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protocols::features::ProteinBackboneAtomAtomPairFeatures Class Reference

#include <ProteinBackboneAtomAtomPairFeatures.hh>

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

 ProteinBackboneAtomAtomPairFeatures ()
 
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...
 
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 &)
 
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_protein_backbone_atom_atom_pairs_table_schema (utility::sql_database::sessionOP db_session) const
 generate the protein_backbone_atom_atom_pairs table schema 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::ProteinBackboneAtomAtomPairFeatures::ProteinBackboneAtomAtomPairFeatures ( )
default

Member Function Documentation

std::string protocols::features::ProteinBackboneAtomAtomPairFeatures::class_name ( )
static
utility::vector1< std::string > protocols::features::ProteinBackboneAtomAtomPairFeatures::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::ProteinBackboneAtomAtomPairFeatures::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
Size protocols::features::ProteinBackboneAtomAtomPairFeatures::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

These atom-atom pairs follow the analysis done in:

Song Y, Tyka M, Leaver-Fay A, Thompson J, Baker D. Structure guided forcefield optimization. Proteins: Structure, Function, and Bioinformatics. 2011:n/a-n/a. Available at: http://doi.wiley.com/10.1002/prot.23013 [Accessed April 4, 2011].

The HBond geometries are recoded in the HBondFeatures reporter

Implements protocols::features::FeaturesReporter.

References core::conformation::Residue::aa(), core::chemical::aa_gly, protocols::features::FeaturesReporter::check_relevant_residues(), core::pose::Pose::energies(), core::conformation::Residue::is_protein(), core::pose::Pose::residue(), core::pose::Pose::size(), core::scoring::Energies::tenA_neighbor_graph(), and core::conformation::Residue::xyz().

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

Reimplemented from protocols::features::FeaturesReporter.

References class_name().

void protocols::features::ProteinBackboneAtomAtomPairFeatures::write_protein_backbone_atom_atom_pairs_table_schema ( utility::sql_database::sessionOP  db_session) const
private

generate the protein_backbone_atom_atom_pairs table schema

Referenced by write_schema_to_db().

void protocols::features::ProteinBackboneAtomAtomPairFeatures::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.

References write_protein_backbone_atom_atom_pairs_table_schema().


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