protocols::features::HBondFeatures Class Reference

#include <HBondFeatures.hh>

Public Member Functions
	HBondFeatures ()
	HBondFeatures (core::scoring::ScoreFunctionOP scfxn)
	HBondFeatures (HBondFeatures const &src)
virtual	~HBondFeatures ()
std::string	type_name () const
	return string with class name More...
void	write_schema_to_db (utility::sql_database::sessionOP db_session) const
	generate the table schemas and write them to the database More...
utility::vector1< std::string >	features_reporter_dependencies () const
	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, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	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)
	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)
Public Member Functions inherited from protocols::features::FeaturesReporter
	FeaturesReporter ()
virtual	~FeaturesReporter ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. 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

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

(

)

References get_score_function().

protocols::features::HBondFeatures::HBondFeatures

(

core::scoring::ScoreFunctionOP

scfxn

)

protocols::features::HBondFeatures::HBondFeatures

(

HBondFeatures const &

src

)

protocols::features::HBondFeatures::~HBondFeatures ( )

virtual

Member Function Documentation

utility::vector1< std::string > protocols::features::HBondFeatures::features_reporter_dependencies ( ) const

virtual

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
	)

References core::scoring::hbonds::HBond::acc_res(), core::scoring::hbonds::HBond::don_res(), core::pose::Pose::energies(), core::conformation::Residue::is_protein(), core::pose::Pose::residue(), basic::database::safely_write_to_database(), core::scoring::Energies::tenA_neighbor_graph(), and core::conformation::Residue::xyz().

Referenced by report_features().

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
	)

References core::conformation::Residue::abase2(), core::scoring::hbonds::HBond::acc_atm(), core::scoring::hbonds::HBond::acc_res(), core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), dihedral_radians(), core::scoring::hbonds::HBond::don_hatm(), core::scoring::hbonds::HBond::don_res(), dot(), core::scoring::hbonds::HBond::eval_type(), get_hbe_acc_hybrid(), numeric::xyzVector< class >::length_squared(), make_hbBasetoAcc_unitvector(), core::pose::Pose::residue(), basic::database::safely_write_to_database(), core::conformation::Atom::xyz(), and protocols::kinmatch::xyz().

Referenced by report_features().

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
	)

References core::scoring::hbonds::HBond::acc_atm(), core::scoring::hbonds::HBond::acc_res(), core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::scoring::etable::TableLookupEtableEnergy::atom_pair_energy(), core::scoring::etable::AnalyticEtableEnergy::atom_pair_energy(), core::scoring::hbonds::HBond::don_hatm(), core::scoring::hbonds::HBond::don_res(), fa_atr, fa_rep, fa_sol, core::scoring::ScoringManager::get_instance(), core::pose::Pose::residue(), basic::database::safely_write_to_database(), and scfxn_.

Referenced by report_features().

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
	)

References core::scoring::hbonds::HBond::acc_atm(), core::scoring::hbonds::HBond::acc_res(), ASSERT_ONLY, core::scoring::hbonds::HBond::don_hatm(), core::scoring::hbonds::HBond::don_res(), core::scoring::hbonds::HBond::energy(), core::scoring::hbonds::HBond::eval_type(), hb_eval_type_weight(), basic::database::safely_write_to_database(), scfxn_, and core::scoring::hbonds::HBond::weight().

Referenced by report_features().

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
	)

References core::pose::Pose::residue(), basic::database::safely_write_to_database(), numeric::xyzVector< class >::x(), protocols::kinmatch::xyz(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by report_features().

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
	)

References core::pose::Pose::is_fullatom(), num_hbonds, basic::database::safely_prepare_statement(), basic::database::safely_write_to_database(), and size().

Referenced by report_features().

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(), basic::database::safely_prepare_statement(), and basic::database::safely_write_to_database().

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
	)

References core::conformation::Residue::atom_base(), core::conformation::Residue::atom_type(), core::pose::Pose::chain(), chain, get_hb_acc_chem_type(), get_hb_don_chem_type(), core::chemical::ResidueType::name(), core::chemical::AtomType::name(), core::scoring::hbonds::HBondTypeManager::name_from_acc_chem_type(), core::scoring::hbonds::HBondTypeManager::name_from_don_chem_type(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), basic::database::safely_prepare_statement(), and basic::database::safely_write_to_database().

