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