protocols::qsar::scoring_grid Namespace Reference

Classes
class	AllAtomNormalization
class	AtrGrid
class	AtrGridCreator
struct	ChargeAtom
	a very light representation of an atom that is just a charge and a cartesian space position More...
class	ChargeGrid
class	ChargeGridCreator
class	ChiAngleNormalization
class	ClassicGrid
class	ClassicGridCreator
class	ConstantScoreBase
class	GridBase
class	GridCreator
	Abstract class fora mover factory. The creator class is responsible for creating a particular mover class. More...
class	GridFactory
class	GridManager
class	GridRegistrator
	this templated class will register an instance of a GridCreator (class T) with the GridFactory. It will ensure that no GridCreator is registered twice and centralizes the registration logic More...
class	GridSet
	A set of related grids. More...
class	HbaGrid
class	HbaGridCreator
class	HbdGrid
class	HbdGridCreator
class	HeavyAtomNormalization
class	LigandPropertyScore
class	LigandPropertyScoreCreator
class	MolecularWeightNormalization
class	PCSMultiGrid
class	PCSMultiGridCreator
class	PCSSingleGrid
class	PCSSingleGridCreator
class	RepGrid
class	RepGridCreator
class	ScoreNormalization
class	ScoringGridLoader
	A class for loading ScoringGrids into the XML parser's basic::datacache::DataMap. More...
class	ScoringGridLoaderCreator
class	ShapeGrid
class	ShapeGridCreator
class	SingleGrid
class	SiteGrid
class	SiteGridCreator
class	SolvationGrid
class	SolvationGridCreator
class	SolvationMetaGrid
class	SolvationMetaGridCreator
class	VdwGrid
class	VdwGridCreator

Typedefs
typedef utility::pointer::shared_ptr < GridBase >	GridBaseOP
typedef utility::pointer::shared_ptr < GridBase const >	GridBaseCOP
typedef utility::pointer::shared_ptr < GridCreator >	GridCreatorOP
typedef utility::pointer::shared_ptr < GridCreator const >	GridCreatorCOP
typedef utility::pointer::shared_ptr < GridFactory >	GridFactoryOP
typedef utility::pointer::shared_ptr < GridFactory const >	GridFactoryCOP
typedef utility::pointer::shared_ptr < GridManager >	GridManagerOP
typedef utility::pointer::shared_ptr < GridManager const >	GridManagerCOP
typedef std::map< std::string, core::Real >	ScoreMap
typedef utility::pointer::shared_ptr < GridSet >	GridSetOP
typedef utility::pointer::shared_ptr < GridSet const >	GridSetCOP
typedef utility::pointer::shared_ptr < PCSMultiGrid >	PCSMultiGridOP
typedef utility::pointer::shared_ptr < PCSMultiGrid const >	PCSMultiGridCOP
typedef utility::pointer::shared_ptr < PCSSingleGrid >	PCSSingleGridOP
typedef utility::pointer::shared_ptr < PCSSingleGrid const >	PCSSingleGridCOP
typedef utility::pointer::shared_ptr < ScoreNormalization >	ScoreNormalizationOP
typedef utility::pointer::shared_ptr < ScoreNormalization const >	ScoreNormalizationCOP
typedef utility::pointer::shared_ptr < ScoringGridLoader >	ScoringGridLoaderOP
typedef utility::pointer::shared_ptr < ScoringGridLoader const >	ScoringGridLoaderCOP
typedef utility::pointer::shared_ptr < SingleGrid >	SingleGridOP
typedef utility::pointer::shared_ptr < SingleGrid const >	SingleGridCOP
typedef utility::pointer::shared_ptr < SolvationGrid >	SolvationGridOP
typedef utility::pointer::shared_ptr < SolvationGrid const >	SolvationGridCOP

Functions
static basic::Tracer	TR ("protocols.qsar.scoring_grid.GridManager")
static basic::Tracer	RepGridTracer ("protocols.ligand_docking.scoring_grid.RepGrid")
GridSetCOP	parse_grid_set_from_tag (utility::tag::TagCOP tag, basic::datacache::DataMap const &data, std::string const &option_name="grid_set")
	Get a GridSet from the datamap, using the option_name attribute of the tag. More...
void	attributes_for_parse_grid_set_from_tag (utility::tag::AttributeList &attributes, std::string const &description="", std::string const &option_name="grid_set")
	Append the attributes read by parse_grid_set_from_tag() More...
GridSetCOP	parse_optional_grid_set_from_tag (utility::tag::TagCOP tag, basic::datacache::DataMap const &data, std::string const &option_name="grid_set")
	Get a GridSet from the datamap, using the option_name attribute of the tag. If a GridSet hasn't been specified, return a nullptr. More...
void	attributes_for_parse_optional_grid_set_from_tag (utility::tag::AttributeList &attributes, std::string const &description="", std::string const &option_name="grid_set")
	Append the attributes read by parse_optional_grid_set_from_tag() More...
std::string	complex_type_name_for_scoring_grid (std::string const &element_name)
	Used to name the xs:complexType for a scoring grid that is created with the given element name. More...
void	xsd_type_definition_w_attributes (utility::tag::XMLSchemaDefinition &xsd, std::string const &scoring_grid_name, std::string const &description, utility::tag::AttributeList const &attributes)
	Define the XML schema definition for a scoring grid that has no subelements but does have a set of attributes (aka options). More...
ScoreNormalizationOP	get_score_normalization_function (std::string const &norm_tag)
static basic::Tracer	TR ("protocols.qsar.scoring_grid.ScoringGridLoader")
static basic::Tracer	TR ("protocols.qsar.scoring_grid.ShapeGrid")
static basic::Tracer	TR ("protocols.qsar.scoring_grid.SingleGrid")

Typedef Documentation

typedef utility::pointer::shared_ptr<GridBase const> protocols::qsar::scoring_grid::GridBaseCOP

typedef utility::pointer::shared_ptr<GridBase> protocols::qsar::scoring_grid::GridBaseOP

typedef utility::pointer::shared_ptr<GridCreator const> protocols::qsar::scoring_grid::GridCreatorCOP

typedef utility::pointer::shared_ptr<GridCreator> protocols::qsar::scoring_grid::GridCreatorOP

typedef utility::pointer::shared_ptr<GridFactory const > protocols::qsar::scoring_grid::GridFactoryCOP

typedef utility::pointer::shared_ptr<GridFactory> protocols::qsar::scoring_grid::GridFactoryOP

typedef utility::pointer::shared_ptr<GridManager const> protocols::qsar::scoring_grid::GridManagerCOP

typedef utility::pointer::shared_ptr<GridManager> protocols::qsar::scoring_grid::GridManagerOP

typedef utility::pointer::shared_ptr< GridSet const > protocols::qsar::scoring_grid::GridSetCOP

typedef utility::pointer::shared_ptr< GridSet > protocols::qsar::scoring_grid::GridSetOP

typedef utility::pointer::shared_ptr<PCSMultiGrid const> protocols::qsar::scoring_grid::PCSMultiGridCOP

typedef utility::pointer::shared_ptr<PCSMultiGrid> protocols::qsar::scoring_grid::PCSMultiGridOP

typedef utility::pointer::shared_ptr<PCSSingleGrid const> protocols::qsar::scoring_grid::PCSSingleGridCOP

typedef utility::pointer::shared_ptr<PCSSingleGrid> protocols::qsar::scoring_grid::PCSSingleGridOP

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

typedef utility::pointer::shared_ptr< ScoreNormalization const > protocols::qsar::scoring_grid::ScoreNormalizationCOP

typedef utility::pointer::shared_ptr< ScoreNormalization > protocols::qsar::scoring_grid::ScoreNormalizationOP

typedef utility::pointer::shared_ptr<ScoringGridLoader const > protocols::qsar::scoring_grid::ScoringGridLoaderCOP

typedef utility::pointer::shared_ptr<ScoringGridLoader> protocols::qsar::scoring_grid::ScoringGridLoaderOP

typedef utility::pointer::shared_ptr<SingleGrid const> protocols::qsar::scoring_grid::SingleGridCOP

typedef utility::pointer::shared_ptr<SingleGrid> protocols::qsar::scoring_grid::SingleGridOP

typedef utility::pointer::shared_ptr<SolvationGrid const> protocols::qsar::scoring_grid::SolvationGridCOP

typedef utility::pointer::shared_ptr<SolvationGrid> protocols::qsar::scoring_grid::SolvationGridOP

Function Documentation

void protocols::qsar::scoring_grid::attributes_for_parse_grid_set_from_tag	(	utility::tag::AttributeList &	attributes,
		std::string const &	description,
		std::string const &	option_name
	)

Append the attributes read by parse_grid_set_from_tag()

Referenced by protocols::qsar::RenderGridsToKinemage::provide_xml_schema(), protocols::features::ResidueGridScoresFeatures::provide_xml_schema(), protocols::ligand_docking::InterfaceScoreCalculator::provide_xml_schema(), protocols::ligand_docking::Transform::provide_xml_schema(), and protocols::ligand_docking::TransformEnsemble::provide_xml_schema().

void protocols::qsar::scoring_grid::attributes_for_parse_optional_grid_set_from_tag	(	utility::tag::AttributeList &	attributes,
		std::string const &	description,
		std::string const &	option_name
	)

Append the attributes read by parse_optional_grid_set_from_tag()

Referenced by protocols::ligand_docking::Translate::provide_xml_schema(), and protocols::ligand_docking::Rotate::provide_xml_schema().

std::string protocols::qsar::scoring_grid::complex_type_name_for_scoring_grid

(

std::string const &

element_name

)

Used to name the xs:complexType for a scoring grid that is created with the given element name.

