#include <PCSSingleGrid.hh>

Inheritance diagram for protocols::qsar::scoring_grid::PCSSingleGrid:

Public Types
typedef core::scoring::nmr::pcs::PCSSingle	PCSSingle

typedef core::scoring::nmr::pcs::PCSSingleOP	PCSSingleOP

typedef core::scoring::nmr::pcs::PCSTensor	PCSTensor

typedef core::scoring::nmr::pcs::PCSTensorOP	PCSTensorOP

typedef core::scoring::nmr::pcs::PCSTensorCOP	PCSTensorCOP

typedef core::pose::Pose	Pose

typedef core::conformation::Residue	Residue

typedef core::conformation::UltraLightResidue	UltraLightResidue

typedef core::Real	Real

typedef core::Size	Size

typedef core::Vector	Vector

Public Member Functions
	PCSSingleGrid ()
	Default constructor. More...

	PCSSingleGrid (std::string const &filename, PCSTensorOP tensor, Real const weight=1.0)
	construct from PCS datafile and fixed PCS tensor More...

	PCSSingleGrid (std::string const &filename, utility::vector1< Real > const &tensor_vals, Real const weight=1.0)
	construct from PCS datafile and vector of PCS tensor values More...

	PCSSingleGrid (std::string const &filename, PCSTensorOP tensor, Pose const &pose, Real const weight=1.0)
	construct from PCS datafile and fixed PCS tensor More...

	PCSSingleGrid (std::string const &filename, utility::vector1< Real > const &tensor_vals, Pose const &pose, Real const weight=1.0)
	construct from PCS datafile and vector of PCS tensor values More...

	PCSSingleGrid (PCSSingleGrid const &other)
	copy constructor More...

PCSSingleGrid &	operator= (PCSSingleGrid const &rhs)
	copy assignment More...

GridBaseOP	clone () const override
	Make a copy of the grid, respecting the subclassing. More...

void	refresh (Pose const &pose, Vector const &center) override
	populate the grid with PCS values based on a passed pose More...

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

void	refresh (Pose const &pose, Vector const &center, utility::vector1< core::Size > ligand_chain_ids_to_exclude) override
	populate the grid with PCS values based on a passed pose More...

Real	score (UltraLightResidue const &residue, Real const max_score, qsarMapCOP qsar_map) const override
	return the current score of an UltraLightResidue using the current PCSSingleGrid More...

Real	atom_score (UltraLightResidue const &residue, core::Size atomno, qsarMapCOP qsar_map) const override
	return the current score of an atom using the current PCSSingleGrid More...

Real	score (Residue const &residue, Real const max_score, qsarMapCOP qsar_map) const override
	return the current score of a residue using the current PCSSingleGrid More...

Real	atom_score (Residue const &residue, core::Size atomno, qsarMapCOP qsar_map) const override
	return the current score of an atom using the current PCSSingleGrid More...

utility::json_spirit::Value	serialize () const override
	serialize the PCSSingleGrid to a json_spirit object More...

void	deserialize (utility::json_spirit::mObject data) override
	deserialize a json_spirit object to a PCSSingleGrid More...

void	parse_my_tag (utility::tag::TagCOP tag) override
	setup a PCSSingleGrid based on RosettaScripts input More...

std::string	hash_fingerprint () const override
	Return a string representing the settings which don't change based on reinitialization. More...

utility::vector1< PCSSingleOP > const &	get_pcs_values () const

PCSTensorCOP	get_tensor () const

Real	get_weight () const

void	set_weight (Real w)

Public Member Functions inherited from protocols::qsar::scoring_grid::SingleGrid
	SingleGrid (std::string const &type)

	~SingleGrid () override

void	initialize (core::Vector const &center, core::Real width, core::Real resolution) override
	initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms). More...

void	set_chain (char chain) override
	set the chain around which to calculate the grid More...

char	get_chain ()
	get the chain around which the grid is calculated More...

utility::json_spirit::Value	serialize () const override
	serialize the SingleGrid to a json_spirit object More...

void	deserialize (utility::json_spirit::mObject data) override
	deserialize a json_spirit object to a SingleGrid More...

core::grid::CartGrid < core::Real > const &	get_grid () const
	return a constant reference to the grid More...

void	set_type (std::string type)
	set the grid type More...

std::string	get_type () const override
	return the grids type More...

void	set_center (core::Vector center)
	set the center of the grid More...

core::Vector	get_center () const
	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) const
	get the value of a single point in the grid based on pdb coordinates More...

core::Real	get_point (core::Vector coords) const
	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...

