protocols::features::StructureFeatures Class Reference

#include <StructureFeatures.hh>

Public Member Functions
	StructureFeatures ()
	StructureFeatures (StructureFeatures const &src)
virtual	~StructureFeatures ()
std::string	type_name () const
	return string with class name More...
virtual void	write_schema_to_db (utility::sql_database::sessionOP db_session) const
	generate the table schemas and write them to the database 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...
core::Size	report_features (core::pose::Pose const &, utility::vector1< bool > const &, StructureID, utility::sql_database::sessionOP)
	collect all the feature data for the pose More...
StructureID	report_features (core::Size batch_id, utility::sql_database::sessionOP db_session, std::string const &tag, std::string const &input_tag)
	collect all the feature data for the pose use This version allows the tag and the input tag to be specificed More...
void	mark_structure_as_sampled (core::Size batch_id, std::string const &tag, std::string const &input_tag, utility::sql_database::sessionOP db_session)
void	delete_record (StructureID struct_id, utility::sql_database::sessionOP db_session)
void	load_into_pose (utility::sql_database::sessionOP db_session, StructureID struct_id, core::pose::Pose &pose)
void	load_tag (utility::sql_database::sessionOP db_session, StructureID struct_id, core::pose::Pose &pose)
StructureID	get_struct_id (utility::sql_database::sessionOP db_session, std::string const &tag, core::Size const &protocol_id)
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	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
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

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::StructureFeatures::StructureFeatures

(

)

protocols::features::StructureFeatures::StructureFeatures

(

StructureFeatures const &

src

)

protocols::features::StructureFeatures::~StructureFeatures ( )

virtual

Member Function Documentation

void protocols::features::StructureFeatures::delete_record ( StructureID  struct_id, utility::sql_database::sessionOP  db_session  )

virtual

Reimplemented from protocols::features::FeaturesReporter.

References basic::database::safely_prepare_statement(), and basic::database::safely_write_to_database().

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

StructureID protocols::features::StructureFeatures::get_struct_id	(	utility::sql_database::sessionOP	db_session,
		std::string const &	tag,
		core::Size const &	protocol_id
	)

References protocols::pack_daemon::error_message, basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), and utility_exit_with_message.

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

virtual

Reimplemented from protocols::features::FeaturesReporter.

References load_tag().

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

References protocols::pack_daemon::error_message, basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), tag_into_pose(), and utility_exit_with_message.

Referenced by load_into_pose().

void protocols::features::StructureFeatures::mark_structure_as_sampled	(	core::Size	batch_id,
		std::string const &	tag,
		std::string const &	input_tag,
		utility::sql_database::sessionOP	db_session
	)

References basic::database::insert_statement_generator::InsertGenerator::add_column(), basic::database::insert_statement_generator::InsertGenerator::add_row(), utility::tools::make_vector(), and basic::database::insert_statement_generator::InsertGenerator::write_to_database().

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

inlinevirtual

collect all the feature data for the pose

Implements protocols::features::FeaturesReporter.

References utility_exit_with_message.

StructureID protocols::features::StructureFeatures::report_features	(	core::Size	batch_id,
		utility::sql_database::sessionOP	db_session,
		std::string const &	tag,
		std::string const &	input_tag
	)

collect all the feature data for the pose use This version allows the tag and the input tag to be specificed

string protocols::features::StructureFeatures::type_name ( ) const

virtual

return string with class name

Reimplemented from protocols::features::FeaturesReporter.

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

virtual

generate the table schemas and write them to the database

Implements protocols::features::FeaturesReporter.

References basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_constraint(), basic::database::schema_generator::Schema::add_foreign_key(), runtime_assert, tag, protocols::features::TR, and basic::database::schema_generator::Schema::write().

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

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