protocols::rotamer_recovery::RRReporterSQLite Class Reference

#include <RRReporterSQLite.hh>

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 ()
	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)
void	set_comparer_info (std::string const &comparer_name, std::string const &comparer_params)
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)
virtual void	reset_recovery ()
virtual 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)
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)
virtual core::Real	recovery_rate () const
virtual void	show (std::ostream &out) const
virtual void	show () const
Public Member Functions inherited from protocols::rotamer_recovery::RRReporter
virtual	~RRReporter ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. 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

protocols::rotamer_recovery::RRReporterSQLite::RRReporterSQLite

(

)

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

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

protocols::rotamer_recovery::RRReporterSQLite::~RRReporterSQLite

(

)

protocols::rotamer_recovery::RRReporterSQLite::RRReporterSQLite

(

RRReporterSQLite const &

src

)

Member Function Documentation

void protocols::rotamer_recovery::RRReporterSQLite::db_session

(

utility::sql_database::sessionOP

db_session

)

sessionOP protocols::rotamer_recovery::RRReporterSQLite::db_session

(

)

References db_session_, and utility_exit_with_message.

Referenced by report_predicted_features(), report_rotamer_recovery_features(), and report_rotamer_recovery_full().

OutputLevel protocols::rotamer_recovery::RRReporterSQLite::get_output_level

(

)

const

References output_level_.

StructureID protocols::rotamer_recovery::RRReporterSQLite::get_struct_id1

(

)

const

References struct_id1_.

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

virtual

Implements protocols::rotamer_recovery::RRReporter.

References residues_considered_, and rotamers_recovered_.

Referenced by show().

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(), protocols::jd2::JobDistributor::current_output_name(), db_session(), dist_cutoff, protocols::jd2::JobDistributor::get_instance(), core::pose::metrics::CalculatorFactory::Instance(), core::pack::task::TaskFactory::push_back(), core::pose::metrics::CalculatorFactory::remove_calculator(), report_to_db_, safely_prepare_statement(), safely_write_to_database(), core::conformation::Residue::seqpos(), and core::pose::Pose::update_residue_neighbors().

Referenced by 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  )

virtual

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_, struct_id1_, and utility_exit_with_message.

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(), safely_prepare_statement(), safely_write_to_database(), and core::conformation::Residue::seqpos().

Referenced by report_rotamer_recovery().

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::JobDistributor::current_job(), core::pose::Pose::data(), db_session(), basic::datacache::BasicDataCache::get(), protocols::jd2::JobDistributor::get_instance(), basic::datacache::BasicDataCache::has(), protocols::jd2::Job::input_tag(), core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG, core::chemical::ResidueType::name(), core::conformation::Residue::name1(), core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), protocol_name_, protocol_params_, safely_prepare_statement(), safely_write_to_database(), core::conformation::Residue::seqpos(), protocols::kinmatch::str(), and core::conformation::Residue::type().

Referenced by report_rotamer_recovery().

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

virtual

Implements protocols::rotamer_recovery::RRReporter.

References residues_considered_, and rotamers_recovered_.

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

virtual

Implements protocols::rotamer_recovery::RRReporter.

References comparer_name_, and comparer_params_.

void protocols::rotamer_recovery::RRReporterSQLite::set_output_level

(

OutputLevel

output_level

)

References output_level_.

void protocols::rotamer_recovery::RRReporterSQLite::set_predicted_report_to_db

(

features::ReportToDBOP

report_to_db

)

References report_to_db_.

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

virtual

Implements protocols::rotamer_recovery::RRReporter.

References protocol_name_, and protocol_params_.

void protocols::rotamer_recovery::RRReporterSQLite::set_struct_id1

(

protocols::features::StructureID const

struct_id1

)

References struct_id1_.

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

virtual

Implements protocols::rotamer_recovery::RRReporter.

References recovery_rate(), residues_considered_, and rotamers_recovered_.

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

virtual

Implements protocols::rotamer_recovery::RRReporter.

References protocols::rotamer_recovery::TR.

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

private

generate the nchi table schema

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

Referenced by write_schema_to_db().

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

Referenced by write_schema_to_db().

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

Referenced by 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 protocols::rotamer_recovery::OL_features, protocols::rotamer_recovery::OL_full, protocols::rotamer_recovery::OL_none, output_level_, report_to_db_, utility_exit_with_message, 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

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

private

Referenced by report_rotamer_recovery_full(), and set_comparer_info().

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

private

Referenced by report_rotamer_recovery_full(), and set_comparer_info().

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

private

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

private

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

private

Referenced by db_session().

OutputLevel protocols::rotamer_recovery::RRReporterSQLite::output_level_

private

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

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

private

Referenced by report_rotamer_recovery_full(), and set_protocol_info().

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

private

Referenced by report_rotamer_recovery_full(), and set_protocol_info().

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().

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

private

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

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

private

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

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

private

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

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

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