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

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

core::Real	score (core::conformation::Residue const &residue, core::Real const max_score, qsarMapCOP qsar_map) const override
	return the current score of a residue using the current grid More...

core::Real	atom_score (core::conformation::Residue const &residue, core::Size atomno, qsarMapCOP qsar_map) const override
	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)

bool	is_in_grid (core::conformation::UltraLightResidue const &residue) const override
	check to see if residue is in grid More...

bool	is_in_grid (core::conformation::Residue const &residue) const override
	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) const

void	dump_BRIX (std::string const &prefix) const override
	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_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::InterpolatorCOP lj_spline, core::Vector const &coords, core::Real cutoff)

void	fill_with_value (core::Real)
	the entire grid with some value More...

void	show (std::ostream &out) const override
	Print a brief summary about this grid to the provided output stream. More...

Public Member Functions inherited from protocols::qsar::scoring_grid::GridBase
	GridBase ()

	~GridBase () override

Static Public Member Functions
static std::string	grid_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Private Member Functions
void	init_pcs_values_from_file (std::string const &filename, Pose const &pose)

Private Attributes
std::string	pcs_file_

utility::vector1< PCSSingleOP >	pcs_values_

PCSTensorOP	tensor_

Real	weight_

Member Typedef Documentation

typedef core::scoring::nmr::pcs::PCSSingle protocols::qsar::scoring_grid::PCSSingleGrid::PCSSingle

typedef core::scoring::nmr::pcs::PCSSingleOP protocols::qsar::scoring_grid::PCSSingleGrid::PCSSingleOP

typedef core::scoring::nmr::pcs::PCSTensor protocols::qsar::scoring_grid::PCSSingleGrid::PCSTensor

typedef core::scoring::nmr::pcs::PCSTensorCOP protocols::qsar::scoring_grid::PCSSingleGrid::PCSTensorCOP

typedef core::scoring::nmr::pcs::PCSTensorOP protocols::qsar::scoring_grid::PCSSingleGrid::PCSTensorOP

typedef core::pose::Pose protocols::qsar::scoring_grid::PCSSingleGrid::Pose

typedef core::Real protocols::qsar::scoring_grid::PCSSingleGrid::Real

typedef core::conformation::Residue protocols::qsar::scoring_grid::PCSSingleGrid::Residue

typedef core::Size protocols::qsar::scoring_grid::PCSSingleGrid::Size

typedef core::conformation::UltraLightResidue protocols::qsar::scoring_grid::PCSSingleGrid::UltraLightResidue

typedef core::Vector protocols::qsar::scoring_grid::PCSSingleGrid::Vector

Constructor & Destructor Documentation

protocols::qsar::scoring_grid::PCSSingleGrid::PCSSingleGrid ( )

Default constructor.

default constructor

Referenced by clone().

protocols::qsar::scoring_grid::PCSSingleGrid::PCSSingleGrid	(	std::string const &	filename,
		PCSTensorOP	tensor,
		Real const	weight = `1.0`
	)

construct from PCS datafile and fixed PCS tensor

protocols::qsar::scoring_grid::PCSSingleGrid::PCSSingleGrid	(	std::string const &	filename,
		utility::vector1< Real > const &	tensor_vals,
		Real const	weight = `1.0`
	)

construct from PCS datafile and vector of PCS tensor values

References tensor_.

protocols::qsar::scoring_grid::PCSSingleGrid::PCSSingleGrid	(	std::string const &	filename,
		PCSTensorOP	tensor,
		Pose const &	pose,
		Real const	weight = `1.0`
	)

construct from PCS datafile and fixed PCS tensor

References init_pcs_values_from_file().

protocols::qsar::scoring_grid::PCSSingleGrid::PCSSingleGrid	(	std::string const &	filename,
		utility::vector1< Real > const &	tensor_vals,
		Pose const &	pose,
		Real const	weight = `1.0`
	)

construct from PCS datafile and vector of PCS tensor values

References init_pcs_values_from_file().

protocols::qsar::scoring_grid::PCSSingleGrid::PCSSingleGrid ( PCSSingleGrid const & other )

copy constructor

References pcs_values_.

