Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::features::TrajectoryReportToDB Class Reference

#include <TrajectoryReportToDB.hh>

Inheritance diagram for protocols::features::TrajectoryReportToDB:
Inheritance graph
[legend]

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::Sizeget_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< boolget_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< boolinitialize_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
 
bool mover_provides_citation_info () const override
 Indiciate that this mover is published. More...
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const override
 Provide authorship information for a published Rosetta module. 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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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::Sizecycle_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 ( )
protocols::features::TrajectoryReportToDB::TrajectoryReportToDB ( core::Size  stride)
protocols::features::TrajectoryReportToDB::TrajectoryReportToDB ( std::string const &  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 
)
protocols::features::TrajectoryReportToDB::TrajectoryReportToDB ( TrajectoryReportToDB const &  src)
protocols::features::TrajectoryReportToDB::~TrajectoryReportToDB ( )
overridedefault

Member Function Documentation

void protocols::features::TrajectoryReportToDB::apply ( Pose )
overridevirtual
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 ( )
private

Add trajectory_map_features_reporter_ to list of features reporters.

References protocols::features::ReportToDB::add_features_reporter(), and trajectory_map_features_reporter_.

Referenced by TrajectoryReportToDB().

std::string protocols::features::TrajectoryReportToDB::mover_name ( )
static
std::string protocols::features::TrajectoryReportToDB::name ( )
inlineoverridevirtual

Reimplemented from protocols::features::ReportToDB.

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

Allow ReportToDB to be called from RosettaScripts See

Reimplemented from protocols::features::ReportToDB.

References protocols::features::ReportToDB::parse_my_tag(), and parse_stride_tag_item().

void protocols::features::TrajectoryReportToDB::parse_stride_tag_item ( utility::tag::TagCOP  tag)

References set_stride().

Referenced by parse_my_tag().

void protocols::features::TrajectoryReportToDB::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::features::TrajectoryReportToDB::set_stride ( core::Size  stride)

References stride_.

Referenced by parse_stride_tag_item().

Member Data Documentation

std::map<std::string, core::Size> protocols::features::TrajectoryReportToDB::cycle_counts_
private

Stores the number of cycles each output tag has been applied.

Referenced by apply(), and get_cycle_counts().

core::Size protocols::features::TrajectoryReportToDB::stride_
private

Features will be reported this number of cycles.

Referenced by apply(), get_stride(), and set_stride().

TrajectoryMapFeaturesOP protocols::features::TrajectoryReportToDB::trajectory_map_features_reporter_
private

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

Referenced by apply(), and initialize_trajectory_reporter().


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