#include <ReportToDB.hh>

Inheritance diagram for protocols::features::ReportToDB:

Public Member Functions
	ReportToDB ()

	ReportToDB (std::string const &name)

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

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

	ReportToDB (ReportToDB const &src)

	~ReportToDB () override

virtual void	register_options () const

moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

virtual std::string	name ()

void	set_batch_name (std::string const &batch_name)

std::string	get_batch_name () const

void	set_batch_description (std::string const &batch_description)

std::string	get_batch_description () const

void	set_relevant_residues_task_factory (core::pack::task::TaskFactoryOP task_factory)

core::pack::task::TaskFactoryOP	get_relevant_residues_task_factory () const

void	set_relevant_residues (utility::vector1< bool > const &relevant_residues)

utility::vector1< bool >	get_relevant_residues () const

void	set_relevant_residues_mode (protocols::features::RelevantResiduesMode::T setting)

protocols::features::RelevantResiduesMode::T	get_relevant_residues_mode () const

void	set_structure_tag (std::string const &setting)

std::string	get_structure_tag () const

void	set_structure_input_tag (std::string const &setting)

std::string	get_structure_input_tag () const

void	add_features_reporter (FeaturesReporterOP features_reporter)

void	parse_batch_description_tag_item (utility::tag::TagCOP tag)

void	parse_batch_id_tag_item (utility::tag::TagCOP tag)

void	parse_protocol_id_tag_item (utility::tag::TagCOP tag)

void	parse_use_transactions_tag_item (utility::tag::TagCOP tag)

void	parse_cache_size_tag_item (utility::tag::TagCOP tag)

void	parse_remove_xray_virt_tag_item (utility::tag::TagCOP tag)

void	parse_relevant_residues_mode_tag_item (utility::tag::TagCOP tag)

void	parse_batch_name_tag_item (utility::tag::TagCOP tag)

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override

void	check_features_reporter_dependencies (FeaturesReporterOP test_feature_reporter) const

void	initialize_reporters ()

void	initialize_database ()

void	initialize_pose (Pose &pose) const
	initialize the pose and set the relevant residues More...

utility::vector1< bool >	initialize_relevant_residues (Pose const &pose)
	initialize the relevant residues of the pose and store save for later. More...

void	apply (Pose &pose) override
	Main Method. More...

StructureID	report_structure_features () const

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

StructureID	get_last_struct_id () const

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

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. More...

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

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

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

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...

virtual bool	reinitialize_for_each_job () const
	Inform 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
	Inform 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...

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...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

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

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

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

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...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

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...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static void	attributes_for_report_to_db (utility::tag::AttributeList &, utility::tag::XMLSchemaDefinition &)

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. More...

Protected Member Functions
void	ensure_structure_tags_are_ready ()
	Checks if structure tags are not null and updates them to current job tags. 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...

Private Attributes
utility::sql_database::sessionOP	db_session_

std::string	batch_name_

std::string	batch_description_

bool	use_transactions_

core::Size	cache_size_

bool	remove_xray_virt_

core::Size	protocol_id_

core::Size	batch_id_

bool	custom_structure_tag_
	True if structure_tag_ has been set to a custom value If false, will be reset with the JobDistributorTag. More...

std::string	structure_tag_

bool	custom_structure_input_tag_
	True if structure_input_tag_ has been set to a custom value If false, will be reset with the JobDistributorInputTag. More...

std::string	structure_input_tag_

StructureID	last_struct_id_

core::pack::task::TaskFactoryOP	task_factory_

utility::vector1< bool >	relevant_residues_

protocols::features::RelevantResiduesMode::T	relevant_residues_mode_
	This indicates which features should be reported given the relevant residue specification: More...

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

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

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

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

Constructor & Destructor Documentation

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

References initialize_reporters().

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

References initialize_reporters().

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

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

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

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

overridedefault

Member Function Documentation

void protocols::features::ReportToDB::add_features_reporter ( FeaturesReporterOP features_reporter )

References check_features_reporter_dependencies(), and features_reporters_.

Referenced by protocols::features::TrajectoryReportToDB::initialize_trajectory_reporter(), and parse_my_tag().

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

overridevirtual

void protocols::features::ReportToDB::attributes_for_report_to_db	(	utility::tag::AttributeList &	attlist,
		utility::tag::XMLSchemaDefinition &	xsd
	)

static

References protocols::rosetta_scripts::attributes_for_parse_database_session(), and core::pack::task::attributes_for_parse_task_operations().

Referenced by protocols::features::TrajectoryReportToDB::provide_xml_schema(), and provide_xml_schema().

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

References batch_name_, and features_reporters_.

Referenced by add_features_reporter().

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

overridevirtual

Return a clone of the Mover object.

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.

Reimplemented in protocols::features::TrajectoryReportToDB.

void protocols::features::ReportToDB::ensure_structure_tags_are_ready ( )

protected

Checks if structure tags are not null and updates them to current job tags.

