarMapOP  qsar_map  )

virtual

return the current score of an atom using the current grid

Implements protocols::qsar::scoring_grid::GridBase.

Reimplemented in protocols::qsar::scoring_grid::ChargeGrid, protocols::qsar::scoring_grid::VdwGrid, protocols::qsar::scoring_grid::HbaGrid, and protocols::qsar::scoring_grid::HbdGrid.

References core::grid::CartGrid< T >::getValue(), grid_, protocols::ligand_docking::grid_score(), core::grid::CartGrid< T >::is_in_grid(), and core::conformation::Residue::xyz().

void protocols::qsar::scoring_grid::SingleGrid::deserialize ( utility::json_spirit::mObject  data)

virtual

deserialize a json_spirit object to a SingleGrid

Implements protocols::qsar::scoring_grid::GridBase.

Reimplemented in protocols::qsar::scoring_grid::ChargeGrid, protocols::qsar::scoring_grid::VdwGrid, protocols::qsar::scoring_grid::HbdGrid, protocols::qsar::scoring_grid::HbaGrid, protocols::qsar::scoring_grid::SolvationGrid, protocols::qsar::scoring_grid::RepGrid, protocols::qsar::scoring_grid::AtrGrid, and protocols::qsar::scoring_grid::ClassicGrid.

References center_, core::grid::CartGrid< T >::deserialize(), grid_, and type_.

Referenced by protocols::qsar::scoring_grid::ClassicGrid::deserialize(), protocols::qsar::scoring_grid::AtrGrid::deserialize(), protocols::qsar::scoring_grid::RepGrid::deserialize(), protocols::qsar::scoring_grid::HbaGrid::deserialize(), protocols::qsar::scoring_grid::SolvationGrid::deserialize(), protocols::qsar::scoring_grid::HbdGrid::deserialize(), protocols::qsar::scoring_grid::VdwGrid::deserialize(), and protocols::qsar::scoring_grid::ChargeGrid::deserialize().

void protocols::qsar::scoring_grid::SingleGrid::diffuse_ring	(	core::Vector const &	coords,
		core::Real	radius,
		core::Real	width,
		core::Real	magnitude
	)

References core::grid::CartGrid< T >::coords(), core::kinematics::tree::distance_squared(), core::grid::CartGrid< T >::getNumberOfPoints(), grid_, core::grid::CartGrid< T >::gridpt(), and core::grid::CartGrid< T >::setValue().

void protocols::qsar::scoring_grid::SingleGrid::dump_BRIX ( std::string const &  prefix)

virtual

output a BRIX formatted grid. This really does not work well but is being left for legacy purposes

Implements protocols::qsar::scoring_grid::GridBase.

References grid_, type_, and core::grid::CartGrid< T >::write_to_BRIX().

void protocols::qsar::scoring_grid::SingleGrid::fill_with_value

(

core::Real

value)

the entire grid with some value

References grid_, and core::grid::CartGrid< T >::setFullOccupied().

Referenced by protocols::qsar::scoring_grid::HbaGrid::refresh(), protocols::qsar::scoring_grid::HbdGrid::refresh(), and protocols::qsar::scoring_grid::VdwGrid::refresh().

core::Vector protocols::qsar::scoring_grid::SingleGrid::get_center

(

)

get the center of the grid

References center_.

char protocols::qsar::scoring_grid::SingleGrid::get_chain

(

)

get the chain around which the grid is calculated

References chain_.

Referenced by protocols::qsar::scoring_grid::VdwGrid::refresh(), and protocols::qsar::scoring_grid::ChargeGrid::setup_charge_atoms().

numeric::xyzVector< core::Size > protocols::qsar::scoring_grid::SingleGrid::get_dimensions

(

)

get dimensions of the grid

References core::grid::CartGrid< T >::getNumberOfPoints(), and grid_.

Referenced by protocols::qsar::scoring_grid::SolvationGrid::refresh(), and protocols::qsar::scoring_grid::ChargeGrid::refresh().

core::grid::CartGrid< core::Real > const & protocols::qsar::scoring_grid::SingleGrid::get_grid

(

)

return a constant reference to the grid

References grid_.