Member Function Documentation

core::Real protocols::qsar::scoring_grid::PCSSingleGrid::atom_score	(	UltraLightResidue const &	residue,
		core::Size	atomno,
		qsarMapCOP	qsar_map
	)		const

overridevirtual

return the current score of an atom using the current PCSSingleGrid

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

References core::conformation::UltraLightResidue::residue().

Referenced by atom_score().

core::Real protocols::qsar::scoring_grid::PCSSingleGrid::atom_score	(	Residue const &	residue,
		core::Size	atomno,
		qsarMapCOP	qsar_map
	)		const

overridevirtual

return the current score of an atom using the current PCSSingleGrid

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

References atom_score(), protocols::qsar::scoring_grid::SingleGrid::get_grid(), core::grid::CartGrid< T >::getValue(), protocols::qsar::scoring_grid::SingleGrid::is_in_grid(), core::scoring::pcs, pcs_values_, core::conformation::Residue::seqpos(), weight_, and core::conformation::Residue::xyz().

GridBaseOP protocols::qsar::scoring_grid::PCSSingleGrid::clone ( ) const

overridevirtual

Make a copy of the grid, respecting the subclassing.

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

References PCSSingleGrid().

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

overridevirtual

deserialize a json_spirit object to a PCSSingleGrid

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

References protocols::qsar::scoring_grid::SingleGrid::deserialize(), core::scoring::pcs, pcs_file_, pcs_values_, tensor_, and weight_.

utility::vector1<PCSSingleOP> const& protocols::qsar::scoring_grid::PCSSingleGrid::get_pcs_values ( ) const

inline

References pcs_values_.

PCSTensorCOP protocols::qsar::scoring_grid::PCSSingleGrid::get_tensor ( ) const

inline

References tensor_.

Real protocols::qsar::scoring_grid::PCSSingleGrid::get_weight ( ) const

inline

References weight_.

std::string protocols::qsar::scoring_grid::PCSSingleGrid::grid_name ( )

static

Referenced by hash_fingerprint(), protocols::qsar::scoring_grid::PCSSingleGridCreator::keyname(), and provide_xml_schema().

std::string protocols::qsar::scoring_grid::PCSSingleGrid::hash_fingerprint ( ) const

overridevirtual

Return a string representing the settings which don't change based on reinitialization.

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

References protocols::qsar::scoring_grid::SingleGrid::get_type(), grid_name(), pcs_file_, pcs_values_, tensor_, and weight_.

void protocols::qsar::scoring_grid::PCSSingleGrid::init_pcs_values_from_file	(	std::string const &	filename,
		Pose const &	pose
	)

private

References core::scoring::pcs, pcs_values_, and core::io::nmr::read_pcs_datafile().

Referenced by PCSSingleGrid(), and refresh().

PCSSingleGrid & protocols::qsar::scoring_grid::PCSSingleGrid::operator= ( PCSSingleGrid const & rhs )

copy assignment

References pcs_file_, pcs_values_, tensor_, and weight_.

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

overridevirtual

setup a PCSSingleGrid based on RosettaScripts input

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

References pcs_file_, tensor_, and weight_.

void protocols::qsar::scoring_grid::PCSSingleGrid::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References grid_name(), and protocols::qsar::scoring_grid::xsd_type_definition_w_attributes().

Referenced by protocols::qsar::scoring_grid::PCSSingleGridCreator::provide_xml_schema().

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

overridevirtual

populate the grid with PCS values based on a passed pose

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

References core::grid::CartGrid< T >::coords(), protocols::qsar::scoring_grid::SingleGrid::get_dimensions(), protocols::qsar::scoring_grid::SingleGrid::get_grid(), init_pcs_values_from_file(), core::scoring::pcs, pcs_file_, core::scoring::nmr::pcs_func(), pcs_values_, core::scoring::nmr::rotation_matrix_from_euler_angles(), protocols::qsar::scoring_grid::SingleGrid::set_point(), and tensor_.

Referenced by refresh().

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

overridevirtual

populate the grid with PCS values based on a passed pose

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

References refresh().

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