References protocols::jd2::current_input_tag(), protocols::jd2::current_output_name(), custom_structure_input_tag_, custom_structure_tag_, structure_input_tag_, and structure_tag_.

Referenced by protocols::features::TrajectoryReportToDB::apply(), and apply().

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

overridevirtual

Generates a new Mover object freshly created with the default ctor.

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.

Reimplemented in protocols::features::TrajectoryReportToDB.

std::string protocols::features::ReportToDB::get_batch_description ( ) const

References batch_description_.

std::string protocols::features::ReportToDB::get_batch_name ( ) const

References batch_name_.

StructureID protocols::features::ReportToDB::get_last_struct_id ( ) const

References last_struct_id_.

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

overridevirtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::features::TrajectoryReportToDB.

References mover_name().

Referenced by provide_citation_info().

vector1< bool > protocols::features::ReportToDB::get_relevant_residues ( ) const

References relevant_residues_.

RelevantResiduesMode::T protocols::features::ReportToDB::get_relevant_residues_mode ( ) const

References relevant_residues_mode_.

TaskFactoryOP protocols::features::ReportToDB::get_relevant_residues_task_factory ( ) const

References task_factory_.

std::string protocols::features::ReportToDB::get_structure_input_tag ( ) const

References structure_input_tag_.

std::string protocols::features::ReportToDB::get_structure_tag ( ) const

References structure_tag_.

Referenced by protocols::features::TrajectoryReportToDB::apply().

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

References batch_features_, batch_id_, db_session_, features_reporters_, initialized, protocol_features_, protocol_id_, and structure_features_.

Referenced by apply().

void protocols::features::ReportToDB::initialize_pose ( Pose & pose ) const

initialize the pose and set the relevant residues

References protocols::cluster::calibur::aa, core::chemical::aa_vrt, core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_slow(), remove_xray_virt_, core::pose::Pose::residue(), core::pose::Pose::size(), protocols::features::TR(), and core::pose::Pose::update_residue_neighbors().

Referenced by apply().

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

initialize the relevant residues of the pose and store save for later.

References relevant_residues_, core::pose::Pose::size(), task_factory_, and protocols::features::TR().

Referenced by apply().

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

References batch_features_, protocol_features_, and structure_features_.

Referenced by ReportToDB().

std::string protocols::features::ReportToDB::mover_name ( )

static

Referenced by get_name(), protocols::features::ReportToDBCreator::keyname(), and provide_xml_schema().

virtual std::string protocols::features::ReportToDB::name ( )

inlinevirtual

Reimplemented in protocols::features::TrajectoryReportToDB.

Referenced by set_batch_name().

void protocols::features::ReportToDB::parse_batch_description_tag_item ( utility::tag::TagCOP tag )

References batch_description_.

Referenced by parse_my_tag().

void protocols::features::ReportToDB::parse_batch_id_tag_item ( utility::tag::TagCOP tag )

References batch_id_.

Referenced by parse_my_tag().

void protocols::features::ReportToDB::parse_batch_name_tag_item ( utility::tag::TagCOP tag )

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

Referenced by parse_my_tag().

void protocols::features::ReportToDB::parse_cache_size_tag_item ( utility::tag::TagCOP tag )

References cache_size_.

Referenced by parse_my_tag().

void protocols::features::ReportToDB::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Allow ReportToDB to be called from RosettaScripts See

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::features::TrajectoryReportToDB.

References add_features_reporter(), db_session_, core::sequence::end, features_reporter_factory_, protocols::features::FeaturesReporterFactory::get_features_reporter(), parse_batch_description_tag_item(), parse_batch_id_tag_item(), parse_batch_name_tag_item(), parse_cache_size_tag_item(), protocols::rosetta_scripts::parse_database_session(), parse_protocol_id_tag_item(), parse_relevant_residues_mode_tag_item(), parse_remove_xray_virt_tag_item(), core::pack::task::parse_task_operations(), parse_use_transactions_tag_item(), relevant_residues_mode_, set_structure_input_tag(), set_structure_tag(), structure_features_, task_factory_, and protocols::features::TR().

Referenced by protocols::features::TrajectoryReportToDB::parse_my_tag().

void protocols::features::ReportToDB::parse_protocol_id_tag_item ( utility::tag::TagCOP tag )

References protocol_id_.

Referenced by parse_my_tag().

void protocols::features::ReportToDB::parse_relevant_residues_mode_tag_item ( utility::tag::TagCOP tag )

References protocols::features::RelevantResiduesMode::Exclusive, protocols::features::RelevantResiduesMode::Inclusive, and relevant_residues_mode_.

Referenced by parse_my_tag().

void protocols::features::ReportToDB::parse_remove_xray_virt_tag_item ( utility::tag::TagCOP tag )

References remove_xray_virt_.

Referenced by parse_my_tag().

void protocols::features::ReportToDB::parse_use_transactions_tag_item ( utility::tag::TagCOP tag )

References use_transactions_.

