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protocols::features::DatabaseJobOutputter Class Reference

#include <DatabaseJobOutputter.hh>

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

Public Types

typedef
protocols::jd2::FileJobOutputter 
parent
 
- Public Types inherited from protocols::jd2::FileJobOutputter
typedef
protocols::jd2::JobOutputter 
parent
 

Public Member Functions

 DatabaseJobOutputter ()
 
 ~DatabaseJobOutputter () override
 
void load_options_from_option_system ()
 load options from option sytem More...
 
void set_database_name (std::string const &database_name)
 Set database name. More...
 
std::string get_database_name () const
 Get database name. More...
 
void set_database_pq_schema (std::string const &database_pq_schema)
 Set database postgreSQL schema. More...
 
std::string get_database_pq_schema () const
 Get database postgresQL schema. More...
 
void flush () override
 see parent class for explanation More...
 
void final_pose (protocols::jd2::JobOP job, core::pose::Pose const &pose, std::string const &tag) override
 this function outputs the final result of a job. More...
 
void other_pose (protocols::jd2::JobOP job, core::pose::Pose const &pose, std::string const &tag, int copy_count=-1, bool score_only=false) override
 this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol. More...
 
bool job_has_completed (protocols::jd2::JobCOP job) override
 this function is not used for output, but it belongs here since it needs to check the same output locations as the class normally writes to. This class checks wherever output goes to see if the job's expected output already exists (on disk or whatever). This is the most basic form of checkpointing. More...
 
std::string output_name (protocols::jd2::JobCOP job) override
 this is the master function for determining the unique output identifier for a job More...
 
- Public Member Functions inherited from protocols::jd2::FileJobOutputter
 FileJobOutputter ()
 
 ~FileJobOutputter () override
 
void set_defaults ()
 
void file (JobCOP job, std::string const &data) override
 this function takes a string and writes it to disk (separately from Tracer output). More...
 
utility::file::FileName const & scorefile_name ()
 
bool write_scorefile () const
 
- Public Member Functions inherited from protocols::jd2::JobOutputter
 JobOutputter ()
 constructor – reads cmd-line to initialize evaluators More...
 
 ~JobOutputter () override
 
virtual void starting_pose (core::pose::Pose const &)
 optionally pass a starting (reference) pose to a JobOutputter for later comparison purposes and/or as interface for initializing evaluators More...
 
virtual std::string filename (JobCOP) const
 
void add_evaluation (evaluation::PoseEvaluatorOP)
 
void set_evaluators (evaluation::PoseEvaluators const &)
 
void clear_evaluators ()
 clear the list of evaluators More...
 
evaluation::PoseEvaluatorsCOP evaluators () const
 
void evaluate (core::pose::Pose &pose, std::string tag, core::io::silent::SilentStruct &pss) const
 
void call_output_observers (core::pose::Pose const &pose, JobOP job) const
 call all output_observers More...
 
void set_defaults ()
 clear the list of evaluators More...
 

Static Public Member Functions

static void register_options ()
 

Private Attributes

protocols::features::ProteinSilentReportOP protein_silent_report_
 
std::string database_name_
 
std::string database_pq_schema_
 
std::string path_
 

Additional Inherited Members

- Protected Member Functions inherited from protocols::jd2::FileJobOutputter
virtual void scorefile (JobCOP job, core::pose::Pose const &pose, std::string prefix_tag="", std::string suffix_tag="", std::string scorefile="")
 this function will handle the scorefile. If you need to make it virtual do so. Latter two arguments are for redirecting the output to a different scorefile for "other_pose"s. Also adds StringReal job info to the score file. More...
 
- Protected Member Functions inherited from protocols::jd2::JobOutputter
std::string affixed_numbered_name (JobCOP job)
 this function generates the affixed, numbered name for the job as prefix + input + suffix + number (affixes from options system). This function is deliberately not virtual, this should be a common mechanism; your JobOutputter can not call it if it would like. More...
 

Detailed Description

this is a implementation of JobOutputter for database-based output.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::features::DatabaseJobOutputter::DatabaseJobOutputter ( )
protocols::features::DatabaseJobOutputter::~DatabaseJobOutputter ( )
override

Member Function Documentation

void protocols::features::DatabaseJobOutputter::final_pose ( protocols::jd2::JobOP  job,
core::pose::Pose const &  pose,
std::string const &  tag 
)
overridevirtual
void protocols::features::DatabaseJobOutputter::flush ( )
overridevirtual

see parent class for explanation

Reimplemented from protocols::jd2::JobOutputter.

std::string protocols::features::DatabaseJobOutputter::get_database_name ( ) const

Get database name.

References database_name_.

string protocols::features::DatabaseJobOutputter::get_database_pq_schema ( ) const

Get database postgresQL schema.

References database_pq_schema_.

bool protocols::features::DatabaseJobOutputter::job_has_completed ( protocols::jd2::JobCOP  job)
overridevirtual

this function is not used for output, but it belongs here since it needs to check the same output locations as the class normally writes to. This class checks wherever output goes to see if the job's expected output already exists (on disk or whatever). This is the most basic form of checkpointing.

Implements protocols::jd2::FileJobOutputter.

References database_name_, database_pq_schema_, output_name(), path_, and protein_silent_report_.

void protocols::features::DatabaseJobOutputter::load_options_from_option_system ( )

load options from option sytem

References protocols::hybridization::path, path_, set_database_name(), and set_database_pq_schema().

Referenced by DatabaseJobOutputter().

void protocols::features::DatabaseJobOutputter::other_pose ( protocols::jd2::JobOP  job,
core::pose::Pose const &  pose,
std::string const &  tag,
int  copy_count = -1,
bool  score_only = false 
)
overridevirtual

this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol.

Implements protocols::jd2::FileJobOutputter.

References protocols::jd2::JobOutputter::call_output_observers(), database_name_, database_pq_schema_, path_, and protein_silent_report_.

std::string protocols::features::DatabaseJobOutputter::output_name ( protocols::jd2::JobCOP  job)
overridevirtual

this is the master function for determining the unique output identifier for a job

Database tags should preserve the FULL NAME such that we don't end up with duplicate tags. This will cause problems on BOINC if changed.

Implements protocols::jd2::FileJobOutputter.

References protocols::jd2::JobOutputter::affixed_numbered_name().

Referenced by final_pose(), and job_has_completed().

void protocols::features::DatabaseJobOutputter::register_options ( )
static
void protocols::features::DatabaseJobOutputter::set_database_name ( std::string const &  database_name)

Set database name.

References database_name_.

Referenced by load_options_from_option_system().

void protocols::features::DatabaseJobOutputter::set_database_pq_schema ( std::string const &  database_pq_schema)

Set database postgreSQL schema.

References database_name_.

Referenced by load_options_from_option_system().

Member Data Documentation

std::string protocols::features::DatabaseJobOutputter::database_name_
private
std::string protocols::features::DatabaseJobOutputter::database_pq_schema_
private
std::string protocols::features::DatabaseJobOutputter::path_
private
protocols::features::ProteinSilentReportOP protocols::features::DatabaseJobOutputter::protein_silent_report_
private

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