#include <TrajectoryReportToDB.hh>

Inheritance diagram for protocols::features::TrajectoryReportToDB:

Public Member Functions
	TrajectoryReportToDB ()

	TrajectoryReportToDB (core::Size stride)

	TrajectoryReportToDB (std::string const &name)

	TrajectoryReportToDB (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)

	TrajectoryReportToDB (TrajectoryReportToDB const &src)

	~TrajectoryReportToDB () override

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...

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

void	parse_stride_tag_item (utility::tag::TagCOP tag)

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

std::string	name () override

void	set_stride (core::Size stride)

core::Size	get_stride () const

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

std::map< std::string, core::Size >	get_cycle_counts () const

Public Member Functions inherited from protocols::features::ReportToDB
	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

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	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...

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

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 Public Member Functions inherited from protocols::features::ReportToDB
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...

Private Member Functions
void	initialize_trajectory_reporter ()
	Add trajectory_map_features_reporter_ to list of features reporters. More...

Private Attributes
std::map< std::string, core::Size >	cycle_counts_
	Stores the number of cycles each output tag has been applied. More...

core::Size	stride_
	Features will be reported this number of cycles. More...

TrajectoryMapFeaturesOP	trajectory_map_features_reporter_
	Special pointer to TrajectoryMapFeatures reporter that we add so that we can update the current_cycle variable in that reporter. More...

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

Protected Member Functions inherited from protocols::features::ReportToDB
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...

Constructor & Destructor Documentation

protocols::features::TrajectoryReportToDB::TrajectoryReportToDB ( )

References initialize_trajectory_reporter(), and protocols::features::ReportToDB::set_batch_name().

protocols::features::TrajectoryReportToDB::TrajectoryReportToDB ( core::Size stride )

References initialize_trajectory_reporter(), and protocols::features::ReportToDB::set_batch_name().

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

References initialize_trajectory_reporter(), and protocols::features::ReportToDB::set_batch_name().

protocols::features::TrajectoryReportToDB::TrajectoryReportToDB	(	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`
	)

References initialize_trajectory_reporter().

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

protocols::features::TrajectoryReportToDB::~TrajectoryReportToDB ( )

overridedefault

Member Function Documentation

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

overridevirtual

Main Method.

Reimplemented from protocols::features::ReportToDB.

References protocols::features::ReportToDB::apply(), cycle_counts_, protocols::features::ReportToDB::ensure_structure_tags_are_ready(), protocols::features::ReportToDB::get_structure_tag(), stride_, and trajectory_map_features_reporter_.

moves::MoverOP protocols::features::TrajectoryReportToDB::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::features::ReportToDB.

moves::MoverOP protocols::features::TrajectoryReportToDB::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::features::ReportToDB.

std::map< std::string, core::Size > protocols::features::TrajectoryReportToDB::get_cycle_counts ( ) const

Probably only needed for unit testing

References cycle_counts_.

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

overridevirtual

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

Reimplemented from protocols::features::ReportToDB.

References mover_name().

core::Size protocols::features::TrajectoryReportToDB::get_stride ( ) const

References stride_.

void protocols::features::TrajectoryReportToDB::initialize_trajectory_reporter ( )