Referenced by protocols::qsar::scoring_grid::HbaGrid::atom_score(), protocols::qsar::scoring_grid::HbdGrid::atom_score(), protocols::qsar::scoring_grid::VdwGrid::atom_score(), protocols::qsar::scoring_grid::ChargeGrid::atom_score(), protocols::qsar::scoring_grid::HbdGrid::score(), protocols::qsar::scoring_grid::HbaGrid::score(), protocols::qsar::scoring_grid::VdwGrid::score(), and protocols::qsar::scoring_grid::ChargeGrid::score().

core::Real protocols::qsar::scoring_grid::SingleGrid::get_max_value

(

)

const

get the minimum score value in the grid

References core::grid::CartGrid< T >::getMaxValue(), and grid_.

core::Real protocols::qsar::scoring_grid::SingleGrid::get_min_value

(

)

const

get the max score value in the grid

References core::grid::CartGrid< T >::getMinValue(), and grid_.

core::Vector protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords	(	int	x,
		int	y,
		int	z
	)

get the pdb coordinates based on grid point coordinates

Referenced by protocols::qsar::scoring_grid::SolvationGrid::refresh(), and protocols::qsar::scoring_grid::ChargeGrid::refresh().

core::Vector protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords

(

core::grid::CartGrid< core::Real >::GridPt

gridpt)

get the pdb coordinates based on grid point coordinates

References core::grid::CartGrid< T >::coords(), and grid_.

core::Real protocols::qsar::scoring_grid::SingleGrid::get_point	(	core::Real	x,
		core::Real	y,
		core::Real	z
	)

get the value of a single point in the grid based on pdb coordinates

References core::grid::CartGrid< T >::getValue(), grid_, and core::grid::CartGrid< T >::is_in_grid().

Referenced by protocols::qsar::scoring_grid::HbaGrid::atom_score(), protocols::qsar::scoring_grid::HbdGrid::atom_score(), protocols::qsar::scoring_grid::VdwGrid::atom_score(), protocols::qsar::scoring_grid::ChargeGrid::atom_score(), protocols::qsar::scoring_grid::HbdGrid::score(), protocols::qsar::scoring_grid::HbaGrid::score(), protocols::qsar::scoring_grid::VdwGrid::score(), and protocols::qsar::scoring_grid::ChargeGrid::score().

core::Real protocols::qsar::scoring_grid::SingleGrid::get_point

(

core::Vector

coords)

get the value of a single point in the grid based on pdb coordinates

References core::grid::CartGrid< T >::getValue(), and grid_.

std::list< std::pair< core::Vector, core::Real > > protocols::qsar::scoring_grid::SingleGrid::get_point_value_list_within_range	(	core::Real	lower_bound,
		core::Real	upper_bound,
		core::Size	stride
	)

References core::grid::CartGrid< T >::coords(), core::grid::CartGrid< T >::getNumberOfPoints(), core::grid::CartGrid< T >::getValue(), and grid_.

std::string protocols::qsar::scoring_grid::SingleGrid::get_type ( )

virtual

return the grids type

Implements protocols::qsar::scoring_grid::GridBase.

References type_.

void protocols::qsar::scoring_grid::SingleGrid::grid_to_kin	(	utility::io::ozstream &	out,
		core::Real	min_val,
		core::Real	max_val,
		core::Size	stride
	)

References core::grid::CartGrid< T >::coords(), core::grid::CartGrid< T >::getNumberOfPoints(), core::grid::CartGrid< T >::getValue(), and grid_.

void protocols::qsar::scoring_grid::SingleGrid::initialize ( core::Vector const &  center, core::Real  width, core::Real  resolution  )

virtual

initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms).

Implements protocols::qsar::scoring_grid::GridBase.

References center_, grid_, core::grid::CartGrid< T >::setBase(), core::grid::CartGrid< T >::setDimensions(), core::grid::CartGrid< T >::setupZones(), and core::grid::CartGrid< T >::zero().

bool protocols::qsar::scoring_grid::SingleGrid::is_in_grid ( core::conformation::Residue const &  residue)

virtual

check to see if residue is in grid

Implements protocols::qsar::scoring_grid::GridBase.

References grid_, core::grid::CartGrid< T >::is_in_grid(), core::conformation::Residue::natoms(), and core::conformation::Residue::xyz().

virtual void protocols::qsar::scoring_grid::SingleGrid::parse_my_tag ( utility::tag::TagPtr const  tag)

pure virtual

setup a grid based on RosettaScripts input

Implements protocols::qsar::scoring_grid::GridBase.

