protocols::rotamer_recovery::RRReporterSQLite Class Reference

#include <RRReporterSQLite.hh>

Inheritance diagram for protocols::rotamer_recovery::RRReporterSQLite:

Collaboration diagram for protocols::rotamer_recovery::RRReporterSQLite:

Classes
struct	OutputLevel

Public Member Functions
	RRReporterSQLite ()
	RRReporterSQLite (std::string const &database_name, std::string const &database_pq_schema="", OutputLevel::e const output_level=OutputLevel::full)
	RRReporterSQLite (utility::sql_database::sessionOP db_session, OutputLevel::e const output_level=OutputLevel::full)
	~RRReporterSQLite ()
	RRReporterSQLite (RRReporterSQLite const &)
void	write_schema_to_db (utility::sql_database::sessionOP db_session, OutputLevel::e output_level=OutputLevel::full) 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)
utility::sql_database::sessionOP	db_session ()
void	set_output_level (OutputLevel::e const output_level)
OutputLevel::e	get_output_level () const
void	set_struct_id1 (boost::uuids::uuid const struct_id1)
boost::uuids::uuid	get_struct_id1 () const
void	set_struct_id2 (boost::uuids::uuid const struct_id1)
boost::uuids::uuid	get_struct_id2 () const
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 (boost::uuids::uuid struct_id1, core::conformation::Residue const &res1, core::Real score, bool recovered)
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...

Private Attributes
OutputLevel::e	output_level_
boost::uuids::uuid	struct_id1_
boost::uuids::uuid	struct_id2_
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_

Detailed Description

Definition at line 40 of file RRReporterSQLite.hh.

Constructor & Destructor Documentation

protocols::rotamer_recovery::RRReporterSQLite::RRReporterSQLite

(

)

Definition at line 76 of file RRReporterSQLite.cc.

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

Definition at line 91 of file RRReporterSQLite.cc.

protocols::rotamer_recovery::RRReporterSQLite::RRReporterSQLite	(	utility::sql_database::sessionOP	db_session,
		OutputLevel::e const	output_level = OutputLevel::full
	)

protocols::rotamer_recovery::RRReporterSQLite::~RRReporterSQLite

(

)

Definition at line 146 of file RRReporterSQLite.cc.

protocols::rotamer_recovery::RRReporterSQLite::RRReporterSQLite

(

RRReporterSQLite const &

src)

Definition at line 130 of file RRReporterSQLite.cc.

Member Function Documentation

sessionOP protocols::rotamer_recovery::RRReporterSQLite::db_session

(

)

Definition at line 351 of file RRReporterSQLite.cc.

References database_name_, database_pq_schema_, db_session_, get_output_level(), and write_schema_to_db().

Referenced by report_rotamer_recovery_full().

RRReporterSQLite::OutputLevel::e protocols::rotamer_recovery::RRReporterSQLite::get_output_level

(

)

const

Definition at line 301 of file RRReporterSQLite.cc.

References output_level_.

Referenced by db_session().

boost::uuids::uuid protocols::rotamer_recovery::RRReporterSQLite::get_struct_id1

(

)

const

Definition at line 314 of file RRReporterSQLite.cc.

References struct_id1_.

boost::uuids::uuid protocols::rotamer_recovery::RRReporterSQLite::get_struct_id2

(

)

const

Definition at line 327 of file RRReporterSQLite.cc.

References struct_id2_.

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

virtual

Implements protocols::rotamer_recovery::RRReporter.

Definition at line 483 of file RRReporterSQLite.cc.

References residues_considered_, and rotamers_recovered_.

Referenced by show().

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.

Definition at line 369 of file RRReporterSQLite.cc.

References protocols::rotamer_recovery::RRReporterSQLite::OutputLevel::features, protocols::rotamer_recovery::RRReporterSQLite::OutputLevel::full, protocols::rotamer_recovery::RRReporterSQLite::OutputLevel::none, output_level_, report_rotamer_recovery_features(), report_rotamer_recovery_full(), residues_considered_, rotamers_recovered_, and struct_id1_.

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

virtual

Definition at line 449 of file RRReporterSQLite.cc.

References db_session_, 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

Definition at line 396 of file RRReporterSQLite.cc.

