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protocols::features::PdbDataFeatures Class Reference

#include <PdbDataFeatures.hh>

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

 PdbDataFeatures ()
 
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_session) override
 
void load_into_pose (utility::sql_database::sessionOP db_session, StructureID struct_id, core::pose::Pose &pose) override
 
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 &)
 
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 Member Functions

void load_residue_pdb_identification (utility::sql_database::sessionOP db_session, StructureID struct_id, core::pose::Pose &pose)
 
void insert_residue_pdb_identification_rows (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session)
 
void load_residue_pdb_confidence (utility::sql_database::sessionOP db_session, StructureID struct_id, core::pose::Pose &pose)
 load the temperature and occupancy information into the PDBInfo object. Backbone atoms are assigned max_bb_temperature and min_bb_occupancy while sidechain atoms are assigned max_sc_temperature and min_sc_occupancy. More...
 
void insert_residue_pdb_confidence_rows (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session)
 

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::PdbDataFeatures::PdbDataFeatures ( )
default

Member Function Documentation

std::string protocols::features::PdbDataFeatures::class_name ( )
static
void protocols::features::PdbDataFeatures::delete_record ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
overridevirtual
utility::vector1< std::string > protocols::features::PdbDataFeatures::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.

void protocols::features::PdbDataFeatures::insert_residue_pdb_confidence_rows ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  relevant_residues,
StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
private
void protocols::features::PdbDataFeatures::insert_residue_pdb_identification_rows ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  relevant_residues,
StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
private
void protocols::features::PdbDataFeatures::load_into_pose ( utility::sql_database::sessionOP  db_session,
StructureID  struct_id,
core::pose::Pose pose 
)
overridevirtual
void protocols::features::PdbDataFeatures::load_residue_pdb_confidence ( utility::sql_database::sessionOP  db_session,
StructureID  struct_id,
core::pose::Pose pose 
)
private

load the temperature and occupancy information into the PDBInfo object. Backbone atoms are assigned max_bb_temperature and min_bb_occupancy while sidechain atoms are assigned max_sc_temperature and min_sc_occupancy.

Note: The information stored in the residue_pdb_confidence table is at the residue level not atom level. Since the temperature and occupancy is usually at the atom level, writing data to the database and reading it back in will result in a loss of information.

References core::pose::Pose::pdb_info(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and protocols::features::TR().

Referenced by load_into_pose().

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

Reimplemented from protocols::features::FeaturesReporter.

References class_name().

void protocols::features::PdbDataFeatures::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.


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