protocols::features::ProteinSilentReport Class Reference

#include <ProteinSilentReport.hh>

Inheritance diagram for protocols::features::ProteinSilentReport:

Public Types
typedef std::map< core::Size, core::pose::PoseOP >	StructureMap
Public Types inherited from protocols::features::Report
typedef utility::vector1 < FeaturesReporterOP >	FeaturesReporters

Public Member Functions
	ProteinSilentReport ()
core::Size	version () override
bool	is_initialized () const
void	initialize (utility::sql_database::sessionOP db_session)
void	apply (core::pose::Pose const &pose, utility::sql_database::sessionOP db_sesion) override
void	apply (core::pose::Pose const &pose, utility::sql_database::sessionOP db_sesion, std::string const &tag)
void	load_pose (utility::sql_database::sessionOP db_session, StructureID struct_id, core::pose::Pose &pose)
void	load_pose (utility::sql_database::sessionOP db_session, StructureID struct_id, std::set< core::Size > residue_numbers, core::pose::Pose &pose)
void	write_schema_to_db (utility::sql_database::sessionOP db_session) const
void	delete_pose_from_tag (utility::sql_database::sessionOP db_session, std::string const &tag)
void	delete_pose (utility::sql_database::sessionOP db_session, StructureID const &struct_id)
core::Size	get_protocol_id () const
core::Size	get_batch_id () const
Public Member Functions inherited from protocols::features::Report
	Report ()
	Report (Report const &src)
	~Report () override

Private Member Functions
void	write_protocol_report (utility::sql_database::sessionOP db_session)
void	write_full_report (core::pose::Pose const &pose, utility::sql_database::sessionOP db_session, std::string const &tag)
void	choose_database_filter ()

Private Attributes
bool	initialized_
DatabaseFilterOP	database_filter_
core::Size	protocol_id_
core::Size	batch_id_
StructureMap	structure_map_
protocols::features::ProtocolFeaturesOP	protocol_features_
protocols::features::BatchFeaturesOP	batch_features_
protocols::features::PdbDataFeaturesOP	pdb_data_features_
protocols::features::StructureFeaturesOP	structure_features_
protocols::features::StructureScoresFeaturesOP	structure_scores_features_
protocols::features::ScoreTypeFeaturesOP	score_type_features_
protocols::features::PoseConformationFeaturesOP	pose_conformation_features_
protocols::features::PoseCommentsFeaturesOP	pose_comments_features_
protocols::features::ProteinResidueConformationFeaturesOP	protein_residue_conformation_features_
protocols::features::ResidueFeaturesOP	residue_features_
protocols::features::ResidueConformationFeaturesOP	residue_conformation_features_
protocols::features::JobDataFeaturesOP	job_data_features_
utility::vector1 < protocols::features::FeaturesReporterOP >	features_reporters_

Additional Inherited Members
Protected Attributes inherited from protocols::features::Report
FeaturesReporters	reporters_

Member Typedef Documentation

typedef std::map< core::Size, core::pose::PoseOP > protocols::features::ProteinSilentReport::StructureMap

Constructor & Destructor Documentation

protocols::features::ProteinSilentReport::ProteinSilentReport

(

)

References database_filter_, features_reporters_, protocols::features::get_DB_filter_ptr(), job_data_features_, pdb_data_features_, pose_comments_features_, pose_conformation_features_, protein_residue_conformation_features_, protocol_id_, residue_conformation_features_, residue_features_, score_type_features_, and structure_features_.

Member Function Documentation

void protocols::features::ProteinSilentReport::apply ( core::pose::Pose const &  pose, utility::sql_database::sessionOP  db_sesion  )

overridevirtual

Implements protocols::features::Report.

void protocols::features::ProteinSilentReport::apply	(	core::pose::Pose const &	pose,
		utility::sql_database::sessionOP	db_sesion,
		std::string const &	tag
	)

void protocols::features::ProteinSilentReport::choose_database_filter ( )

private

void protocols::features::ProteinSilentReport::delete_pose	(	utility::sql_database::sessionOP	db_session,
		StructureID const &	struct_id
	)

References job_data_features_, pdb_data_features_, pose_comments_features_, pose_conformation_features_, protein_residue_conformation_features_, residue_conformation_features_, residue_features_, structure_features_, and structure_scores_features_.

Referenced by delete_pose_from_tag().

void protocols::features::ProteinSilentReport::delete_pose_from_tag	(	utility::sql_database::sessionOP	db_session,
		std::string const &	tag
	)

References delete_pose(), protocol_id_, and structure_features_.

core::Size protocols::features::ProteinSilentReport::get_batch_id

(

)

const

References batch_id_.

core::Size protocols::features::ProteinSilentReport::get_protocol_id

(

)

const

References protocol_id_.

void protocols::features::ProteinSilentReport::initialize

(

utility::sql_database::sessionOP

db_session

)

References initialized_, write_protocol_report(), and write_schema_to_db().

bool protocols::features::ProteinSilentReport::is_initialized

(

)

const

References initialized_.

void protocols::features::ProteinSilentReport::load_pose	(	utility::sql_database::sessionOP	db_session,
		StructureID	struct_id,
		core::pose::Pose &	pose
	)

