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protocols::features::TrajectoryMapFeatures Class Reference

#include <TrajectoryMapFeatures.hh>

Inheritance diagram for protocols::features::TrajectoryMapFeatures:
Inheritance graph
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Public Member Functions

 TrajectoryMapFeatures ()
 
void write_schema_to_db (utility::sql_database::sessionOP db_session) const override
 generate the table schemas and write them to the database More...
 
utility::vector1< std::string > features_reporter_dependencies () const override
 return the set of features reporters that are required to also already be extracted by the time this one is used. More...
 
core::Size report_features (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session) override
 collect all the feature data for the pose More...
 
void delete_record (StructureID struct_id, utility::sql_database::sessionOP db_sesion) override
 
void set_current_cycle (core::Size stride)
 
core::Size get_current_cycle () const
 
std::string type_name () const override
 
- Public Member Functions inherited from protocols::features::FeaturesReporter
 FeaturesReporter ()
 
 ~FeaturesReporter () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
 
virtual std::string schema () const
 return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator More...
 
core::Size report_features (core::pose::Pose const &, StructureID, utility::sql_database::sessionOP)
 collect all the feature data for the pose. More...
 
virtual void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &)
 
virtual void load_into_pose (utility::sql_database::sessionOP, StructureID, core::pose::Pose &)
 
void set_relevant_residues_mode (RelevantResiduesMode::T setting)
 
RelevantResiduesMode::T get_relevant_residues_mode () const
 
bool check_relevant_residues (utility::vector1< bool > const &relevant_residues, core::Size res1) const
 
bool check_relevant_residues (utility::vector1< bool > const &relevant_residues, core::Size res1, core::Size res2) const
 
bool check_relevant_residues_range (utility::vector1< bool > const &relevant_residues, core::Size res1, core::Size res2) const
 
bool check_relevant_residues (utility::vector1< bool > const &relevant_residues, utility::vector1< core::Size > const &residues) const
 

Static Public Member Functions

static std::string class_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 

Private Attributes

core::Size current_cycle_
 Stores the cycle count for the current pose being saved. More...
 

Additional Inherited Members

- Protected Member Functions inherited from protocols::features::FeaturesReporter
std::string find_tag (core::pose::Pose const &pose) const
 
void delete_records_from_table (std::string const &table_name, StructureID struct_id, utility::sql_database::sessionOP db_session)
 a helper function for deleting data associated with a given structure from feature database WARNING table_name must be sanitized! More...
 
- Protected Attributes inherited from protocols::features::FeaturesReporter
RelevantResiduesMode::T relevant_residues_mode_
 

Constructor & Destructor Documentation

protocols::features::TrajectoryMapFeatures::TrajectoryMapFeatures ( )

Member Function Documentation

std::string protocols::features::TrajectoryMapFeatures::class_name ( )
static
void protocols::features::TrajectoryMapFeatures::delete_record ( StructureID  struct_id,
utility::sql_database::sessionOP  db_sesion 
)
overridevirtual
utility::vector1< std::string > protocols::features::TrajectoryMapFeatures::features_reporter_dependencies ( ) const
overridevirtual

return the set of features reporters that are required to also already be extracted by the time this one is used.

Reimplemented from protocols::features::FeaturesReporter.

core::Size protocols::features::TrajectoryMapFeatures::get_current_cycle ( ) const

References current_cycle_.

void protocols::features::TrajectoryMapFeatures::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
Size protocols::features::TrajectoryMapFeatures::report_features ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  relevant_residues,
StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
overridevirtual

collect all the feature data for the pose

Implements protocols::features::FeaturesReporter.

References current_cycle_.

void protocols::features::TrajectoryMapFeatures::set_current_cycle ( core::Size  stride)

References current_cycle_.

std::string protocols::features::TrajectoryMapFeatures::type_name ( ) const
overridevirtual

Reimplemented from protocols::features::FeaturesReporter.

References class_name().

void protocols::features::TrajectoryMapFeatures::write_schema_to_db ( utility::sql_database::sessionOP  db_session) const
overridevirtual

generate the table schemas and write them to the database

Implements protocols::features::FeaturesReporter.

Member Data Documentation

core::Size protocols::features::TrajectoryMapFeatures::current_cycle_
private

Stores the cycle count for the current pose being saved.

Rather than storing the cycle count in pose (where it might be arbitrarily cleared), we are counting cycles/steps by mapping to output tag. Since the features reporter does not know what tag it is at apply time, but the ReportToDB subclassed mover does, this TrajectoryMapFeatures reporter is set up to query this variable to get the current cycle count, which should be up to date because the original apply() call is made to the TrajectoryMapFeatures mover. This variable being up-to-date and meaningful depends on it being set by the TrajectoryMapFeatures Mover (or an unimplemented at the time of this writing mover)

Referenced by get_current_cycle(), report_features(), and set_current_cycle().


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