Implemented in protocols::qsar::scoring_grid::ChargeGrid, protocols::qsar::scoring_grid::HbdGrid, protocols::qsar::scoring_grid::HbaGrid, protocols::qsar::scoring_grid::RepGrid, protocols::qsar::scoring_grid::AtrGrid, protocols::qsar::scoring_grid::ClassicGrid, protocols::qsar::scoring_grid::VdwGrid, and protocols::qsar::scoring_grid::SolvationGrid.

virtual void protocols::qsar::scoring_grid::SingleGrid::refresh ( core::pose::Pose const &  pose, core::Vector const &  center, core::Size const &  ligand_chain_id_to_exclude  )

pure virtual

populate the grid with values based on a passed pose

Implements protocols::qsar::scoring_grid::GridBase.

Implemented in protocols::qsar::scoring_grid::ChargeGrid, protocols::qsar::scoring_grid::VdwGrid, protocols::qsar::scoring_grid::HbaGrid, protocols::qsar::scoring_grid::HbdGrid, protocols::qsar::scoring_grid::SolvationGrid, protocols::qsar::scoring_grid::RepGrid, protocols::qsar::scoring_grid::AtrGrid, and protocols::qsar::scoring_grid::ClassicGrid.

virtual void protocols::qsar::scoring_grid::SingleGrid::refresh ( core::pose::Pose const &  pose, core::Vector const &  center, utility::vector1< core::Size >  ligand_chain_ids_to_exclude  )

pure virtual

populate the grid with values based on a passed pose

Implements protocols::qsar::scoring_grid::GridBase.

Implemented in protocols::qsar::scoring_grid::ChargeGrid, protocols::qsar::scoring_grid::VdwGrid, protocols::qsar::scoring_grid::HbaGrid, protocols::qsar::scoring_grid::HbdGrid, protocols::qsar::scoring_grid::SolvationGrid, protocols::qsar::scoring_grid::RepGrid, protocols::qsar::scoring_grid::AtrGrid, and protocols::qsar::scoring_grid::ClassicGrid.

virtual void protocols::qsar::scoring_grid::SingleGrid::refresh ( core::pose::Pose const &  pose, core::Vector const &  center  )

pure virtual

populate the grid with values based on a passed pose

Implements protocols::qsar::scoring_grid::GridBase.

Implemented in protocols::qsar::scoring_grid::ChargeGrid, protocols::qsar::scoring_grid::VdwGrid, protocols::qsar::scoring_grid::HbaGrid, protocols::qsar::scoring_grid::HbdGrid, protocols::qsar::scoring_grid::SolvationGrid, protocols::qsar::scoring_grid::RepGrid, protocols::qsar::scoring_grid::AtrGrid, and protocols::qsar::scoring_grid::ClassicGrid.

core::Real protocols::qsar::scoring_grid::SingleGrid::score ( core::conformation::Residue const &  residue, core::Real const  max_score, qsarMapOP  qsar_map  )

virtual

return the current score of a residue using the current grid

Implements protocols::qsar::scoring_grid::GridBase.

Reimplemented in protocols::qsar::scoring_grid::ChargeGrid, protocols::qsar::scoring_grid::VdwGrid, protocols::qsar::scoring_grid::HbaGrid, and protocols::qsar::scoring_grid::HbdGrid.

References core::grid::CartGrid< T >::getValue(), grid_, protocols::ligand_docking::grid_score(), core::grid::CartGrid< T >::is_in_grid(), core::conformation::Residue::nheavyatoms(), and core::conformation::Residue::xyz().

utility::json_spirit::Value protocols::qsar::scoring_grid::SingleGrid::serialize ( )

virtual

serialize the SingleGrid to a json_spirit object

Implements protocols::qsar::scoring_grid::GridBase.

Reimplemented in protocols::qsar::scoring_grid::ChargeGrid, protocols::qsar::scoring_grid::VdwGrid, protocols::qsar::scoring_grid::HbdGrid, protocols::qsar::scoring_grid::HbaGrid, protocols::qsar::scoring_grid::SolvationGrid, protocols::qsar::scoring_grid::RepGrid, protocols::qsar::scoring_grid::AtrGrid, and protocols::qsar::scoring_grid::ClassicGrid.

References center_, chain_, grid_, core::grid::CartGrid< T >::serialize(), and type_.

