#include <ReportToDB.hh>

Inheritance diagram for protocols::features::ReportToDB:

Collaboration diagram for protocols::features::ReportToDB:

Public Member Functions
	ReportToDB ()

	ReportToDB (std::string const &name)

	ReportToDB (std::string const &name, utility::sql_database::sessionOP db_session, std::string const &sample_source, bool use_transactions=true, core::Size cache_size=2000)

	ReportToDB (ReportToDB const &src)

virtual	~ReportToDB ()

virtual void	register_options () const

virtual moves::MoverOP	fresh_instance () const
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

virtual moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...

void	parse_sample_source_tag_item (utility::tag::TagPtr const tag)

void	parse_protocol_id_tag_item (utility::tag::TagPtr const tag)

void	parse_use_transactions_tag_item (utility::tag::TagPtr const tag)

void	parse_cache_size_tag_item (utility::tag::TagPtr const tag)

void	parse_remove_xray_virt_tag_item (utility::tag::TagPtr const tag)

void	parse_name_tag_item (utility::tag::TagPtr const tag)

void	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &data, Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &pose)

void	check_features_reporter_dependencies (FeaturesReporterOP test_feature_reporter) const

void	initialize_reporters ()

void	initialize_database ()

utility::vector1< bool >	initialize_pose (Pose &pose) const
	initialize the pose and return the relevant residues More...

void	write_features_reporters_table () const
	Add the defined features reporters to the 'features_reporters' table in the database. More...

void	write_batch_reports_table () const
	Link the defined features reporters to the batch of structures extracted with this invocation of the ReportToDB mover. More...

void	write_linking_tables () const
	write tables linking the batches table with the features datababase More...

void	apply (Pose &pose)

boost::uuids::uuid	report_structure_features (utility::vector1< bool > const &relevant_residues) const

void	report_features (core::pose::Pose const &pose, boost::uuids::uuid struct_id, utility::vector1< bool > const &relevant_residues) const

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

void	set_current_tag (std::string const &new_tag)

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

void	type (const std::string &type_in)

std::string	get_type () const

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual bool	reinitialize_for_each_job () const
	this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	this function informs the job distributor (august 08 vintage) whether this object needs to be regenerated when the input pose is about to change (for example, if the mover has special code on the first apply() that is only valid for that one input pose). More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr	TagPtr

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	overload this static method if you access options within the mover. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Constructor & Destructor Documentation

protocols::features::ReportToDB::ReportToDB ( )

References initialize_reporters().

Referenced by clone(), and fresh_instance().

protocols::features::ReportToDB::ReportToDB ( std::string const & name)

References initialize_reporters().

protocols::features::ReportToDB::ReportToDB	(	std::string const &	name,
		utility::sql_database::sessionOP	db_session,
		std::string const &	sample_source,
		bool	use_transactions = `true`,
		core::Size	cache_size = `2000`
	)

protocols::features::ReportToDB::ReportToDB ( ReportToDB const & src)

References protocols::features::TR().

protocols::features::ReportToDB::~ReportToDB ( )

virtual

Member Function Documentation

void protocols::features::ReportToDB::apply ( Pose & pose)

virtual

Implements protocols::moves::Mover.

References batch_id_, cache_size_, db_session_, protocols::features::get_protocol_and_batch_id(), initialize_database(), initialize_pose(), name_, protocol_id_, report_features(), report_structure_features(), and use_transactions_.

void protocols::features::ReportToDB::check_features_reporter_dependencies ( FeaturesReporterOP test_feature_reporter) const

References features_reporters_, and name_.

Referenced by parse_my_tag().

MoverOP protocols::features::ReportToDB::clone ( ) const

virtual

clone has to be overridden only if clone invocation is expected.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

References ReportToDB().

MoverOP protocols::features::ReportToDB::fresh_instance ( ) const

virtual

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

References ReportToDB().

virtual std::string protocols::features::ReportToDB::get_name ( ) const

inlinevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

void protocols::features::ReportToDB::initialize_database ( )

References batch_features_, db_session_, features_reporters_, initialized, protocol_features_, structure_features_, use_transactions_, and write_linking_tables().

Referenced by apply().

vector1< bool > protocols::features::ReportToDB::initialize_pose ( Pose & pose) const

initialize the pose and return the relevant residues

References core::chemical::aa_vrt, core::pose::Pose::conformation(), protocols::jd2::JobDistributor::current_output_name(), core::conformation::Conformation::delete_residue_slow(), protocols::jd2::JobDistributor::get_instance(), name_, remove_xray_virt_, core::pose::Pose::residue(), task_factory_, core::pose::Pose::total_residue(), and protocols::features::TR().

Referenced by apply().

void protocols::features::ReportToDB::initialize_reporters ( )

References batch_features_, protocol_features_, and structure_features_.

Referenced by ReportToDB().

void protocols::features::ReportToDB::parse_cache_size_tag_item ( utility::tag::TagPtr const tag)

References cache_size_.

Referenced by parse_my_tag().

void protocols::features::ReportToDB::parse_my_tag	(	utility::tag::TagPtr const	tag,
		protocols::moves::DataMap &	data,
		Filters_map const &	,
		protocols::moves::Movers_map const &	,
		core::pose::Pose const &	pose
	)

virtual

Allow ReportToDB to be called from RosettaScripts See

Reimplemented from protocols::moves::Mover.