Referenced by protocols::antibody::AntibodyDatabaseManager::load_cdr_pose(), and protocols::antibody::AntibodyDatabaseManager::load_cdr_poses().

void protocols::features::ProteinSilentReport::load_pose	(	utility::sql_database::sessionOP	db_session,
		StructureID	struct_id,
		std::set< core::Size >	residue_numbers,
		core::pose::Pose &	pose
	)

Size protocols::features::ProteinSilentReport::version ( )

overridevirtual

Implements protocols::features::Report.

void protocols::features::ProteinSilentReport::write_full_report ( core::pose::Pose const &  pose, utility::sql_database::sessionOP  db_session, std::string const &  tag  )

private

References batch_id_, protocols::jd2::current_input_tag(), core::pose::Pose::energies(), core::scoring::Energies::energies_updated(), job_data_features_, pdb_data_features_, pose_comments_features_, pose_conformation_features_, protein_residue_conformation_features_, residue_conformation_features_, residue_features_, core::pose::Pose::size(), structure_features_, structure_scores_features_, and protocols::features::TR().

void protocols::features::ProteinSilentReport::write_protocol_report ( utility::sql_database::sessionOP  db_session )

private

References batch_id_, features_reporters_, protocols::features::get_protocol_and_batch_id(), protocol_id_, and score_type_features_.

Referenced by initialize().

void protocols::features::ProteinSilentReport::write_schema_to_db

(

utility::sql_database::sessionOP

db_session

)

const

References batch_features_, batch_id_, job_data_features_, pdb_data_features_, pose_comments_features_, pose_conformation_features_, protein_residue_conformation_features_, protocol_features_, protocol_id_, residue_conformation_features_, residue_features_, score_type_features_, structure_features_, and structure_scores_features_.

Referenced by initialize().

Member Data Documentation

protocols::features::BatchFeaturesOP protocols::features::ProteinSilentReport::batch_features_

private

Referenced by write_schema_to_db().

core::Size protocols::features::ProteinSilentReport::batch_id_

private

Referenced by get_batch_id(), write_full_report(), write_protocol_report(), and write_schema_to_db().

DatabaseFilterOP protocols::features::ProteinSilentReport::database_filter_

private

Referenced by ProteinSilentReport().

utility::vector1< protocols::features::FeaturesReporterOP > protocols::features::ProteinSilentReport::features_reporters_

private

Referenced by ProteinSilentReport(), and write_protocol_report().

bool protocols::features::ProteinSilentReport::initialized_

private

Referenced by initialize(), and is_initialized().

protocols::features::JobDataFeaturesOP protocols::features::ProteinSilentReport::job_data_features_

private

Referenced by delete_pose(), ProteinSilentReport(), write_full_report(), and write_schema_to_db().

protocols::features::PdbDataFeaturesOP protocols::features::ProteinSilentReport::pdb_data_features_

private

Referenced by delete_pose(), ProteinSilentReport(), write_full_report(), and write_schema_to_db().

protocols::features::PoseCommentsFeaturesOP protocols::features::ProteinSilentReport::pose_comments_features_

private

Referenced by delete_pose(), ProteinSilentReport(), write_full_report(), and write_schema_to_db().

protocols::features::PoseConformationFeaturesOP protocols::features::ProteinSilentReport::pose_conformation_features_

private

Referenced by delete_pose(), ProteinSilentReport(), write_full_report(), and write_schema_to_db().

protocols::features::ProteinResidueConformationFeaturesOP protocols::features::ProteinSilentReport::protein_residue_conformation_features_

private

Referenced by delete_pose(), ProteinSilentReport(), write_full_report(), and write_schema_to_db().

protocols::features::ProtocolFeaturesOP protocols::features::ProteinSilentReport::protocol_features_

private

Referenced by write_schema_to_db().

core::Size protocols::features::ProteinSilentReport::protocol_id_

private

Referenced by delete_pose_from_tag(), get_protocol_id(), ProteinSilentReport(), write_protocol_report(), and write_schema_to_db().

protocols::features::ResidueConformationFeaturesOP protocols::features::ProteinSilentReport::residue_conformation_features_

private

Referenced by delete_pose(), ProteinSilentReport(), write_full_report(), and write_schema_to_db().

protocols::features::ResidueFeaturesOP protocols::features::ProteinSilentReport::residue_features_

private

Referenced by delete_pose(), ProteinSilentReport(), write_full_report(), and write_schema_to_db().

protocols::features::ScoreTypeFeaturesOP protocols::features::ProteinSilentReport::score_type_features_

private

Referenced by ProteinSilentReport(), write_protocol_report(), and write_schema_to_db().

protocols::features::StructureFeaturesOP protocols::features::ProteinSilentReport::structure_features_

private

Referenced by delete_pose(), delete_pose_from_tag(), ProteinSilentReport(), write_full_report(), and write_schema_to_db().

StructureMap protocols::features::ProteinSilentReport::structure_map_

private

protocols::features::StructureScoresFeaturesOP protocols::features::ProteinSilentReport::structure_scores_features_

private

Referenced by delete_pose(), write_full_report(), and write_schema_to_db().

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

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