References core::conformation::Residue::chain(), comparer_name_, comparer_params_, protocols::jd2::JobDistributor::current_job(), core::pose::Pose::data(), db_session(), protocols::jd2::JobDistributor::get_instance(), 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_, 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.

Definition at line 363 of file RRReporterSQLite.cc.

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.

Definition at line 342 of file RRReporterSQLite.cc.

References comparer_name_, and comparer_params_.

void protocols::rotamer_recovery::RRReporterSQLite::set_output_level

(

OutputLevel::e const

output_level)

Definition at line 294 of file RRReporterSQLite.cc.

References output_level_.

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

virtual

Implements protocols::rotamer_recovery::RRReporter.

Definition at line 333 of file RRReporterSQLite.cc.

References protocol_name_, and protocol_params_.

void protocols::rotamer_recovery::RRReporterSQLite::set_struct_id1

(

boost::uuids::uuid const

struct_id1)

Definition at line 307 of file RRReporterSQLite.cc.

References struct_id1_.

void protocols::rotamer_recovery::RRReporterSQLite::set_struct_id2

(

boost::uuids::uuid const

struct_id1)

Definition at line 320 of file RRReporterSQLite.cc.

References struct_id1_.

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

virtual

Implements protocols::rotamer_recovery::RRReporter.

Definition at line 469 of file RRReporterSQLite.cc.

References recovery_rate(), residues_considered_, and rotamers_recovered_.

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

virtual

Implements protocols::rotamer_recovery::RRReporter.

Definition at line 478 of file RRReporterSQLite.cc.

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

Definition at line 169 of file RRReporterSQLite.cc.

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

Definition at line 262 of file RRReporterSQLite.cc.

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

Definition at line 216 of file RRReporterSQLite.cc.

Referenced by write_schema_to_db().

void protocols::rotamer_recovery::RRReporterSQLite::write_schema_to_db	(	utility::sql_database::sessionOP	db_session,
		OutputLevel::e	output_level = OutputLevel::full
	)		const

generate the table schemas and write them to the database

Definition at line 149 of file RRReporterSQLite.cc.

References protocols::rotamer_recovery::RRReporterSQLite::OutputLevel::features, protocols::rotamer_recovery::RRReporterSQLite::OutputLevel::full, protocols::rotamer_recovery::RRReporterSQLite::OutputLevel::none, write_nchi_table_schema(), write_rotamer_recovery_features_table_schema(), and write_rotamer_recovery_full_table_schema().

Referenced by db_session(), and protocols::features::RotamerRecoveryFeatures::write_schema_to_db().

Member Data Documentation

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

private

Definition at line 186 of file RRReporterSQLite.hh.

Referenced by report_rotamer_recovery_full(), and set_comparer_info().

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

private

Definition at line 187 of file RRReporterSQLite.hh.

Referenced by report_rotamer_recovery_full(), and set_comparer_info().

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

private

Definition at line 192 of file RRReporterSQLite.hh.

Referenced by db_session().

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

private

Definition at line 193 of file RRReporterSQLite.hh.

Referenced by db_session().

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

private

Definition at line 194 of file RRReporterSQLite.hh.

Referenced by db_session(), and report_rotamer_recovery_features().

OutputLevel::e protocols::rotamer_recovery::RRReporterSQLite::output_level_

private

Definition at line 178 of file RRReporterSQLite.hh.

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

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

private

Definition at line 183 of file RRReporterSQLite.hh.

Referenced by report_rotamer_recovery_full(), and set_protocol_info().

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

private

Definition at line 184 of file RRReporterSQLite.hh.

Referenced by report_rotamer_recovery_full(), and set_protocol_info().

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

private

Definition at line 189 of file RRReporterSQLite.hh.

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

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

private

Definition at line 190 of file RRReporterSQLite.hh.

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

boost::uuids::uuid protocols::rotamer_recovery::RRReporterSQLite::struct_id1_

private

Definition at line 180 of file RRReporterSQLite.hh.

Referenced by get_struct_id1(), report_rotamer_recovery(), set_struct_id1(), and set_struct_id2().

boost::uuids::uuid protocols::rotamer_recovery::RRReporterSQLite::struct_id2_

private

Definition at line 181 of file RRReporterSQLite.hh.

Referenced by get_struct_id2().

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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