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protocols::features::AtomInResidueAtomInResiduePairFeatures Class Reference

#include <AtomInResidueAtomInResiduePairFeatures.hh>

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

 AtomInResidueAtomInResiduePairFeatures ()
 
void write_schema_to_db (utility::sql_database::sessionOP db_session) const override
 return string with class name 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 report_atom_pairs (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session)
 Similar to radial density distributions defined in Lu H, Skolnick J. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins. 2001;44(3):223-32. Available at: http://www.ncbi.nlm.nih.gov/pubmed/11455595. 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_atom_in_residue_pairs_table_schema (utility::sql_database::sessionOP db_session) const
 generate the atom_in_residue_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::AtomInResidueAtomInResiduePairFeatures::AtomInResidueAtomInResiduePairFeatures ( )
default

Member Function Documentation

std::string protocols::features::AtomInResidueAtomInResiduePairFeatures::class_name ( )
static
utility::vector1< std::string > protocols::features::AtomInResidueAtomInResiduePairFeatures::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::AtomInResidueAtomInResiduePairFeatures::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::features::AtomInResidueAtomInResiduePairFeatures::report_atom_pairs ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  relevant_residues,
StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)

Similar to radial density distributions defined in Lu H, Skolnick J. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins. 2001;44(3):223-32. Available at: http://www.ncbi.nlm.nih.gov/pubmed/11455595.

This is very similar in spirit to the potential described in

´╗┐Lu H, Skolnick J. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins. 2001;44(3):223-32. Available at: http://www.ncbi.nlm.nih.gov/pubmed/11455595.

However, they use different distance bins. Here, [0,1), ..., [9,10) are used because they are easy and as they report the the paper, most of the signal comes in the 3.5-6.5 range. To get the molar fraction of atom types–since the types are unique within each residue type, there is exactly one per residue of that type. Therefore this information can be extracted from the Residues table when needed. It may make sense to include it here if it turns to to be too cumbersom to get those quantities.

TODO: Expand for not just canonical residue types

References protocols::features::FeaturesReporter::check_relevant_residues(), core::pose::Pose::conformation(), core::pose::Pose::energies(), core::chemical::num_canonical_aas, core::pose::Pose::residue(), core::scoring::Energies::residue_neighbors_updated(), core::pose::Pose::size(), core::conformation::Conformation::structure_moved(), and core::scoring::Energies::tenA_neighbor_graph().

Referenced by report_features().

Size protocols::features::AtomInResidueAtomInResiduePairFeatures::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 report_atom_pairs().

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

Reimplemented from protocols::features::FeaturesReporter.

References class_name().

void protocols::features::AtomInResidueAtomInResiduePairFeatures::write_atom_in_residue_pairs_table_schema ( utility::sql_database::sessionOP  db_session) const
private

generate the atom_in_residue_pairs table schema

Referenced by write_schema_to_db().

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

return string with class name

generate the table schemas and write them to the database

Implements protocols::features::FeaturesReporter.

References write_atom_in_residue_pairs_table_schema().


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