Referenced by parse_my_tag().

void protocols::features::ReportToDB::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

References get_name().

void protocols::features::ReportToDB::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References attributes_for_report_to_db(), protocols::features::FeaturesReporterFactory::features_reporter_xml_schema_group_name(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

Referenced by protocols::features::ReportToDBCreator::provide_xml_schema().

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

virtual

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

References batch_description_, batch_id_, batch_name_, db_session_, features_reporters_, protocol_id_, protocols::features::TR(), and use_transactions_.

Referenced by apply().

StructureID protocols::features::ReportToDB::report_structure_features ( ) const

References batch_description_, batch_id_, batch_name_, db_session_, protocol_id_, structure_features_, structure_input_tag_, structure_tag_, and use_transactions_.

Referenced by apply().

void protocols::features::ReportToDB::set_batch_description ( std::string const & batch_description )

References batch_description_.

void protocols::features::ReportToDB::set_batch_name ( std::string const & batch_name )

References batch_name_, and name().

Referenced by protocols::features::TrajectoryReportToDB::TrajectoryReportToDB().

void protocols::features::ReportToDB::set_relevant_residues ( utility::vector1< bool > const & relevant_residues )

References relevant_residues_.

void protocols::features::ReportToDB::set_relevant_residues_mode ( protocols::features::RelevantResiduesMode::T setting )

References relevant_residues_mode_.

void protocols::features::ReportToDB::set_relevant_residues_task_factory ( core::pack::task::TaskFactoryOP task_factory )

References task_factory_.

void protocols::features::ReportToDB::set_structure_input_tag ( std::string const & setting )

References custom_structure_input_tag_, and structure_input_tag_.

Referenced by parse_my_tag().

void protocols::features::ReportToDB::set_structure_tag ( std::string const & setting )

References custom_structure_tag_, and structure_tag_.

Referenced by parse_my_tag().

Member Data Documentation

std::string protocols::features::ReportToDB::batch_description_

private

Referenced by apply(), get_batch_description(), parse_batch_description_tag_item(), report_features(), report_structure_features(), and set_batch_description().

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(), initialize_database(), parse_batch_id_tag_item(), report_features(), and report_structure_features().

std::string protocols::features::ReportToDB::batch_name_

private

Referenced by apply(), check_features_reporter_dependencies(), get_batch_name(), parse_batch_name_tag_item(), report_features(), report_structure_features(), and set_batch_name().

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

private

Referenced by apply(), and parse_cache_size_tag_item().

bool protocols::features::ReportToDB::custom_structure_input_tag_

private

True if structure_input_tag_ has been set to a custom value If false, will be reset with the JobDistributorInputTag.

Referenced by ensure_structure_tags_are_ready(), and set_structure_input_tag().

bool protocols::features::ReportToDB::custom_structure_tag_

private

True if structure_tag_ has been set to a custom value If false, will be reset with the JobDistributorTag.

Referenced by ensure_structure_tags_are_ready(), and set_structure_tag().

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

private

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

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 add_features_reporter(), apply(), check_features_reporter_dependencies(), initialize_database(), and report_features().

bool protocols::features::ReportToDB::initialized

private

Referenced by initialize_database().

StructureID protocols::features::ReportToDB::last_struct_id_

private

Referenced by apply(), and get_last_struct_id().

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(), initialize_database(), parse_protocol_id_tag_item(), report_features(), and report_structure_features().

utility::vector1< bool > protocols::features::ReportToDB::relevant_residues_

private

Referenced by get_relevant_residues(), initialize_relevant_residues(), and set_relevant_residues().

protocols::features::RelevantResiduesMode::T protocols::features::ReportToDB::relevant_residues_mode_

private

This indicates which features should be reported given the relevant residue specification:

Exclusive: All residues in a feature must be specified as 'relevant' through the given task operations to be reported. (DEFAULT)

Inclusive: At least one residue in the the feature must be specified as 'relavent' through the given task operations to be reported.

Referenced by get_relevant_residues_mode(), parse_my_tag(), parse_relevant_residues_mode_tag_item(), and set_relevant_residues_mode().

bool protocols::features::ReportToDB::remove_xray_virt_

private

Referenced by initialize_pose(), and parse_remove_xray_virt_tag_item().

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

private

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

std::string protocols::features::ReportToDB::structure_input_tag_

private

Referenced by ensure_structure_tags_are_ready(), get_structure_input_tag(), report_structure_features(), and set_structure_input_tag().

std::string protocols::features::ReportToDB::structure_tag_

private

Referenced by apply(), ensure_structure_tags_are_ready(), get_structure_tag(), report_structure_features(), and set_structure_tag().

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

private

Referenced by get_relevant_residues_task_factory(), initialize_relevant_residues(), parse_my_tag(), and set_relevant_residues_task_factory().

bool protocols::features::ReportToDB::use_transactions_

private

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

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

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

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation