#include <RRReporterSQLite.hh>

Inheritance diagram for protocols::rotamer_recovery::RRReporterSQLite:

Public Member Functions
	RRReporterSQLite ()

	RRReporterSQLite (std::string const &database_name, std::string const &database_pq_schema="", OutputLevel output_level=protocols::rotamer_recovery::OL_full)

	RRReporterSQLite (utility::sql_database::sessionOP db_session, OutputLevel output_level=protocols::rotamer_recovery::OL_full)

	~RRReporterSQLite () override

	RRReporterSQLite (RRReporterSQLite const &)

void	write_schema_to_db (utility::sql_database::sessionOP db_session) const
	generate the table schemas and write them to the database More...

void	set_protocol_info (std::string const &protocol_name, std::string const &protocol_params) override

void	set_comparer_info (std::string const &comparer_name, std::string const &comparer_params) override

void	db_session (utility::sql_database::sessionOP db_session)

utility::sql_database::sessionOP	db_session ()

void	set_output_level (OutputLevel output_level)

OutputLevel	get_output_level () const

void	set_struct_id1 (protocols::features::StructureID const struct_id1)

protocols::features::StructureID	get_struct_id1 () const

void	set_predicted_report_to_db (features::ReportToDBOP report_to_db)

void	reset_recovery () override

void	report_rotamer_recovery (core::pose::Pose const &pose1, core::pose::Pose const &pose2, core::conformation::Residue const &res1, core::conformation::Residue const &res2, core::Real score, bool recovered) override

virtual void	report_rotamer_recovery_full (core::pose::Pose const &pose1, core::pose::Pose const &pose2, core::conformation::Residue const &res1, core::conformation::Residue const &res2, core::Real score, bool recovered)

virtual void	report_rotamer_recovery_features (protocols::features::StructureID struct_id1, core::conformation::Residue const &res1, core::Real score, bool recovered)

virtual void	report_predicted_features (features::StructureID struct_id1, core::conformation::Residue const &res1, core::pose::Pose const &predicted_pose, core::conformation::Residue const &predicted_res)

core::Real	recovery_rate () const override

void	show (std::ostream &out) const override

void	show () const override

Public Member Functions inherited from protocols::rotamer_recovery::RRReporter
	~RRReporter () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. More...

Private Member Functions
void	write_nchi_table_schema (utility::sql_database::sessionOP db_session) const
	generate the nchi table schema More...

void	write_rotamer_recovery_full_table_schema (utility::sql_database::sessionOP db_session) const
	generate the full rotamer_recovery table schema More...

void	write_rotamer_recovery_features_table_schema (utility::sql_database::sessionOP db_session) const
	generate the features rotamer_recovery table schema More...

void	write_predicted_features_table_schema (utility::sql_database::sessionOP db_session) const
	generate the predicted_features table schema More...

Private Attributes
OutputLevel	output_level_

protocols::features::StructureID	struct_id1_

protocols::features::ReportToDBOP	report_to_db_

std::string	protocol_name_

std::string	protocol_params_

std::string	comparer_name_

std::string	comparer_params_

core::Size	residues_considered_

core::Size	rotamers_recovered_

std::string	database_name_

std::string	database_pq_schema_

utility::sql_database::sessionOP	db_session_

Constructor & Destructor Documentation

◆ RRReporterSQLite() [1/4]

protocols::rotamer_recovery::RRReporterSQLite::RRReporterSQLite ( )

◆ RRReporterSQLite() [2/4]

protocols::rotamer_recovery::RRReporterSQLite::RRReporterSQLite	(	std::string const &	database_name,
		std::string const &	database_pq_schema = `""`,
		OutputLevel	output_level = `protocols::rotamer_recovery::OL_full`
	)

◆ RRReporterSQLite() [3/4]

protocols::rotamer_recovery::RRReporterSQLite::RRReporterSQLite	(	utility::sql_database::sessionOP	db_session,
		OutputLevel	output_level = `protocols::rotamer_recovery::OL_full`
	)

◆ ~RRReporterSQLite()

protocols::rotamer_recovery::RRReporterSQLite::~RRReporterSQLite ( )

overridedefault

◆ RRReporterSQLite() [4/4]

protocols::rotamer_recovery::RRReporterSQLite::RRReporterSQLite ( RRReporterSQLite const & src )

Member Function Documentation

◆ db_session() [1/2]

sessionOP protocols::rotamer_recovery::RRReporterSQLite::db_session ( )

References db_session_.

Referenced by report_predicted_features(), report_rotamer_recovery_features(), report_rotamer_recovery_full(), write_nchi_table_schema(), write_predicted_features_table_schema(), write_rotamer_recovery_features_table_schema(), write_rotamer_recovery_full_table_schema(), and write_schema_to_db().

◆ db_session() [2/2]

void protocols::rotamer_recovery::RRReporterSQLite::db_session ( utility::sql_database::sessionOP db_session )

◆ get_output_level()

OutputLevel protocols::rotamer_recovery::RRReporterSQLite::get_output_level ( ) const

References output_level_.

◆ get_struct_id1()

StructureID protocols::rotamer_recovery::RRReporterSQLite::get_struct_id1 ( ) const

References struct_id1_.

◆ recovery_rate()

Real protocols::rotamer_recovery::RRReporterSQLite::recovery_rate ( ) const

overridevirtual

Implements protocols::rotamer_recovery::RRReporter.

References residues_considered_, and rotamers_recovered_.

Referenced by show().

◆ report_predicted_features()

void protocols::rotamer_recovery::RRReporterSQLite::report_predicted_features	(	features::StructureID	struct_id1,
		core::conformation::Residue const &	res1,
		core::pose::Pose const &	predicted_pose,
		core::conformation::Residue const &	predicted_res
	)

virtual

References protocols::jd2::current_output_name(), db_session(), core::pose::metrics::CalculatorFactory::Instance(), core::pose::metrics::CalculatorFactory::remove_calculator(), report_to_db_, core::conformation::Residue::seqpos(), and core::pose::Pose::update_residue_neighbors().

Referenced by report_rotamer_recovery().

◆ report_rotamer_recovery()

void protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		core::conformation::Residue const &	res1,
		core::conformation::Residue const &	res2,
		core::Real	score,
		bool	recovered
	)

overridevirtual

Implements protocols::rotamer_recovery::RRReporter.

References protocols::rotamer_recovery::OL_features, protocols::rotamer_recovery::OL_full, protocols::rotamer_recovery::OL_none, output_level_, report_predicted_features(), report_rotamer_recovery_features(), report_rotamer_recovery_full(), residues_considered_, rotamers_recovered_, protocols::hybridization::score, and struct_id1_.

◆ report_rotamer_recovery_features()

void protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_features	(	protocols::features::StructureID	struct_id1,
		core::conformation::Residue const &	res1,
		core::Real	score,
		bool	recovered
	)

virtual

References db_session(), protocols::hybridization::score, and core::conformation::Residue::seqpos().

Referenced by report_rotamer_recovery().

◆ report_rotamer_recovery_full()

void protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		core::conformation::Residue const &	res1,
		core::conformation::Residue const &	res2,
		core::Real	score,
		bool	recovered
	)

virtual

References core::conformation::Residue::chain(), comparer_name_, comparer_params_, protocols::jd2::current_input_tag(), core::pose::Pose::data(), db_session(), core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG, core::chemical::ResidueTypeBase::name(), core::conformation::Residue::name1(), core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), protocol_name_, protocol_params_, protocols::hybridization::score, core::conformation::Residue::seqpos(), protocols::kinmatch::str(), and core::conformation::Residue::type().

Referenced by report_rotamer_recovery().

◆ reset_recovery()

void protocols::rotamer_recovery::RRReporterSQLite::reset_recovery ( )

overridevirtual

Implements protocols::rotamer_recovery::RRReporter.

References residues_considered_, and rotamers_recovered_.

◆ set_comparer_info()

void protocols::rotamer_recovery::RRReporterSQLite::set_comparer_info	(	std::string const &	comparer_name,
		std::string const &	comparer_params
	)

overridevirtual

Implements protocols::rotamer_recovery::RRReporter.

References comparer_name_, and comparer_params_.

◆ set_output_level()

void protocols::rotamer_recovery::RRReporterSQLite::set_output_level ( OutputLevel output_level )

References output_level_.

◆ set_predicted_report_to_db()

void protocols::rotamer_recovery::RRReporterSQLite::set_predicted_report_to_db ( features::ReportToDBOP report_to_db )

References report_to_db_.

◆ set_protocol_info()

void protocols::rotamer_recovery::RRReporterSQLite::set_protocol_info	(	std::string const &	protocol_name,
		std::string const &	protocol_params
	)

overridevirtual

Implements protocols::rotamer_recovery::RRReporter.

References protocol_name_, and protocol_params_.

◆ set_struct_id1()

void protocols::rotamer_recovery::RRReporterSQLite::set_struct_id1 ( protocols::features::StructureID const struct_id1 )

References struct_id1_.

◆ show() [1/2]

void protocols::rotamer_recovery::RRReporterSQLite::show ( ) const

overridevirtual

Implements protocols::rotamer_recovery::RRReporter.

References protocols::rotamer_recovery::TR().

◆ show() [2/2]

void protocols::rotamer_recovery::RRReporterSQLite::show ( std::ostream & out ) const

overridevirtual

Implements protocols::rotamer_recovery::RRReporter.

References core::conformation::membrane::out, recovery_rate(), residues_considered_, and rotamers_recovered_.

◆ write_nchi_table_schema()

void protocols::rotamer_recovery::RRReporterSQLite::write_nchi_table_schema ( utility::sql_database::sessionOP db_session ) const

private

generate the nchi table schema

References db_session().

Referenced by write_schema_to_db().

◆ write_predicted_features_table_schema()

void protocols::rotamer_recovery::RRReporterSQLite::write_predicted_features_table_schema ( utility::sql_database::sessionOP db_session ) const

private

generate the predicted_features table schema

References db_session().

