#include <GridManager.hh>

Collaboration diagram for protocols::qsar::scoring_grid::GridManager:

Public Member Functions
void	reset ()
	reset GridManager to the default settings More...

void	set_normalized (bool normalized)
	should grid scores be normalized? More...

void	set_width (core::Real width)
	set width (must be done before initialization) More...

void	set_resolution (core::Real resolution)
	set resolution (must be done before initialization) More...

void	set_chain (char chain)
	set ligand chain (must be done before initialization) More...

void	make_new_grid (utility::tag::TagPtr const tag)
	make a new grid from grid tag, and insert it into the grid manager More...

void	insert_grid (std::string const name, GridBaseOP const grid)
	insert a grid pointer into the grid manager More...

void	set_qsar_map (qsarMapOP qsar_map)
	set the qsar_map More...

bool	is_qsar_map_attached ()
	is a qsar map attached to the grid manager? More...

GridBaseOP	get_grid (std::string const &grid_name)
	given a grid type, return a pointer to the grid More...

utility::vector1< std::string >	get_grid_names ()
	get a list of grid names More...

core::Real	total_score (core::conformation::Residue const &residue)
	return the total score of a residue on the grid More...

core::Real	total_score (core::pose::Pose const &pose, core::Size const chain_id)
	return the total score of a chain on the grid More...

std::map< std::string, core::Real >	atom_score (core::pose::Pose const &pose, core::conformation::Residue const &residue, core::Size atomindex)
	get a map of scoring terms and scores for each term given a residue and atom number More...

void	update_grids (core::pose::Pose const &pose, core::Vector const &center, core::Size const &ligand_chain_id_to_exclude)
	recalculate all grids for a pose. This must be called if the backbone or sidechain conformations change! More...

void	update_grids (core::pose::Pose const &pose, core::Vector const &center, utility::vector1< core::Size > ligand_chain_ids_to_exclude)
	recalculate all grids for a pose. This must be called if the backbone or sidechain conformations change! More...

void	update_grids (core::pose::Pose const &pose, core::Vector const &center)
	recalculate all grids for a pose. This must be called if the backbone or sidechain conformations change! More...

void	initialize_all_grids (core::Vector const &center)
	initialize all grids and fill with 0s given a center point More...

core::Size	size ()
	return the number of grids in the manager More...

ScoreMap	get_cached_scores ()
	get a map of cached scores More...

void	append_cached_scores (jd2::JobOP job)
	append all cached scores to a current job More...

void	write_grids (std::string prefix)
	write all grids out using the BRIX format More...

bool	is_in_grid (core::conformation::Residue const &residue)
	check to see if all atoms in the ligand are in the grid More...

Static Public Member Functions
static GridManager *	get_instance ()

Private Member Functions
	GridManager ()

	GridManager (GridManager const &)

GridManager const &	operator= (GridManager const &)

utility::json_spirit::Value	serialize ()
	serialize the current map to a JSON object. There is no public interface for this because the grid manager takes care of it on its own More...

void	deserialize (utility::json_spirit::mArray data)
	deserialize the JSON object to a map. There is no public interface for this because the grid manager takes care of it on its own More...

Private Attributes
std::map< std::string, GridMap >	grid_map_cache_

std::map< std::string, core::Real >	grid_weights_

GridMap	grid_map_

ScoreMap	score_map_

std::string	last_tag_

core::Real	width_

core::Real	resolution_

qsar::qsarMapOP	qsar_map_

bool	initialized_

char	chain_

bool	normalized_

Static Private Attributes
static GridManager *	instance_

Detailed Description

Definition at line 44 of file GridManager.hh.

Constructor & Destructor Documentation

protocols::qsar::scoring_grid::GridManager::GridManager ( )

private

Definition at line 77 of file GridManager.cc.

References grid_map_, and score_map_.

Referenced by get_instance().

protocols::qsar::scoring_grid::GridManager::GridManager ( GridManager const & )

private

Member Function Documentation

void protocols::qsar::scoring_grid::GridManager::append_cached_scores ( jd2::JobOP job)

append all cached scores to a current job

Definition at line 388 of file GridManager.cc.

