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protocols::features::HBondFeatures Class Reference

#include <HBondFeatures.hh>

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

 HBondFeatures ()
 
 HBondFeatures (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
 get what criteria should be used to define what constitutes a hydrogen bond 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 insert_site_row (core::pose::Pose const &pose, StructureID struct_id, core::Size site_id, core::Size resNum, core::Size atmNum, bool is_donor, utility::sql_database::sessionOP db_session)
 
void insert_site_pdb_row (core::pose::Pose const &pose, core::Size resNum, core::Size atmNum, core::Size heavy_atmNum, StructureID struct_id, core::Size site_id, utility::sql_database::sessionOP db_session)
 
void insert_site_environment_row (core::pose::Pose const &pose, core::Size resNum, core::Size atmNum, StructureID struct_id, core::Size site_id, core::id::AtomID_Map< core::Real > const &atom_sasa_s, core::id::AtomID_Map< core::Real > const &atom_sasa_m, core::id::AtomID_Map< core::Real > const &atom_sasa_l, core::id::AtomID_Map< utility::vector1< core::scoring::hbonds::HBondCOP > > const &site_partners, core::id::AtomID_Map< core::Real > const &site_hbond_energies, utility::sql_database::sessionOP db_session)
 
void insert_site_atoms_row (core::pose::Pose const &pose, core::Size resNum, core::Size atmNum, StructureID struct_id, core::Size site_id, utility::sql_database::sessionOP db_session)
 
void insert_hbond_row (core::scoring::hbonds::HBond const &hbond, StructureID struct_id, core::Size hbond_id, core::id::AtomID_Map< core::Size > const &site_ids, core::id::AtomID_Map< utility::vector1< core::scoring::hbonds::HBondCOP > > const &site_partners, utility::sql_database::sessionOP db_session)
 
void insert_hbond_geom_coords (core::pose::Pose const &pose, core::scoring::hbonds::HBondOptions const &hbond_options, core::scoring::hbonds::HBond const &hbond, StructureID struct_id, core::Size hbond_id, utility::sql_database::sessionOP db_session)
 
void insert_hbond_lennard_jones_row (core::pose::Pose const &pose, core::scoring::hbonds::HBond const &hbond, StructureID struct_id, core::Size hbond_id, utility::sql_database::sessionOP db_session)
 
void insert_hbond_dehydron_row (core::pose::Pose const &pose, core::scoring::hbonds::HBond const &hbond, StructureID struct_id, core::Size hbond_id, utility::sql_database::sessionOP db_session)
 
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_hbond_chem_types_table_schema (utility::sql_database::sessionOP db_session) const
 
void write_hbond_sites_table_schema (utility::sql_database::sessionOP db_session) const
 
void write_hbond_sites_pdb_table_schema (utility::sql_database::sessionOP db_session) const
 
void write_hbond_site_environment_table_schema (utility::sql_database::sessionOP db_session) const
 
void write_hbond_site_atoms_table_schema (utility::sql_database::sessionOP db_session) const
 
void write_hbonds_table_schema (utility::sql_database::sessionOP db_session) const
 
void write_hbond_lennard_jones_table_schema (utility::sql_database::sessionOP db_session) const
 
void write_hbond_geom_coords_table_schema (utility::sql_database::sessionOP db_session) const
 
void write_hbond_dehydrons_table_schema (utility::sql_database::sessionOP db_session) const
 

Private Attributes

core::scoring::ScoreFunctionOP scfxn_
 
HBDefType definition_type_
 
core::Real definition_threshold_
 

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

Member Function Documentation

std::string protocols::features::HBondFeatures::class_name ( )
static
utility::vector1< std::string > protocols::features::HBondFeatures::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::HBondFeatures::insert_hbond_dehydron_row ( core::pose::Pose const &  pose,
core::scoring::hbonds::HBond const &  hbond,
StructureID  struct_id,
core::Size  hbond_id,
utility::sql_database::sessionOP  db_session 
)
void protocols::features::HBondFeatures::insert_hbond_geom_coords ( core::pose::Pose const &  pose,
core::scoring::hbonds::HBondOptions const &  hbond_options,
core::scoring::hbonds::HBond const &  hbond,
StructureID  struct_id,
core::Size  hbond_id,
utility::sql_database::sessionOP  db_session 
)
void protocols::features::HBondFeatures::insert_hbond_lennard_jones_row ( core::pose::Pose const &  pose,
core::scoring::hbonds::HBond const &  hbond,
StructureID  struct_id,
core::Size  hbond_id,
utility::sql_database::sessionOP  db_session 
)
void protocols::features::HBondFeatures::insert_hbond_row ( core::scoring::hbonds::HBond const &  hbond,
StructureID  struct_id,
core::Size  hbond_id,
core::id::AtomID_Map< core::Size > const &  site_ids,
core::id::AtomID_Map< utility::vector1< core::scoring::hbonds::HBondCOP > > const &  site_partners,
utility::sql_database::sessionOP  db_session 
)
void protocols::features::HBondFeatures::insert_site_atoms_row ( core::pose::Pose const &  pose,
core::Size  resNum,
core::Size  atmNum,
StructureID  struct_id,
core::Size  site_id,
utility::sql_database::sessionOP  db_session 
)
void protocols::features::HBondFeatures::insert_site_environment_row ( core::pose::Pose const &  pose,
core::Size  resNum,
core::Size  atmNum,
StructureID  struct_id,
core::Size  site_id,
core::id::AtomID_Map< core::Real > const &  atom_sasa_s,
core::id::AtomID_Map< core::Real > const &  atom_sasa_m,
core::id::AtomID_Map< core::Real > const &  atom_sasa_l,
core::id::AtomID_Map< utility::vector1< core::scoring::hbonds::HBondCOP > > const &  site_partners,
core::id::AtomID_Map< core::Real > const &  site_hbond_energies,
utility::sql_database::sessionOP  db_session 
)
void protocols::features::HBondFeatures::insert_site_pdb_row ( core::pose::Pose const &  pose,
core::Size  resNum,
core::Size  atmNum,
core::Size  heavy_atmNum,
StructureID  struct_id,
core::Size  site_id,
utility::sql_database::sessionOP  db_session 
)

References core::pose::Pose::pdb_info().

Referenced by report_features().

void protocols::features::HBondFeatures::insert_site_row ( core::pose::Pose const &  pose,
StructureID  struct_id,
core::Size  site_id,
core::Size  resNum,
core::Size  atmNum,
bool  is_donor,
utility::sql_database::sessionOP  db_session 
)
void protocols::features::HBondFeatures::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

get what criteria should be used to define what constitutes a hydrogen bond

set what criteria should be used to define what constitutes a hydrogen bond get the definition threshold that should be used to define what constitutes a hydrogen bond set the definition threshold that should be used to define what constitutes a hydrogen bond

Reimplemented from protocols::features::FeaturesReporter.

References definition_threshold_, definition_type_, core::scoring::get_score_function(), protocols::features::hbdef_AHDIST, protocols::features::hbdef_ENERGY, and scfxn_.

void protocols::features::HBondFeatures::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
Size protocols::features::HBondFeatures::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::HBondFeatures::type_name ( ) const
overridevirtual

Reimplemented from protocols::features::FeaturesReporter.

References class_name().

void protocols::features::HBondFeatures::write_hbond_chem_types_table_schema ( utility::sql_database::sessionOP  db_session) const
private
void protocols::features::HBondFeatures::write_hbond_dehydrons_table_schema ( utility::sql_database::sessionOP  db_session) const
private

Referenced by write_schema_to_db().

void protocols::features::HBondFeatures::write_hbond_geom_coords_table_schema ( utility::sql_database::sessionOP  db_session) const
private

Referenced by write_schema_to_db().

void protocols::features::HBondFeatures::write_hbond_lennard_jones_table_schema ( utility::sql_database::sessionOP  db_session) const
private

Referenced by write_schema_to_db().

void protocols::features::HBondFeatures::write_hbond_site_atoms_table_schema ( utility::sql_database::sessionOP  db_session) const
private

Referenced by write_schema_to_db().

void protocols::features::HBondFeatures::write_hbond_site_environment_table_schema ( utility::sql_database::sessionOP  db_session) const
private

Referenced by write_schema_to_db().

void protocols::features::HBondFeatures::write_hbond_sites_pdb_table_schema ( utility::sql_database::sessionOP  db_session) const
private

References protocols::loops::iCode.

Referenced by write_schema_to_db().

void protocols::features::HBondFeatures::write_hbond_sites_table_schema ( utility::sql_database::sessionOP  db_session) const
private

Referenced by write_schema_to_db().

void protocols::features::HBondFeatures::write_hbonds_table_schema ( utility::sql_database::sessionOP  db_session) const
private

Referenced by write_schema_to_db().

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

Member Data Documentation

core::Real protocols::features::HBondFeatures::definition_threshold_
private

Referenced by parse_my_tag(), and report_features().

HBDefType protocols::features::HBondFeatures::definition_type_
private

Referenced by parse_my_tag(), and report_features().

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

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