#include <ChargeGrid.hh>

Inheritance diagram for protocols::qsar::scoring_grid::ChargeGrid:

Collaboration diagram for protocols::qsar::scoring_grid::ChargeGrid:

Public Member Functions
	ChargeGrid ()

	ChargeGrid (core::Real charge)

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

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...

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 Member Functions
core::Real	nominal_depth (core::Size const &n_atoms) const
	calculate nominal depth based on atom count within 4 Angstroms. See Table 2 of the 1985 Goodford Paper More...

core::Real	charge_charge_electrostatic (core::pose::Pose const &pose, ChargeAtom const &atom_q, ChargeAtom const &atom_p) const

void	setup_charge_atoms (core::pose::Pose const &pose)

Private Attributes
core::Real	zeta_

core::Real	epsilon_

core::Real	indirect_numerator_

core::Real	epsilon_0_

std::list< ChargeAtom >	charge_atom_list_

Detailed Description

Definition at line 51 of file ChargeGrid.hh.

Constructor & Destructor Documentation

protocols::qsar::scoring_grid::ChargeGrid::ChargeGrid ( )

Definition at line 79 of file ChargeGrid.cc.

protocols::qsar::scoring_grid::ChargeGrid::ChargeGrid ( core::Real charge)

Definition at line 89 of file ChargeGrid.cc.

Member Function Documentation

core::Real protocols::qsar::scoring_grid::ChargeGrid::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 216 of file ChargeGrid.cc.

References core::conformation::Residue::atomic_charge(), protocols::qsar::scoring_grid::SingleGrid::get_grid(), protocols::qsar::scoring_grid::SingleGrid::get_point(), core::grid::CartGrid< T >::is_in_grid(), and core::conformation::Residue::xyz().

core::Real protocols::qsar::scoring_grid::ChargeGrid::charge_charge_electrostatic	(	core::pose::Pose const &	pose,
		ChargeAtom const &	atom_q,
		ChargeAtom const &	atom_p
	)		const

private

Definition at line 264 of file ChargeGrid.cc.

References protocols::qsar::scoring_grid::ChargeAtom::charge, core::kinematics::distance(), epsilon_0_, indirect_numerator_, protocols::qsar::scoring_grid::ChargeAtom::neighbor_count, nominal_depth(), protocols::qsar::scoring_grid::ChargeAtom::xyz, and zeta_.

Referenced by refresh().

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

virtual

deserialize a json_spirit object to a SingleGrid

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

Definition at line 117 of file ChargeGrid.cc.

References charge_atom_list_, protocols::qsar::scoring_grid::ChargeAtom::deserialize(), and protocols::qsar::scoring_grid::SingleGrid::deserialize().

core::Real protocols::qsar::scoring_grid::ChargeGrid::nominal_depth ( core::Size const & n_atoms) const

private

calculate nominal depth based on atom count within 4 Angstroms. See Table 2 of the 1985 Goodford Paper

Definition at line 229 of file ChargeGrid.cc.

Referenced by charge_charge_electrostatic().

void protocols::qsar::scoring_grid::ChargeGrid::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 193 of file ChargeGrid.cc.

void protocols::qsar::scoring_grid::ChargeGrid::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 182 of file ChargeGrid.cc.

Referenced by refresh().

void protocols::qsar::scoring_grid::ChargeGrid::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 133 of file ChargeGrid.cc.

References charge_atom_list_, charge_charge_electrostatic(), protocols::qsar::scoring_grid::SingleGrid::get_dimensions(), protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(), protocols::sic_dock::neighbor_count(), protocols::qsar::scoring_grid::SingleGrid::set_point(), and setup_charge_atoms().

void protocols::qsar::scoring_grid::ChargeGrid::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 187 of file ChargeGrid.cc.

References refresh().

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