Referenced by protocols::qsar::scoring_grid::GridFactory::provide_xml_schema(), and xsd_type_definition_w_attributes().

ScoreNormalizationOP protocols::qsar::scoring_grid::get_score_normalization_function

(

std::string const &

norm_tag

)

Referenced by protocols::ligand_docking::InterfaceScoreCalculator::parse_my_tag(), and protocols::qsar::scoring_grid::GridSet::set_normalization_function().

GridSetCOP protocols::qsar::scoring_grid::parse_grid_set_from_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap const &	data,
		std::string const &	option_name
	)

Get a GridSet from the datamap, using the option_name attribute of the tag.

Referenced by protocols::qsar::qsarMover::parse_my_tag(), protocols::qsar::RenderGridsToKinemage::parse_my_tag(), protocols::features::ResidueGridScoresFeatures::parse_my_tag(), protocols::ligand_docking::Transform::parse_my_tag(), and protocols::ligand_docking::TransformEnsemble::parse_my_tag().

GridSetCOP protocols::qsar::scoring_grid::parse_optional_grid_set_from_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap const &	data,
		std::string const &	option_name
	)

Get a GridSet from the datamap, using the option_name attribute of the tag. If a GridSet hasn't been specified, return a nullptr.

Referenced by protocols::ligand_docking::InterfaceScoreCalculator::parse_my_tag(), protocols::ligand_docking::Translate::parse_my_tag(), and protocols::ligand_docking::Rotate::parse_my_tag().

static basic::Tracer protocols::qsar::scoring_grid::RepGridTracer ( "protocols.ligand_docking.scoring_grid.RepGrid"  )

static

static basic::Tracer protocols::qsar::scoring_grid::TR ( "protocols.qsar.scoring_grid.SingleGrid"  )

static

static basic::Tracer protocols::qsar::scoring_grid::TR ( "protocols.qsar.scoring_grid.ScoringGridLoader"  )

static

static basic::Tracer protocols::qsar::scoring_grid::TR ( "protocols.qsar.scoring_grid.ShapeGrid"  )

static

static basic::Tracer protocols::qsar::scoring_grid::TR ( "protocols.qsar.scoring_grid.GridManager"  )

static

Referenced by protocols::qsar::scoring_grid::GridManager::find_grid_set(), protocols::qsar::scoring_grid::GridManager::get_grids(), protocols::qsar::scoring_grid::GridManager::insert_into_cache(), protocols::qsar::scoring_grid::ShapeGrid::load_kbp_data(), protocols::qsar::scoring_grid::GridSet::make_new_grid(), protocols::qsar::scoring_grid::GridSet::normalize(), protocols::qsar::scoring_grid::ScoringGridLoader::parse_gridset_tag(), and protocols::qsar::scoring_grid::GridSet::reinitialize().

void protocols::qsar::scoring_grid::xsd_type_definition_w_attributes	(	utility::tag::XMLSchemaDefinition &	xsd,
		std::string const &	scoring_grid_name,
		std::string const &	description,
		utility::tag::AttributeList const &	attributes
	)

Define the XML schema definition for a scoring grid that has no subelements but does have a set of attributes (aka options).

References complex_type_name_for_scoring_grid().

Referenced by protocols::qsar::scoring_grid::AtrGrid::provide_xml_schema(), protocols::qsar::scoring_grid::RepGrid::provide_xml_schema(), protocols::qsar::scoring_grid::ClassicGrid::provide_xml_schema(), protocols::qsar::scoring_grid::SiteGrid::provide_xml_schema(), protocols::qsar::scoring_grid::SolvationGrid::provide_xml_schema(), protocols::qsar::scoring_grid::HbaGrid::provide_xml_schema(), protocols::qsar::scoring_grid::LigandPropertyScore::provide_xml_schema(), protocols::qsar::scoring_grid::HbdGrid::provide_xml_schema(), protocols::qsar::scoring_grid::VdwGrid::provide_xml_schema(), protocols::qsar::scoring_grid::ShapeGrid::provide_xml_schema(), protocols::qsar::scoring_grid::SolvationMetaGrid::provide_xml_schema(), protocols::qsar::scoring_grid::ChargeGrid::provide_xml_schema(), protocols::qsar::scoring_grid::PCSMultiGrid::provide_xml_schema(), and protocols::qsar::scoring_grid::PCSSingleGrid::provide_xml_schema().