References score_map_, and total_score().

Referenced by protocols::qsar::qsarMover::apply().

std::map< std::string, core::Real > protocols::qsar::scoring_grid::GridManager::atom_score	(	core::pose::Pose const &	pose,
		core::conformation::Residue const &	residue,
		core::Size	atomindex
	)

get a map of scoring terms and scores for each term given a residue and atom number

Definition at line 232 of file GridManager.cc.

References grid_map_, grid_weights_, and qsar_map_.

Referenced by protocols::features::ResidueGridScoresFeatures::report_features().

void protocols::qsar::scoring_grid::GridManager::deserialize ( utility::json_spirit::mArray data)

private

deserialize the JSON object to a map. There is no public interface for this because the grid manager takes care of it on its own

Definition at line 432 of file GridManager.cc.

References protocols::qsar::scoring_grid::GridFactory::get_instance(), and grid_map_.

Referenced by update_grids().

ScoreMap protocols::qsar::scoring_grid::GridManager::get_cached_scores ( )

get a map of cached scores

Definition at line 383 of file GridManager.cc.

References score_map_.

Referenced by protocols::ligand_docking::append_ligand_grid_scores(), and protocols::qsar::qsarMover::apply().

GridBaseOP protocols::qsar::scoring_grid::GridManager::get_grid ( std::string const & grid_name)

given a grid type, return a pointer to the grid

Definition at line 144 of file GridManager.cc.

References grid_map_.

Referenced by protocols::qsar::qsarMover::apply(), and protocols::qsar::RenderGridsToKinemage::parse_my_tag().

utility::vector1< std::string > protocols::qsar::scoring_grid::GridManager::get_grid_names ( )

get a list of grid names

Definition at line 149 of file GridManager.cc.

References grid_map_.

GridManager * protocols::qsar::scoring_grid::GridManager::get_instance ( )

static

Definition at line 55 of file GridManager.cc.

References GridManager(), and instance_.

Referenced by protocols::ligand_docking::append_ligand_grid_scores(), protocols::qsar::qsarMover::apply(), protocols::qsar::scoring_grid::GridInitMover::apply(), protocols::ligand_docking::Transform::apply(), protocols::ligand_docking::Translate::apply(), protocols::ligand_docking::Rotate::apply(), protocols::qsar::scoring_grid::ScoringGridLoader::load_data(), protocols::qsar::RenderGridsToKinemage::parse_my_tag(), protocols::features::ResidueGridScoresFeatures::report_features(), and protocols::ligand_docking::Translate::translate_ligand().

void protocols::qsar::scoring_grid::GridManager::initialize_all_grids ( core::Vector const & center)

initialize all grids and fill with 0s given a center point

Definition at line 361 of file GridManager.cc.

References grid_map_, initialized_, resolution_, and width_.

Referenced by protocols::ligand_docking::append_ligand_grid_scores(), protocols::qsar::qsarMover::apply(), protocols::qsar::scoring_grid::GridInitMover::apply(), protocols::ligand_docking::Transform::apply(), protocols::ligand_docking::Translate::apply(), and protocols::features::ResidueGridScoresFeatures::report_features().

void protocols::qsar::scoring_grid::GridManager::insert_grid	(	std::string const	name,
		GridBaseOP const	grid
	)

insert a grid pointer into the grid manager

Definition at line 139 of file GridManager.cc.

References grid_map_.

Referenced by make_new_grid().

bool protocols::qsar::scoring_grid::GridManager::is_in_grid ( core::conformation::Residue const & residue)

check to see if all atoms in the ligand are in the grid

Definition at line 444 of file GridManager.cc.

References grid_map_.

Referenced by protocols::ligand_docking::Transform::apply().

bool protocols::qsar::scoring_grid::GridManager::is_qsar_map_attached ( )

is a qsar map attached to the grid manager?

Definition at line 115 of file GridManager.cc.

References qsar_map_.

void protocols::qsar::scoring_grid::GridManager::make_new_grid ( utility::tag::TagPtr const tag)

make a new grid from grid tag, and insert it into the grid manager

Definition at line 126 of file GridManager.cc.