Referenced by report_features().

void protocols::features::HBondFeatures::parse_my_tag ( utility::tag::TagCOP  tag, basic::datacache::DataMap &  data, protocols::filters::Filters_map const &  , protocols::moves::Movers_map const &  , core::pose::Pose const &    )

virtual

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_, basic::datacache::DataMap::get(), get_score_function(), protocols::features::hbdef_AHDIST, protocols::features::hbdef_ENERGY, and scfxn_.

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  )

virtual

collect all the feature data for the pose

Implements protocols::features::FeaturesReporter.

References core::scoring::hbonds::HBond::acc_res(), begin, calc_per_atom_sasa(), protocols::features::FeaturesReporter::check_relevant_residues(), core::pose::Pose::conformation(), definition_threshold_, definition_type_, core::scoring::hbonds::HBond::don_res(), end, core::pose::Pose::energies(), fill_hbond_set_by_AHdist_threshold(), get_score_function(), protocols::features::hbdef_AHDIST, protocols::features::hbdef_ENERGY, hbond, core::scoring::hbonds::HBondSet::hbond(), core::scoring::hbonds::HBond::hbond_energy_comparer(), core::scoring::hbonds::HBondSet::hbond_options(), initialize_atomid_map(), core::pose::initialize_atomid_map(), insert_hbond_dehydron_row(), insert_hbond_geom_coords(), insert_hbond_lennard_jones_row(), insert_hbond_row(), insert_site_atoms_row(), insert_site_environment_row(), insert_site_pdb_row(), insert_site_row(), core::pose::Pose::is_fullatom(), core::pose::symmetry::make_score_function_consistent_with_symmetric_state_of_pose(), core::pose::Pose::n_residue(), core::scoring::hbonds::HBondSet::nhbonds(), core::pose::Pose::residue(), core::scoring::Energies::residue_neighbors_updated(), runtime_assert, scfxn_, core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies(), core::conformation::Conformation::structure_moved(), protocols::features::TR, type, and utility_exit_with_message.

string protocols::features::HBondFeatures::type_name ( ) const

virtual

return string with class name

Reimplemented from protocols::features::FeaturesReporter.

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

private

References basic::database::schema_generator::Schema::add_column(), c, insert_or_ignore(), t, table, and basic::database::schema_generator::Schema::write().

Referenced by write_schema_to_db().

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

private

References basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_foreign_key(), table, and basic::database::schema_generator::Schema::write().

Referenced by write_schema_to_db().

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

private

References basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_foreign_key(), table, and basic::database::schema_generator::Schema::write().

Referenced by write_schema_to_db().

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

private

References basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_foreign_key(), table, and basic::database::schema_generator::Schema::write().

Referenced by write_schema_to_db().

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

private

References basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_foreign_key(), table, and basic::database::schema_generator::Schema::write().

Referenced by write_schema_to_db().

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

private

References basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_foreign_key(), num_hbonds, table, and basic::database::schema_generator::Schema::write().

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 basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_foreign_key(), chain, protocols::loops::iCode, table, and basic::database::schema_generator::Schema::write().

Referenced by write_schema_to_db().

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

private

References basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_foreign_key(), chain, table, and basic::database::schema_generator::Schema::write().

Referenced by write_schema_to_db().

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

private

References basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_foreign_key(), table, and basic::database::schema_generator::Schema::write().

Referenced by write_schema_to_db().

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

virtual

generate the table schemas and write them to the database

Implements protocols::features::FeaturesReporter.

References write_hbond_chem_types_table_schema(), write_hbond_dehydrons_table_schema(), write_hbond_geom_coords_table_schema(), write_hbond_lennard_jones_table_schema(), write_hbond_site_atoms_table_schema(), write_hbond_site_environment_table_schema(), write_hbond_sites_pdb_table_schema(), write_hbond_sites_table_schema(), and write_hbonds_table_schema().

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

Referenced by insert_hbond_lennard_jones_row(), insert_hbond_row(), parse_my_tag(), and report_features().

---

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

• src/protocols/features/HBondFeatures.hh
• src/protocols/features/HBondFeatures.cc