References check_features_reporter_dependencies(), db_session_, core::sequence::end, features_reporter_factory_, features_reporters_, protocols::features::FeaturesReporterFactory::get_features_reporter(), parse_cache_size_tag_item(), parse_name_tag_item(), parse_protocol_id_tag_item(), parse_remove_xray_virt_tag_item(), parse_sample_source_tag_item(), protocols::rosetta_scripts::parse_task_operations(), parse_use_transactions_tag_item(), task_factory_, and protocols::features::TR().

void protocols::features::ReportToDB::parse_name_tag_item ( utility::tag::TagPtr const tag)

References name_, and protocols::features::TR().

Referenced by parse_my_tag().

void protocols::features::ReportToDB::parse_protocol_id_tag_item ( utility::tag::TagPtr const tag)

References protocols::wum::mpi_rank(), and protocol_id_.

Referenced by parse_my_tag().

void protocols::features::ReportToDB::parse_remove_xray_virt_tag_item ( utility::tag::TagPtr const tag)

References remove_xray_virt_.

Referenced by parse_my_tag().

void protocols::features::ReportToDB::parse_sample_source_tag_item ( utility::tag::TagPtr const tag)

References sample_source_, and protocols::features::TR().

Referenced by parse_my_tag().

void protocols::features::ReportToDB::parse_use_transactions_tag_item ( utility::tag::TagPtr const tag)

References use_transactions_.

Referenced by parse_my_tag().

void protocols::features::ReportToDB::register_options ( ) const

virtual

void protocols::features::ReportToDB::report_features	(	core::pose::Pose const &	pose,
		boost::uuids::uuid	struct_id,
		utility::vector1< bool > const &	relevant_residues
	)		const

References batch_id_, db_session_, features_reporters_, name_, protocol_id_, and protocols::features::TR().

Referenced by apply().

uuid protocols::features::ReportToDB::report_structure_features ( utility::vector1< bool > const & relevant_residues) const

References batch_id_, db_session_, name_, protocol_id_, and structure_features_.

Referenced by apply().

void protocols::features::ReportToDB::write_batch_reports_table ( ) const

Link the defined features reporters to the batch of structures extracted with this invocation of the ReportToDB mover.

References db_session_.

Referenced by write_linking_tables().

void protocols::features::ReportToDB::write_features_reporters_table ( ) const

Add the defined features reporters to the 'features_reporters' table in the database.

The 'features_reporters' table lists the type_names of the all defined features reporters. The 'batch_reports' table link the features reporters with each batch defined in the 'batches' table.

References db_session_, and features_reporters_.

Referenced by write_linking_tables().

void protocols::features::ReportToDB::write_linking_tables ( ) const

write tables linking the batches table with the features datababase

References name_, write_batch_reports_table(), and write_features_reporters_table().

Referenced by initialize_database().

Member Data Documentation

protocols::features::BatchFeaturesOP protocols::features::ReportToDB::batch_features_

private

Referenced by initialize_database(), and initialize_reporters().

core::Size protocols::features::ReportToDB::batch_id_

private

Referenced by apply(), report_features(), and report_structure_features().

core::Size protocols::features::ReportToDB::cache_size_

private

Referenced by apply(), and parse_cache_size_tag_item().

utility::sql_database::sessionOP protocols::features::ReportToDB::db_session_

private

Referenced by apply(), initialize_database(), parse_my_tag(), report_features(), report_structure_features(), write_batch_reports_table(), and write_features_reporters_table().

protocols::features::FeaturesReporterFactory* protocols::features::ReportToDB::features_reporter_factory_

private

Referenced by parse_my_tag().

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

private

Referenced by check_features_reporter_dependencies(), initialize_database(), parse_my_tag(), report_features(), and write_features_reporters_table().

bool protocols::features::ReportToDB::initialized

private

Referenced by initialize_database().

std::string protocols::features::ReportToDB::name_

private

Referenced by apply(), check_features_reporter_dependencies(), initialize_pose(), parse_name_tag_item(), report_features(), report_structure_features(), and write_linking_tables().

protocols::features::ProtocolFeaturesOP protocols::features::ReportToDB::protocol_features_

private

Referenced by initialize_database(), and initialize_reporters().

core::Size protocols::features::ReportToDB::protocol_id_

private

Referenced by apply(), parse_protocol_id_tag_item(), report_features(), and report_structure_features().

bool protocols::features::ReportToDB::remove_xray_virt_

private

Referenced by initialize_pose(), and parse_remove_xray_virt_tag_item().

std::string protocols::features::ReportToDB::sample_source_

private

Referenced by parse_sample_source_tag_item().

protocols::features::StructureFeaturesOP protocols::features::ReportToDB::structure_features_

private

Referenced by initialize_database(), initialize_reporters(), and report_structure_features().

core::pack::task::TaskFactoryOP protocols::features::ReportToDB::task_factory_

private

Referenced by initialize_pose(), and parse_my_tag().

bool protocols::features::ReportToDB::use_transactions_

private

Referenced by apply(), initialize_database(), and parse_use_transactions_tag_item().

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

src/protocols/features/ReportToDB.hh
src/protocols/features/ReportToDB.cc

Private Attributes
utility::sql_database::sessionOP	db_session_

std::string	sample_source_

std::string	name_

bool	use_transactions_

core::Size	cache_size_

bool	remove_xray_virt_

core::Size	protocol_id_

core::Size	batch_id_

core::pack::task::TaskFactoryOP	task_factory_

protocols::features::FeaturesReporterFactory *	features_reporter_factory_

protocols::features::ProtocolFeaturesOP	protocol_features_

protocols::features::BatchFeaturesOP	batch_features_

protocols::features::StructureFeaturesOP	structure_features_

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

bool	initialized

Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation