A set of related grids. More...

#include <GridSet.hh>

Inheritance diagram for protocols::qsar::scoring_grid::GridSet:

Public Types
typedef std::map< std::string, core::Real >	ScoreMap

Public Member Functions
	GridSet ()

	GridSet (GridSet const &src)

	~GridSet () override

GridSetOP	clone () const

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

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

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

core::Real	width () const
	get grid width More...

core::Real	resolution () const
	get grid resoultion More...

char	chain () const
	get ligand chain More...

void	set_normalization_function (std::string norm_function_name)
	set normalization function More...

bool	is_normalization_enabled () const
	is normalization applied during scoring? More...

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

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

void	reinitialize (core::pose::Pose const &pose, core::Vector const &center)
	Reinitialize the included grids with the given information. More...

GridBaseCOP	get_grid (std::string const &name) const

void	add_grid (std::string const &name, GridBaseOP grid, core::Real weight=1.0)
	Add a grid to the GridSet under the given name. More...

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

bool	has_grid (std::string const &name) const
	Returns true if we already have a grid with the given name. More...

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

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

core::Real	average_score (utility::vector1< core::conformation::UltraLightResidue > &residues) const
	return the average score of multiple residues on the grid More...

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

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

core::Real	total_score (core::pose::Pose const &pose, utility::vector1< core::Size > const &residues) const
	return the total score for a set of residues on the grid More...

ScoreMap	grid_scores (core::conformation::Residue const &residue) const

ScoreMap	grid_scores (core::pose::Pose const &pose, utility::vector1< core::Size > const &residues) const

ScoreMap	atom_score (core::pose::Pose const &pose, core::conformation::Residue const &residue, core::Size atomindex) const
	get a map of (unweighted, unnormalized) scoring terms and scores for each term given a residue and atom number More...

bool	is_in_grid (utility::vector1< core::conformation::UltraLightResidue > const &residues) const
	check if all atoms in all the ligands are in grid More...

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

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

std::string	hash_fingerprint () const
	Return a string representing the settings of this GridSet. More...

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

utility::json_spirit::Value	serialize () const
	serialize the current map to a JSON object. More...

void	deserialize (utility::json_spirit::mArray data)
	deserialize the JSON object to a map. More...

Private Types
typedef std::map< std::string, GridBaseOP >	MappingType

Private Member Functions
template<class GridScorable >
core::Real	total_score (utility::vector1< GridScorable const * > const &items) const
	Return a single weighted, normalized score for all items Templated to allow for common implementation between Residue and UltraLightResidue. More...

core::Real	normalize (core::Real total_score, utility::vector1< core::conformation::UltraLightResidue const * > const &items) const
	Normalize a score based on the passed items;. More...

core::Real	normalize (core::Real total_score, utility::vector1< core::conformation::Residue const * > const &items) const
	Normalize a score based on the passed items;. More...

template<class GridScorable >
ScoreMap	grid_scores (utility::vector1< GridScorable const * > const &items) const
	Return a map of summed unweighted, unormalized scores for each grid. Templated to allow for common implementation between Residue and UltraLightResidue. More...

Private Attributes
MappingType	grids_

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

core::Real	width_ = 40

core::Real	resolution_ = 0.25

char	chain_ = 'X'

qsar::qsarMapCOP	qsar_map_

ScoreNormalizationCOP	norm_function_

Detailed Description

A set of related grids.

Member Typedef Documentation

◆ MappingType

typedef std::map<std::string,GridBaseOP> protocols::qsar::scoring_grid::GridSet::MappingType

private

◆ ScoreMap

typedef std::map< std::string, core::Real > protocols::qsar::scoring_grid::GridSet::ScoreMap

Constructor & Destructor Documentation

◆ GridSet() [1/2]

protocols::qsar::scoring_grid::GridSet::GridSet ( )

default

◆ GridSet() [2/2]

protocols::qsar::scoring_grid::GridSet::GridSet ( GridSet const & src )

References grids_, and core::scoring::pair.

◆ ~GridSet()

protocols::qsar::scoring_grid::GridSet::~GridSet ( )

overridedefault

Member Function Documentation

◆ add_grid()

void protocols::qsar::scoring_grid::GridSet::add_grid	(	std::string const &	name,
		GridBaseOP	grid,
		core::Real	weight = `1.0`
	)

Add a grid to the GridSet under the given name.

References grid_weights_, and grids_.

Referenced by make_new_grid().

◆ atom_score()

GridSet::ScoreMap protocols::qsar::scoring_grid::GridSet::atom_score	(	core::pose::Pose const &	pose,
		core::conformation::Residue const &	residue,
		core::Size	atomindex
	)		const

get a map of (unweighted, unnormalized) scoring terms and scores for each term given a residue and atom number

References grid_weights_, grids_, and qsar_map_.

◆ average_score()

core::Real protocols::qsar::scoring_grid::GridSet::average_score ( utility::vector1< core::conformation::UltraLightResidue > & residues ) const

return the average score of multiple residues on the grid

References protocols::hybridization::score, and total_score().

◆ chain() [1/2]

char protocols::qsar::scoring_grid::GridSet::chain ( ) const

inline

get ligand chain

References chain_.

◆ chain() [2/2]

void protocols::qsar::scoring_grid::GridSet::chain ( char chain )

inline

set ligand chain (must be done before initialization)

References chain(), and chain_.

Referenced by chain().

◆ clone()

GridSetOP protocols::qsar::scoring_grid::GridSet::clone ( ) const

Referenced by protocols::qsar::scoring_grid::GridManager::get_grids().

◆ deserialize()

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

deserialize the JSON object to a map.

References grids_.

◆ get_grid()

GridBaseCOP protocols::qsar::scoring_grid::GridSet::get_grid ( std::string const & name ) const

References grids_.

◆ get_grid_names()

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

get a list of grid names

References grids_.

◆ grid_scores() [1/3]

GridSet::ScoreMap protocols::qsar::scoring_grid::GridSet::grid_scores ( core::conformation::Residue const & residue ) const

Referenced by grid_scores(), and total_score().

◆ grid_scores() [2/3]

GridSet::ScoreMap protocols::qsar::scoring_grid::GridSet::grid_scores	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	residues
	)		const

References grid_scores(), and core::pose::Pose::residue().

◆ grid_scores() [3/3]

template<class GridScorable >

GridSet::ScoreMap protocols::qsar::scoring_grid::GridSet::grid_scores ( utility::vector1< GridScorable const * > const & items ) const

private

Return a map of summed unweighted, unormalized scores for each grid. Templated to allow for common implementation between Residue and UltraLightResidue.

Yes, raw pointer. This is for speed reasons (don't have to copy objects) and because this is a class-internal implementation detail. Do not publically expose this interface.

References grids_, and qsar_map_.

◆ has_grid()

bool protocols::qsar::scoring_grid::GridSet::has_grid ( std::string const & name ) const

Returns true if we already have a grid with the given name.

References grids_.

Referenced by make_new_grid().

◆ hash_fingerprint()

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

Return a string representing the settings of this GridSet.

This should encapsulate everything that doesn't change with a call to reinitialize() The string is not meant to be interpretable.

References chain_, grid_weights_, grids_, norm_function_, core::scoring::pair, qsar_map_, resolution_, and width_.

Referenced by protocols::qsar::scoring_grid::GridManager::compute_hash().

◆ is_in_grid() [1/3]

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

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

References grids_.

◆ is_in_grid() [2/3]

bool protocols::qsar::scoring_grid::GridSet::is_in_grid ( core::conformation::UltraLightResidue const & residue ) const

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

References grids_.

◆ is_in_grid() [3/3]

bool protocols::qsar::scoring_grid::GridSet::is_in_grid ( utility::vector1< core::conformation::UltraLightResidue > const & residues ) const

check if all atoms in all the ligands are in grid

◆ is_normalization_enabled()

bool protocols::qsar::scoring_grid::GridSet::is_normalization_enabled ( ) const

is normalization applied during scoring?

References norm_function_.

◆ is_qsar_map_attached()

bool protocols::qsar::scoring_grid::GridSet::is_qsar_map_attached ( ) const

is a qsar map attached to the grid manager?

References qsar_map_.

◆ make_new_grid()

void protocols::qsar::scoring_grid::GridSet::make_new_grid ( utility::tag::TagCOP tag )

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

References add_grid(), has_grid(), and protocols::qsar::scoring_grid::TR().

◆ normalize() [1/2]

core::Real protocols::qsar::scoring_grid::GridSet::normalize	(	core::Real	total_score,
		utility::vector1< core::conformation::Residue const * > const &	items
	)		const

private

Normalize a score based on the passed items;.

Yes, raw pointer. This is to interface with the other functions. Do not publically expose this interface.

References norm_function_, protocols::hybridization::score, and protocols::qsar::scoring_grid::TR().

◆ normalize() [2/2]

core::Real protocols::qsar::scoring_grid::GridSet::normalize	(	core::Real	total_score,
		utility::vector1< core::conformation::UltraLightResidue const * > const &	items
	)		const

private

Normalize a score based on the passed items;.

Yes, raw pointer. This is to interface with the other functions. Do not publically expose this interface.

References norm_function_, protocols::hybridization::score, and protocols::qsar::scoring_grid::TR().

Referenced by total_score().

◆ reinitialize()

void protocols::qsar::scoring_grid::GridSet::reinitialize	(	core::pose::Pose const &	pose,
		core::Vector const &	center
	)

Reinitialize the included grids with the given information.

References core::conformation::membrane::center, chain_, grids_, resolution_, protocols::qsar::scoring_grid::TR(), and width_.

◆ resolution() [1/2]

core::Real protocols::qsar::scoring_grid::GridSet::resolution ( ) const

inline

get grid resoultion

References resolution_.

◆ resolution() [2/2]

void protocols::qsar::scoring_grid::GridSet::resolution ( core::Real resolution )

inline

set resolution (must be done before initialization)

References resolution(), and resolution_.

Referenced by resolution().

◆ serialize()

utility::json_spirit::Value protocols::qsar::scoring_grid::GridSet::serialize ( ) const

serialize the current map to a JSON object.

References grids_.

◆ set_normalization_function()

void protocols::qsar::scoring_grid::GridSet::set_normalization_function ( std::string norm_function_name )

set normalization function

References protocols::qsar::scoring_grid::get_score_normalization_function(), and norm_function_.

◆ set_qsar_map()

void protocols::qsar::scoring_grid::GridSet::set_qsar_map ( qsarMapCOP qsar_map )

set the qsar_map

References qsar_map_.

◆ size()

core::Size protocols::qsar::scoring_grid::GridSet::size ( ) const

return the number of grids

References grids_.

Referenced by protocols::ligand_docking::get_ligand_grid_scores().

◆ total_score() [1/5]

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

return the total score of a residue on the grid

References total_score().

◆ total_score() [2/5]

core::Real protocols::qsar::scoring_grid::GridSet::total_score ( core::conformation::UltraLightResidue const & residue ) const

return the total score of a residue on the grid

Referenced by average_score(), and total_score().

◆ total_score() [3/5]

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

return the total score of a chain on the grid

References core::pose::get_resnums_for_chain_id(), and total_score().

◆ total_score() [4/5]

core::Real protocols::qsar::scoring_grid::GridSet::total_score	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	residues
	)		const

return the total score for a set of residues on the grid

References core::pose::Pose::residue(), and total_score().

◆ total_score() [5/5]

template<class GridScorable >

core::Real protocols::qsar::scoring_grid::GridSet::total_score ( utility::vector1< GridScorable const * > const & items ) const

private

Return a single weighted, normalized score for all items Templated to allow for common implementation between Residue and UltraLightResidue.

Yes, raw pointer. This is for speed reasons (don't have to copy objects) and because this is a class-internal implementation detail. Do not publically expose this interface.

References grid_scores(), grid_weights_, norm_function_, normalize(), and protocols::hybridization::score.

◆ width() [1/2]

core::Real protocols::qsar::scoring_grid::GridSet::width ( ) const

inline

get grid width

References width_.

◆ width() [2/2]

void protocols::qsar::scoring_grid::GridSet::width ( core::Real width )

inline

set width (must be done before initialization)

References width(), and width_.

Referenced by width().

◆ write_grids()

void protocols::qsar::scoring_grid::GridSet::write_grids ( std::string prefix ) const

write all grids out using the BRIX format

References grids_.

Member Data Documentation

◆ chain_

char protocols::qsar::scoring_grid::GridSet::chain_ = 'X'

private

Referenced by chain(), hash_fingerprint(), and reinitialize().

◆ grid_weights_

std::map< std::string, core::Real > protocols::qsar::scoring_grid::GridSet::grid_weights_

private

Referenced by add_grid(), atom_score(), hash_fingerprint(), and total_score().

◆ grids_

MappingType protocols::qsar::scoring_grid::GridSet::grids_

private

Referenced by add_grid(), atom_score(), deserialize(), get_grid(), get_grid_names(), grid_scores(), GridSet(), has_grid(), hash_fingerprint(), is_in_grid(), reinitialize(), serialize(), size(), and write_grids().

◆ norm_function_

ScoreNormalizationCOP protocols::qsar::scoring_grid::GridSet::norm_function_

private

Referenced by hash_fingerprint(), is_normalization_enabled(), normalize(), set_normalization_function(), and total_score().

◆ qsar_map_

qsar::qsarMapCOP protocols::qsar::scoring_grid::GridSet::qsar_map_

private

Referenced by atom_score(), grid_scores(), hash_fingerprint(), is_qsar_map_attached(), and set_qsar_map().

◆ resolution_

core::Real protocols::qsar::scoring_grid::GridSet::resolution_ = 0.25

private

Referenced by hash_fingerprint(), reinitialize(), and resolution().

◆ width_

core::Real protocols::qsar::scoring_grid::GridSet::width_ = 40

private

Referenced by hash_fingerprint(), reinitialize(), and width().

The documentation for this class was generated from the following files:

src/protocols/qsar/scoring_grid/GridSet.hh
src/protocols/qsar/scoring_grid/GridSet.cc

Public Types

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ MappingType

◆ ScoreMap

Constructor & Destructor Documentation

◆ GridSet() [1/2]

◆ GridSet() [2/2]

◆ ~GridSet()

Member Function Documentation

◆ add_grid()

◆ atom_score()

◆ average_score()

◆ chain() [1/2]

◆ chain() [2/2]

◆ clone()

◆ deserialize()

◆ get_grid()

◆ get_grid_names()

◆ grid_scores() [1/3]

◆ grid_scores() [2/3]

◆ grid_scores() [3/3]

◆ has_grid()

◆ hash_fingerprint()

◆ is_in_grid() [1/3]

◆ is_in_grid() [2/3]

◆ is_in_grid() [3/3]

◆ is_normalization_enabled()

◆ is_qsar_map_attached()

◆ make_new_grid()

◆ normalize() [1/2]

◆ normalize() [2/2]

◆ reinitialize()

◆ resolution() [1/2]

◆ resolution() [2/2]

◆ serialize()

◆ set_normalization_function()

◆ set_qsar_map()

◆ size()

◆ total_score() [1/5]

◆ total_score() [2/5]

◆ total_score() [3/5]

◆ total_score() [4/5]

◆ total_score() [5/5]

◆ width() [1/2]

◆ width() [2/2]

◆ write_grids()

Member Data Documentation

◆ chain_

◆ grid_weights_

◆ grids_

◆ norm_function_

◆ qsar_map_

◆ resolution_

◆ width_