Referenced by protocols::qsar::scoring_grid::ClassicGrid::serialize(), protocols::qsar::scoring_grid::AtrGrid::serialize(), protocols::qsar::scoring_grid::RepGrid::serialize(), protocols::qsar::scoring_grid::HbaGrid::serialize(), protocols::qsar::scoring_grid::SolvationGrid::serialize(), protocols::qsar::scoring_grid::HbdGrid::serialize(), protocols::qsar::scoring_grid::VdwGrid::serialize(), and protocols::qsar::scoring_grid::ChargeGrid::serialize().

void protocols::qsar::scoring_grid::SingleGrid::set_center

(

core::Vector

center)

set the center of the grid

References center_.

void protocols::qsar::scoring_grid::SingleGrid::set_chain ( char  chain)

virtual

set the chain around which to calculate the grid

Implements protocols::qsar::scoring_grid::GridBase.

References chain_.

void protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere	(	core::Vector const &	coords,
		core::Real	cutoff
	)

void protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom	(	core::Real const &	atom_shell,
		core::Vector const &	coords,
		core::Real	cutoff
	)

References core::grid::CartGrid< T >::coords(), core::kinematics::distance(), core::grid::CartGrid< T >::getNumberOfPoints(), core::grid::CartGrid< T >::getValue(), grid_, core::grid::CartGrid< T >::gridpt(), and core::grid::CartGrid< T >::setValue().

Referenced by protocols::qsar::scoring_grid::VdwGrid::refresh().

void protocols::qsar::scoring_grid::SingleGrid::set_point	(	core::Vector const &	coords,
		core::Real	value
	)

References grid_, and core::grid::CartGrid< T >::setValue().

Referenced by protocols::qsar::scoring_grid::SolvationGrid::refresh(), and protocols::qsar::scoring_grid::ChargeGrid::refresh().

void protocols::qsar::scoring_grid::SingleGrid::set_ring	(	core::Vector const &	coords,
		core::Real	inner_radius,
		core::Real	outer_radius,
		core::Real	value
	)

References core::grid::CartGrid< T >::coords(), core::grid::CartGrid< T >::getNumberOfPoints(), grid_, core::grid::CartGrid< T >::gridpt(), and core::grid::CartGrid< T >::setValue().

Referenced by protocols::qsar::scoring_grid::AtrGrid::set_ligand_rings(), protocols::qsar::scoring_grid::AtrGrid::set_protein_rings(), and set_sphere().

void protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom	(	numeric::interpolation::spline::InterpolatorOP	lj_spline,
		core::Vector const &	coords,
		core::Real	cutoff
	)

References core::grid::CartGrid< T >::coords(), core::kinematics::distance(), core::grid::CartGrid< T >::getNumberOfPoints(), core::grid::CartGrid< T >::getValue(), grid_, core::grid::CartGrid< T >::gridpt(), and core::grid::CartGrid< T >::setValue().

Referenced by protocols::qsar::scoring_grid::HbaGrid::refresh(), and protocols::qsar::scoring_grid::HbdGrid::refresh().

void protocols::qsar::scoring_grid::SingleGrid::set_sphere	(	core::Vector const &	coords,
		core::Real	radius,
		core::Real	value
	)

References set_ring().

Referenced by protocols::qsar::scoring_grid::ClassicGrid::refresh(), and protocols::qsar::scoring_grid::RepGrid::refresh().

void protocols::qsar::scoring_grid::SingleGrid::set_type

(

std::string

type)

set the grid type

References type_.

Member Data Documentation

core::Vector protocols::qsar::scoring_grid::SingleGrid::center_

private

Referenced by deserialize(), get_center(), initialize(), serialize(), and set_center().

char protocols::qsar::scoring_grid::SingleGrid::chain_

private

Referenced by get_chain(), serialize(), and set_chain().

core::grid::CartGrid<core::Real> protocols::qsar::scoring_grid::SingleGrid::grid_

private

Referenced by atom_score(), deserialize(), diffuse_ring(), dump_BRIX(), fill_with_value(), get_dimensions(), get_grid(), get_max_value(), get_min_value(), get_pdb_coords(), get_point(), get_point_value_list_within_range(), grid_to_kin(), initialize(), is_in_grid(), score(), serialize(), set_distance_sphere_for_atom(), set_point(), set_ring(), and set_score_sphere_for_atom().

std::string protocols::qsar::scoring_grid::SingleGrid::type_

private

Referenced by deserialize(), dump_BRIX(), get_type(), serialize(), and set_type().

---

The documentation for this class was generated from the following files:

• src/protocols/qsar/scoring_grid/SingleGrid.hh
• src/protocols/qsar/scoring_grid/SingleGrid.cc