protocols::features::ScreeningFeatures Class Reference

#include <ScreeningFeatures.hh>

Public Member Functions
	ScreeningFeatures ()
	ScreeningFeatures (ScreeningFeatures const &src)
virtual	~ScreeningFeatures ()
std::string	type_name () const
virtual void	write_schema_to_db (utility::sql_database::sessionOP db_session) const
	Define the schema and write it to the database. This is most easily achieved using the schema_generator. Once everything has converted to the schema generator this should be made a pure virtual. 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...
virtual core::Size	report_features (core::pose::Pose const &pose, utility::vector1< bool > const &, StructureID struct_id, utility::sql_database::sessionOP db_session)
	collect all the feature data for the pose. More...
void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
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
std::vector < utility::json_spirit::Pair >	get_desriptor_data () const

Private Attributes
std::string	chain_
utility::vector1< std::string >	descriptors_

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::ScreeningFeatures::ScreeningFeatures

(

)

protocols::features::ScreeningFeatures::ScreeningFeatures

(

ScreeningFeatures const &

src

)

protocols::features::ScreeningFeatures::~ScreeningFeatures ( )

virtual

Member Function Documentation

utility::vector1< std::string > protocols::features::ScreeningFeatures::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.

std::vector< utility::json_spirit::Pair > protocols::features::ScreeningFeatures::get_desriptor_data ( ) const

private

References protocols::jd2::JobDistributor::current_job(), protocols::nonlocal::current_job(), descriptors_, and protocols::jd2::JobDistributor::get_instance().

Referenced by report_features().

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

virtual

Reimplemented from protocols::features::FeaturesReporter.

References chain_, descriptors_, basic::options::option, basic::options::OptionKeys::in::file::screening_job_file, and user.

core::Size protocols::features::ScreeningFeatures::report_features ( core::pose::Pose const &  , utility::vector1< bool > const &  , StructureID  , utility::sql_database::sessionOP    )

virtual

collect all the feature data for the pose.

Implements protocols::features::FeaturesReporter.

References basic::database::insert_statement_generator::InsertGenerator::add_column(), basic::database::insert_statement_generator::InsertGenerator::add_row(), chain_, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), protocols::nonlocal::current_job(), core::pose::get_chain_id_from_chain(), get_desriptor_data(), protocols::jd2::JobDistributor::get_instance(), utility::tools::make_vector(), core::chemical::ResidueType::name3(), core::pose::Pose::residue_type(), utility::json_spirit::write(), and basic::database::insert_statement_generator::InsertGenerator::write_to_database().

std::string protocols::features::ScreeningFeatures::type_name ( ) const

virtual

Reimplemented from protocols::features::FeaturesReporter.

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

virtual

Define the schema and write it to the database. This is most easily achieved using the schema_generator. Once everything has converted to the schema generator this should be made a pure virtual.

Implements protocols::features::FeaturesReporter.

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

Member Data Documentation

std::string protocols::features::ScreeningFeatures::chain_

private

Referenced by parse_my_tag(), and report_features().

utility::vector1<std::string> protocols::features::ScreeningFeatures::descriptors_

private

Referenced by get_desriptor_data(), and parse_my_tag().

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

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