#include <VdwGrid.hh>

Inheritance diagram for protocols::qsar::scoring_grid::VdwGrid:

Collaboration diagram for protocols::qsar::scoring_grid::VdwGrid:

Public Member Functions
	VdwGrid ()

virtual	~VdwGrid ()

virtual void	refresh (core::pose::Pose const &pose, core::Vector const &center, core::Size const &)
	populate the grid with values based on a passed pose More...

virtual void	refresh (core::pose::Pose const &pose, core::Vector const &center)
	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 >)
	populate the grid with values based on a passed pose More...

void	parse_my_tag (utility::tag::TagPtr const tag)
	setup a grid based on RosettaScripts input 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...

virtual utility::json_spirit::Value	serialize ()
	serialize the Interpolator to a json_spirit object More...

virtual void	deserialize (utility::json_spirit::mObject data)
	deserialize a json_spirit object to a Interpolator More...

Public Member Functions inherited from protocols::qsar::scoring_grid::SingleGrid
	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...

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...

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
numeric::interpolation::spline::InterpolatorOP	lj_spline_

core::Real	cutoff_

Detailed Description

Definition at line 28 of file VdwGrid.hh.

Constructor & Destructor Documentation

protocols::qsar::scoring_grid::VdwGrid::VdwGrid ( )

Definition at line 65 of file VdwGrid.cc.

References lj_spline_.

protocols::qsar::scoring_grid::VdwGrid::~VdwGrid ( )

virtual

Definition at line 118 of file VdwGrid.cc.

Member Function Documentation

core::Real protocols::qsar::scoring_grid::VdwGrid::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

Reimplemented from protocols::qsar::scoring_grid::SingleGrid.

Definition at line 145 of file VdwGrid.cc.

References core::conformation::Residue::atom_type(), protocols::qsar::scoring_grid::SingleGrid::get_grid(), protocols::qsar::scoring_grid::SingleGrid::get_point(), core::grid::CartGrid< T >::is_in_grid(), core::chemical::AtomType::lj_radius(), lj_spline_, and core::conformation::Residue::xyz().

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

virtual

deserialize a json_spirit object to a Interpolator

Reimplemented from protocols::qsar::scoring_grid::SingleGrid.

Definition at line 176 of file VdwGrid.cc.

References cutoff_, protocols::qsar::scoring_grid::SingleGrid::deserialize(), and lj_spline_.

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

virtual

setup a grid based on RosettaScripts input

Implements protocols::qsar::scoring_grid::SingleGrid.

Definition at line 72 of file VdwGrid.cc.

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

virtual

populate the grid with values based on a passed pose

Implements protocols::qsar::scoring_grid::SingleGrid.

Definition at line 108 of file VdwGrid.cc.

Referenced by refresh().

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

virtual

populate the grid with values based on a passed pose

Implements protocols::qsar::scoring_grid::SingleGrid.

Definition at line 77 of file VdwGrid.cc.

References core::conformation::Residue::atom_type(), core::conformation::Residue::chain(), cutoff_, protocols::qsar::scoring_grid::SingleGrid::fill_with_value(), protocols::qsar::scoring_grid::SingleGrid::get_chain(), core::pose::get_chain_id_from_chain(), core::chemical::AtomType::lj_radius(), core::pose::Pose::n_residue(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(), protocols::kinmatch::xyz(), and core::pose::Pose::xyz().

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

virtual

populate the grid with values based on a passed pose

Implements protocols::qsar::scoring_grid::SingleGrid.

Definition at line 113 of file VdwGrid.cc.

References refresh().

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