Referenced by write_schema_to_db().

◆ write_rotamer_recovery_features_table_schema()

void protocols::rotamer_recovery::RRReporterSQLite::write_rotamer_recovery_features_table_schema ( utility::sql_database::sessionOP db_session ) const

private

generate the features rotamer_recovery table schema

References db_session().

Referenced by write_schema_to_db().

◆ write_rotamer_recovery_full_table_schema()

void protocols::rotamer_recovery::RRReporterSQLite::write_rotamer_recovery_full_table_schema ( utility::sql_database::sessionOP db_session ) const

private

generate the full rotamer_recovery table schema

References db_session(), and protocols::hybridization::score.

Referenced by write_schema_to_db().

◆ write_schema_to_db()

void protocols::rotamer_recovery::RRReporterSQLite::write_schema_to_db ( utility::sql_database::sessionOP db_session ) const

generate the table schemas and write them to the database

References db_session(), protocols::rotamer_recovery::OL_features, protocols::rotamer_recovery::OL_full, protocols::rotamer_recovery::OL_none, output_level_, report_to_db_, write_nchi_table_schema(), write_predicted_features_table_schema(), write_rotamer_recovery_features_table_schema(), and write_rotamer_recovery_full_table_schema().

Member Data Documentation

◆ comparer_name_

std::string protocols::rotamer_recovery::RRReporterSQLite::comparer_name_

private

Referenced by report_rotamer_recovery_full(), and set_comparer_info().

◆ comparer_params_

std::string protocols::rotamer_recovery::RRReporterSQLite::comparer_params_

private

Referenced by report_rotamer_recovery_full(), and set_comparer_info().

◆ database_name_

std::string protocols::rotamer_recovery::RRReporterSQLite::database_name_

private

◆ database_pq_schema_

std::string protocols::rotamer_recovery::RRReporterSQLite::database_pq_schema_

private

◆ db_session_

utility::sql_database::sessionOP protocols::rotamer_recovery::RRReporterSQLite::db_session_

private

Referenced by db_session().

◆ output_level_

OutputLevel protocols::rotamer_recovery::RRReporterSQLite::output_level_

private

Referenced by get_output_level(), report_rotamer_recovery(), set_output_level(), and write_schema_to_db().

◆ protocol_name_

std::string protocols::rotamer_recovery::RRReporterSQLite::protocol_name_

private

Referenced by report_rotamer_recovery_full(), and set_protocol_info().

◆ protocol_params_

std::string protocols::rotamer_recovery::RRReporterSQLite::protocol_params_

private

Referenced by report_rotamer_recovery_full(), and set_protocol_info().

◆ report_to_db_

protocols::features::ReportToDBOP protocols::rotamer_recovery::RRReporterSQLite::report_to_db_

private

Referenced by report_predicted_features(), set_predicted_report_to_db(), and write_schema_to_db().

◆ residues_considered_

core::Size protocols::rotamer_recovery::RRReporterSQLite::residues_considered_

private

Referenced by recovery_rate(), report_rotamer_recovery(), reset_recovery(), and show().

◆ rotamers_recovered_

core::Size protocols::rotamer_recovery::RRReporterSQLite::rotamers_recovered_

private

Referenced by recovery_rate(), report_rotamer_recovery(), reset_recovery(), and show().

◆ struct_id1_

protocols::features::StructureID protocols::rotamer_recovery::RRReporterSQLite::struct_id1_

private

Referenced by get_struct_id1(), report_rotamer_recovery(), and set_struct_id1().

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

src/protocols/rotamer_recovery/RRReporterSQLite.hh
src/protocols/rotamer_recovery/RRReporterSQLite.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ RRReporterSQLite() [1/4]

◆ RRReporterSQLite() [2/4]

◆ RRReporterSQLite() [3/4]

◆ ~RRReporterSQLite()

◆ RRReporterSQLite() [4/4]

Member Function Documentation

◆ db_session() [1/2]

◆ db_session() [2/2]

◆ get_output_level()

◆ get_struct_id1()

◆ recovery_rate()

◆ report_predicted_features()

◆ report_rotamer_recovery()

◆ report_rotamer_recovery_features()

◆ report_rotamer_recovery_full()

◆ reset_recovery()

◆ set_comparer_info()

◆ set_output_level()

◆ set_predicted_report_to_db()

◆ set_protocol_info()

◆ set_struct_id1()

◆ show() [1/2]

◆ show() [2/2]

◆ write_nchi_table_schema()

◆ write_predicted_features_table_schema()

◆ write_rotamer_recovery_features_table_schema()

◆ write_rotamer_recovery_full_table_schema()

◆ write_schema_to_db()

Member Data Documentation

◆ comparer_name_

◆ comparer_params_

◆ database_name_

◆ database_pq_schema_

◆ db_session_

◆ output_level_

◆ protocol_name_

◆ protocol_params_

◆ report_to_db_

◆ residues_considered_

◆ rotamers_recovered_

◆ struct_id1_