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protocols::features::ResidueScoresFeatures Class Reference

#include <ResidueScoresFeatures.hh>

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

 ResidueScoresFeatures ()
 
 ResidueScoresFeatures (core::scoring::ScoreFunctionOP scfxn)
 
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...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 
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...
 
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 Member Functions

void write_residue_scores_1b_table_schema (utility::sql_database::sessionOP db_session) const
 generate the residue_scores_1b table schema More...
 
void write_residue_scores_2b_table_schema_helper (std::string name, utility::sql_database::sessionOP db_session) const
 2b schema helper More...
 
void write_residue_scores_2b_table_schema (utility::sql_database::sessionOP db_session) const
 generate the residue_scores_2b table schema More...
 
void write_residue_scores_lr_2b_table_schema (utility::sql_database::sessionOP db_session) const
 generate the residue_scores_2b table schema More...
 
void insert_residue_scores_rows (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID const struct_id, utility::sql_database::sessionOP db_session)
 
void insert_one_body_residue_score_rows (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, core::Size const batch_id, StructureID const struct_id, utility::sql_database::sessionOP db_session)
 
void insert_two_body_residue_score_rows (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, core::Size const batch_id, StructureID const struct_id, utility::sql_database::sessionOP db_session)
 
void insert_two_body_long_range_residue_score_rows (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, core::Size const batch_id, StructureID const struct_id, utility::sql_database::sessionOP db_session)
 

Private Attributes

core::scoring::ScoreFunctionOP scfxn_
 

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::ResidueScoresFeatures::ResidueScoresFeatures ( )
protocols::features::ResidueScoresFeatures::ResidueScoresFeatures ( core::scoring::ScoreFunctionOP  scfxn)

Member Function Documentation

std::string protocols::features::ResidueScoresFeatures::class_name ( )
static
utility::vector1< std::string > protocols::features::ResidueScoresFeatures::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::ResidueScoresFeatures::insert_one_body_residue_score_rows ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  relevant_residues,
core::Size const  batch_id,
StructureID const  struct_id,
utility::sql_database::sessionOP  db_session 
)
private
void protocols::features::ResidueScoresFeatures::insert_residue_scores_rows ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  relevant_residues,
StructureID const  struct_id,
utility::sql_database::sessionOP  db_session 
)
private
  • Score types are either one body, two body, or whole structure and can either dependend on the context or not.
  • Whole structure terms are reported in the structure_scores table along with the totals from the remaining terms.
  • The one and two body terms are broken up into two different tables because they are parametrized differently (one residue vs two residues).
  • Residues are identified by Rosetta's residue numbering scheme. To convert to the PDB residue numbering scheme, join with the residues_pdb table.
  • Although two body terms can be with in the same residue, these 'intrares' score terms are reported with the two body terms where resNum == otherResNum.
  • Two body terms always are reported so that resNum1 <= resNum2.
  • Values for score terms are only reported if they are non-zero.
  • Values of two body energies are only reported when both residues are true in the relevant_residues vector.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, protocols::features::get_batch_id(), insert_one_body_residue_score_rows(), insert_two_body_long_range_residue_score_rows(), insert_two_body_residue_score_rows(), core::pose::Pose::residue(), scfxn_, and core::pose::Pose::size().

Referenced by report_features().

void protocols::features::ResidueScoresFeatures::insert_two_body_long_range_residue_score_rows ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  relevant_residues,
core::Size const  batch_id,
StructureID const  struct_id,
utility::sql_database::sessionOP  db_session 
)
private
void protocols::features::ResidueScoresFeatures::insert_two_body_residue_score_rows ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  relevant_residues,
core::Size const  batch_id,
StructureID const  struct_id,
utility::sql_database::sessionOP  db_session 
)
private
void protocols::features::ResidueScoresFeatures::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Reimplemented from protocols::features::FeaturesReporter.

References scfxn_.

void protocols::features::ResidueScoresFeatures::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
Size protocols::features::ResidueScoresFeatures::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 insert_residue_scores_rows().

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

Reimplemented from protocols::features::FeaturesReporter.

References class_name().

void protocols::features::ResidueScoresFeatures::write_residue_scores_1b_table_schema ( utility::sql_database::sessionOP  db_session) const
private

generate the residue_scores_1b table schema

Referenced by write_schema_to_db().

void protocols::features::ResidueScoresFeatures::write_residue_scores_2b_table_schema ( utility::sql_database::sessionOP  db_session) const
private

generate the residue_scores_2b table schema

References write_residue_scores_2b_table_schema_helper().

Referenced by write_schema_to_db().

void protocols::features::ResidueScoresFeatures::write_residue_scores_2b_table_schema_helper ( std::string  name,
utility::sql_database::sessionOP  db_session 
) const
private
void protocols::features::ResidueScoresFeatures::write_residue_scores_lr_2b_table_schema ( utility::sql_database::sessionOP  db_session) const
private

generate the residue_scores_2b table schema

References write_residue_scores_2b_table_schema_helper().

Referenced by write_schema_to_db().

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

Member Data Documentation

core::scoring::ScoreFunctionOP protocols::features::ResidueScoresFeatures::scfxn_
private

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