#include <ShapeGrid.hh>

Public Member Functions
	ShapeGrid ()

virtual	~ShapeGrid ()

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::TagCOP tag)
	setup a grid based on RosettaScripts input More...

virtual core::Real	score (core::conformation::UltraLightResidue const &residue, core::Real const max_score, qsarMapOP qsar_map)
	return the current score of an UltraLightResidue using the current grid More...

virtual core::Real	atom_score (core::conformation::UltraLightResidue const &residue, core::Size atomno, qsarMapOP qsar_map)
	return the current score of an atom using the current grid 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 grid information More...

virtual void	deserialize (utility::json_spirit::mObject data)
	deserialize the grid information 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::UltraLightResidue const &residue)
	check to see if residue is in grid More...

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 Types
typedef utility::pointer::owning_ptr < core::grid::CartGrid < core::Real > >	KBPGridOP
	data store for the KBP data. key is the name3 of the amino acid This is being done with an unordered map to allow for constant lookup but still allow for KBP data about NCAAs to be introduced eventually if needed More...

Private Member Functions
core::Real	get_score_from_angles (std::string const &name3, core::Real distance, core::Real theta, core::Real phi)
	get the appropriate score from the KBP tables More...

core::Real	get_point_score (numeric::kdtree::KDPointList const &nearest_residues, core::Vector const &query_coords)
	given a KDPointList and a set of query coordinates get the score to place in the grid More...

void	load_kbp_data ()
	the KBP data is stored as a compressed json file in the database. It is read during construction More...

Private Attributes
boost::unordered_map < std::string, KBPGridOP >	kbp_data_

core::Real	distance_bin_width_

core::Real	theta_bin_width_

core::Real	phi_bin_width_

Member Typedef Documentation

typedef utility::pointer::owning_ptr< core::grid::CartGrid<core::Real> > protocols::qsar::scoring_grid::ShapeGrid::KBPGridOP

private

data store for the KBP data. key is the name3 of the amino acid This is being done with an unordered map to allow for constant lookup but still allow for KBP data about NCAAs to be introduced eventually if needed

Constructor & Destructor Documentation

protocols::qsar::scoring_grid::ShapeGrid::ShapeGrid ( )

References distance_bin_width_, load_kbp_data(), phi_bin_width_, and theta_bin_width_.

protocols::qsar::scoring_grid::ShapeGrid::~ShapeGrid ( )

virtual

Member Function Documentation

core::Real protocols::qsar::scoring_grid::ShapeGrid::atom_score	(	core::conformation::UltraLightResidue 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.

References protocols::qsar::scoring_grid::SingleGrid::get_point().

core::Real protocols::qsar::scoring_grid::ShapeGrid::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.

References protocols::qsar::scoring_grid::SingleGrid::get_point(), and core::conformation::Residue::xyz().

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

virtual

deserialize the grid information

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

References protocols::qsar::scoring_grid::SingleGrid::deserialize().

core::Real protocols::qsar::scoring_grid::ShapeGrid::get_point_score	(	numeric::kdtree::KDPointList const &	nearest_residues,
		core::Vector const &	query_coords
	)

private

given a KDPointList and a set of query coordinates get the score to place in the grid

References numeric::angle_radians(), numeric::kdtree::KDPointList::begin(), numeric::dihedral_degrees(), distance(), numeric::kdtree::KDPointList::end(), get_score_from_angles(), protocols::stepwise::sampling::protein::phi(), residue, score(), numeric::kdtree::KDPointList::size(), and total_score.

Referenced by refresh().

core::Real protocols::qsar::scoring_grid::ShapeGrid::get_score_from_angles	(	std::string const &	name3,
		core::Real	distance,
		core::Real	theta,
		core::Real	phi
	)

private

get the appropriate score from the KBP tables

References distance_bin_width_, kbp_data_, phi_bin_width_, and theta_bin_width_.

Referenced by get_point_score().

void protocols::qsar::scoring_grid::ShapeGrid::load_kbp_data ( )

private

the KBP data is stored as a compressed json file in the database. It is read during construction

References utility::io::izstream::close(), utility::file::file_exists(), filename(), basic::database::full_name(), utility::json_spirit::Value_impl< Config >::get_array(), get_str(), kbp_data_, utility::io::izstream::open(), utility::json_spirit::read(), protocols::qsar::scoring_grid::TR, and utility_exit_with_message.

Referenced by ShapeGrid().

void protocols::qsar::scoring_grid::ShapeGrid::parse_my_tag ( utility::tag::TagCOP tag )

virtual

setup a grid based on RosettaScripts input

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

void protocols::qsar::scoring_grid::ShapeGrid::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.

Referenced by refresh().

void protocols::qsar::scoring_grid::ShapeGrid::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.

References protocols::qsar::scoring_grid::SingleGrid::fill_with_value(), protocols::qsar::scoring_grid::SingleGrid::get_chain(), core::pose::get_chain_id_from_chain(), protocols::qsar::scoring_grid::SingleGrid::get_dimensions(), protocols::qsar::scoring_grid::SingleGrid::get_pdb_coords(), get_point_score(), core::pose::Pose::n_residue(), numeric::kdtree::nearest_neighbors(), residue, core::pose::Pose::residue(), protocols::qsar::scoring_grid::SingleGrid::set_point(), numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

void protocols::qsar::scoring_grid::ShapeGrid::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.

References refresh().

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

virtual

return the current score of an UltraLightResidue using the current grid

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

References protocols::qsar::scoring_grid::SingleGrid::get_point(), core::conformation::UltraLightResidue::natoms(), and total_score.

Referenced by get_point_score().

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