References protocols::qsar::scoring_grid::GridFactory::get_instance(), grid_weights_, protocols::qsar::scoring_grid::GridManagerTracer(), and insert_grid().

Referenced by protocols::qsar::scoring_grid::ScoringGridLoader::load_data().

GridManager const& protocols::qsar::scoring_grid::GridManager::operator= ( GridManager const & )

private

void protocols::qsar::scoring_grid::GridManager::reset ( void )

reset GridManager to the default settings

Definition at line 64 of file GridManager.cc.

References chain_, grid_map_, initialized_, last_tag_, normalized_, qsar_map_, resolution_, score_map_, and width_.

utility::json_spirit::Value protocols::qsar::scoring_grid::GridManager::serialize ( )

private

serialize the current map to a JSON object. There is no public interface for this because the grid manager takes care of it on its own

Definition at line 415 of file GridManager.cc.

References grid_map_.

Referenced by update_grids().

void protocols::qsar::scoring_grid::GridManager::set_chain ( char chain)

set ligand chain (must be done before initialization)

Definition at line 105 of file GridManager.cc.

References chain_.

Referenced by protocols::qsar::scoring_grid::ScoringGridLoader::load_data().

void protocols::qsar::scoring_grid::GridManager::set_normalized ( bool normalized)

should grid scores be normalized?

Definition at line 90 of file GridManager.cc.

References normalized_.

Referenced by protocols::qsar::scoring_grid::ScoringGridLoader::load_data().

void protocols::qsar::scoring_grid::GridManager::set_qsar_map ( qsarMapOP qsar_map)

set the qsar_map

Definition at line 110 of file GridManager.cc.

References qsar_map_.

Referenced by protocols::qsar::qsarMover::apply().

void protocols::qsar::scoring_grid::GridManager::set_resolution ( core::Real resolution)

set resolution (must be done before initialization)

Definition at line 100 of file GridManager.cc.

References resolution_.

Referenced by protocols::qsar::scoring_grid::ScoringGridLoader::load_data().

void protocols::qsar::scoring_grid::GridManager::set_width ( core::Real width)

set width (must be done before initialization)

Definition at line 95 of file GridManager.cc.

References width_.

Referenced by protocols::qsar::scoring_grid::ScoringGridLoader::load_data().

core::Size protocols::qsar::scoring_grid::GridManager::size ( )

return the number of grids in the manager

Definition at line 378 of file GridManager.cc.

References grid_map_.

Referenced by protocols::ligand_docking::append_ligand_grid_scores(), protocols::ligand_docking::Translate::apply(), protocols::ligand_docking::Rotate::apply(), and protocols::features::ResidueGridScoresFeatures::report_features().

core::Real protocols::qsar::scoring_grid::GridManager::total_score ( core::conformation::Residue const & residue)

return the total score of a residue on the grid

Definition at line 161 of file GridManager.cc.

References grid_map_, core::conformation::Residue::natoms(), normalized_, qsar_map_, and score_map_.

Referenced by append_cached_scores(), protocols::ligand_docking::append_ligand_grid_scores(), protocols::qsar::qsarMover::apply(), protocols::ligand_docking::Transform::apply(), total_score(), and protocols::ligand_docking::Translate::translate_ligand().

core::Real protocols::qsar::scoring_grid::GridManager::total_score	(	core::pose::Pose const &	pose,
		core::Size const	chain_id
	)

return the total score of a chain on the grid

Definition at line 192 of file GridManager.cc.

References core::pose::get_chain_residues(), grid_map_, grid_weights_, normalized_, qsar_map_, score_map_, and total_score().

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

recalculate all grids for a pose. This must be called if the backbone or sidechain conformations change!

Definition at line 260 of file GridManager.cc.

References chain_, grid_map_, resolution_, and width_.

Referenced by protocols::ligand_docking::append_ligand_grid_scores(), protocols::qsar::qsarMover::apply(), protocols::qsar::scoring_grid::GridInitMover::apply(), protocols::ligand_docking::Transform::apply(), protocols::ligand_docking::Translate::apply(), and protocols::features::ResidueGridScoresFeatures::report_features().

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