#include <PCSMultiGrid.hh>

Inheritance diagram for protocols::qsar::scoring_grid::PCSMultiGrid:

Public Types
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
	PCSMultiGrid ()
	default constructor More...

	PCSMultiGrid (std::string const &filename, Real const weight=1.0)
	construct from PCS input file More...

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

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

	~PCSMultiGrid () override
	destructor More...

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

void	initialize (Vector const &center, Real width, Real resolution) override
	setup a vector of PCSSingleGrid objects initialize each PCSSingleGrid with a given center point, width and resolution (in angstroms) and set grid values to zero. More...

void	refresh (Pose const &pose, Vector const &center) override
	populate grids in the vector 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 grids in the vector 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 grids in the vector 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 PCSMultiGrid 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 PCSMultiGrid 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 PCSMultiGrid 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 PCSMultiGrid More...

std::string	get_type () const override
	get the type of the grid More...

void	set_chain (char chain) override
	set the chain the grid applies to More...

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...

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

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

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

bool	is_in_grid (UltraLightResidue const &residue) const override
	determine if all residue atoms are in a grid More...

bool	is_in_grid (Residue const &residue) const override
	determine if all residue atoms are in a grid More...

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

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

core::Size	get_number_pcs_grids () const

utility::vector1< SingleGridOP > const &	get_pcs_grids () const

utility::vector1< SingleGridOP > &	get_pcs_grids ()

Real	get_weight () const

void	set_weight (Real w)

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	initialize_pcs_data_from_input_file (std::string const &filename)

Private Attributes
std::string	type_

std::string	pcs_input_file_

utility::vector1< SingleGridOP >	pcs_grid_vector_

Real	weight_

bool	pcs_data_initialized_

Member Typedef Documentation

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

typedef core::Real protocols::qsar::scoring_grid::PCSMultiGrid::Real

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

typedef core::Size protocols::qsar::scoring_grid::PCSMultiGrid::Size

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

typedef core::Vector protocols::qsar::scoring_grid::PCSMultiGrid::Vector

Constructor & Destructor Documentation

protocols::qsar::scoring_grid::PCSMultiGrid::PCSMultiGrid ( )

default constructor

Referenced by clone().

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

construct from PCS input file

References initialize_pcs_data_from_input_file(), and pcs_data_initialized_.

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

copy constructor

References pcs_grid_vector_.

protocols::qsar::scoring_grid::PCSMultiGrid::~PCSMultiGrid ( )

override

destructor

Member Function Documentation

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

overridevirtual

return the current score of an atom using the current PCSMultiGrid

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

References pcs_grid_vector_, core::scoring::total_score, and weight_.

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

overridevirtual

return the current score of an atom using the current PCSMultiGrid

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

References pcs_grid_vector_, core::scoring::total_score, and weight_.

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

overridevirtual

Make a copy of the grid, respecting the subclassing.

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

References PCSMultiGrid().

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

overridevirtual

deserialize a json_spirit object to a PCSMultiGrid

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

References pcs_grid_vector_, pcs_input_file_, type_, and weight_.

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

overridevirtual

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

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

core::Size protocols::qsar::scoring_grid::PCSMultiGrid::get_number_pcs_grids ( ) const

inline

References pcs_grid_vector_.

utility::vector1< SingleGridOP > const& protocols::qsar::scoring_grid::PCSMultiGrid::get_pcs_grids ( ) const

inline

References pcs_grid_vector_.

utility::vector1< SingleGridOP >& protocols::qsar::scoring_grid::PCSMultiGrid::get_pcs_grids ( )

inline

References pcs_grid_vector_.

std::string protocols::qsar::scoring_grid::PCSMultiGrid::get_type ( ) const

overridevirtual

get the type of the grid

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

References grid_name().

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

inline

References weight_.

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

static

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

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

overridevirtual

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

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

References grid_name(), pcs_data_initialized_, pcs_grid_vector_, pcs_input_file_, type_, and weight_.

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

overridevirtual

setup a vector of PCSSingleGrid objects initialize each PCSSingleGrid with a given center point, width and resolution (in angstroms) and set grid values to zero.

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

References initialize_pcs_data_from_input_file(), pcs_data_initialized_, pcs_grid_vector_, and pcs_input_file_.

void protocols::qsar::scoring_grid::PCSMultiGrid::initialize_pcs_data_from_input_file ( std::string const & filename )

private

References core::conformation::membrane::in, core::scoring::pcs, pcs_data_initialized_, pcs_grid_vector_, core::io::nmr::read_pcs_dataset_params_list(), and core::id::to_string().

Referenced by initialize(), parse_my_tag(), and PCSMultiGrid().

bool protocols::qsar::scoring_grid::PCSMultiGrid::is_in_grid ( UltraLightResidue const & residue ) const

overridevirtual

determine if all residue atoms are in a grid

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

References pcs_grid_vector_.

Referenced by is_in_grid().

bool protocols::qsar::scoring_grid::PCSMultiGrid::is_in_grid ( Residue const & residue ) const

overridevirtual

determine if all residue atoms are in a grid

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

References is_in_grid(), and pcs_grid_vector_.

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

copy assignment

References pcs_data_initialized_, pcs_grid_vector_, pcs_input_file_, type_, and weight_.

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

overridevirtual

setup a PCSMultiGrid based on RosettaScripts input

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

References initialize_pcs_data_from_input_file(), pcs_data_initialized_, pcs_input_file_, and weight_.

void protocols::qsar::scoring_grid::PCSMultiGrid::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::PCSMultiGridCreator::provide_xml_schema().

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

overridevirtual

populate grids in the vector with PCS values based on a passed pose

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

References pcs_grid_vector_.

Referenced by refresh().

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

overridevirtual

populate grids in the vector with PCS values based on a passed pose

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

References refresh().

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