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Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
protocols::features::ModelFeatures Class Reference

#include <ModelFeatures.hh>

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

 ModelFeatures ()
 
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...
 
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< Segmentfind_segments (protocols::features::StructureID struct_id, utility::sql_database::sessionOP db_session)
 get the vector of beginnings/ends of secondary structure segments More...
 
void trim_pose (core::pose::Pose &pose, std::set< core::Size > resnums) const
 for testing purposes only More...
 
core::Size report_features (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, protocols::features::StructureID struct_id, utility::sql_database::sessionOP db_session) override
 collect all the feature data for the pose More...
 
void write_clique_to_db (std::set< core::Size > const &clique, protocols::features::StructureID struct_id, utility::sql_database::sessionOP db_session) const
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) 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 load_into_pose (utility::sql_database::sessionOP, StructureID, core::pose::Pose &)
 
virtual void delete_record (StructureID, utility::sql_database::sessionOP)
 
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 min_helix_size_
 
core::Size min_strand_size_
 
core::Size min_ss_cluster_size_
 
core::Size max_ss_cluster_size_
 
core::Real distance_cutoff_
 
core::Real angle_cutoff_
 

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::ModelFeatures::ModelFeatures ( )

Member Function Documentation

std::string protocols::features::ModelFeatures::class_name ( )
static
utility::vector1< std::string > protocols::features::ModelFeatures::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.

utility::vector1< Segment > protocols::features::ModelFeatures::find_segments ( protocols::features::StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
void protocols::features::ModelFeatures::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::features::ModelFeatures::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
core::Size protocols::features::ModelFeatures::report_features ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  relevant_residues,
protocols::features::StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
overridevirtual
void protocols::features::ModelFeatures::trim_pose ( core::pose::Pose pose,
std::set< core::Size resnums 
) const
std::string protocols::features::ModelFeatures::type_name ( ) const
overridevirtual

Reimplemented from protocols::features::FeaturesReporter.

References class_name().

Referenced by parse_my_tag().

void protocols::features::ModelFeatures::write_clique_to_db ( std::set< core::Size > const &  clique,
protocols::features::StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
) const

Referenced by report_features().

void protocols::features::ModelFeatures::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::Real protocols::features::ModelFeatures::angle_cutoff_
private

Referenced by parse_my_tag(), and report_features().

core::Real protocols::features::ModelFeatures::distance_cutoff_
private

Referenced by parse_my_tag(), and report_features().

core::Size protocols::features::ModelFeatures::max_ss_cluster_size_
private

Referenced by parse_my_tag(), and report_features().

core::Size protocols::features::ModelFeatures::min_helix_size_
private
core::Size protocols::features::ModelFeatures::min_ss_cluster_size_
private

Referenced by parse_my_tag(), and report_features().

core::Size protocols::features::ModelFeatures::min_strand_size_
private

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