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protocols::features::DatabaseJobInputter Class Reference

#include <DatabaseJobInputter.hh>

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

Public Member Functions

 DatabaseJobInputter ()
 
 ~DatabaseJobInputter () 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 postreSQL schema. More...
 
std::string get_database_pq_schema () const
 Get database postreSQL schema. More...
 
core::scoring::ScoreFunctionOP get_scorefunction ()
 Get score function. More...
 
void set_scorefunction (core::scoring::ScoreFunctionOP scorefunction)
 Set score function. More...
 
void set_struct_ids_from_strings (utility::vector1< std::string > const &struct_id_strings)
 set struct_ids from a list of strings of integer representations More...
 
void set_struct_ids_from_sql (utility::vector1< std::string > const &sql)
 set input tags using a database SELECT command More...
 
void pose_from_job (core::pose::Pose &pose, protocols::jd2::JobOP job) override
 this function is responsible for filling the pose reference with the pose indicated by the job. The Job object (within its InnerJob) contains a PoseCOP. This function needs to either fill the pose reference from the InnerJob or, on first demand of a pose from that InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill the reference. This implementation uses pose_from_pdb More...
 
void fill_jobs (protocols::jd2::JobsContainer &jobs) override
 this function determines what jobs exist from -in::file::silent and -in::file::tags. More...
 
protocols::jd2::JobInputterInputSource::Enum input_source () const override
 Return the type of input source that the DatabaseJobInputter is currently using. More...
 
- Public Member Functions inherited from protocols::jd2::JobInputter
 ~JobInputter () override
 
JobInputterCOP get_self_ptr () const
 Get self const owning pointers. More...
 
JobInputterOP get_self_ptr ()
 Get self owning pointers. More...
 
JobInputterCAP get_self_weak_ptr () const
 Get self const weak pointers. More...
 
JobInputterAP get_self_weak_ptr ()
 Get self weak pointers. More...
 
virtual void update_jobs_list (JobsContainerOP jobs)
 This function is only called by certain JobInputters to update the jobs list after it has already been created. More...
 
virtual bool updates_jobs_list () const
 Does this type of JobInputter update the jobs list? More...
 

Static Public Member Functions

static void register_options ()
 
- Static Public Member Functions inherited from protocols::jd2::JobInputter
static std::string job_inputter_input_source_to_string (JobInputterInputSource::Enum source)
 call this with input_source() to get the input source of a particular job inputter More...
 

Private Attributes

core::scoring::ScoreFunctionOP scfxn_
 
protocols::features::ProteinSilentReportOP protein_silent_report_
 
std::string database_name_
 
std::string database_pq_schema_
 
std::map< std::string,
StructureID
tag_structures_
 
std::map< std::string,
std::set< core::Size > > 
tag_residues_
 

Additional Inherited Members

- Protected Member Functions inherited from protocols::jd2::JobInputter
void load_pose_into_job (core::pose::Pose const &pose, JobOP job)
 this function modifies the InnerJob's pose. Access to that pose is via friendship. More...
 
void load_pose_into_job (core::pose::PoseCOP pose, JobOP job)
 this function modifies the InnerJob's pose. Access to that pose is via friendship. More...
 
virtual core::Size get_nstruct () const
 this code is here to restrict the use of inner_job_nonconst (this class is a friend class and can do it) More...
 

Detailed Description

This is the simplest implementation of JobInputter, which reads from -s/-l and Database files.

Constructor & Destructor Documentation

protocols::features::DatabaseJobInputter::DatabaseJobInputter ( )
protocols::features::DatabaseJobInputter::~DatabaseJobInputter ( )
overridedefault

Member Function Documentation

void protocols::features::DatabaseJobInputter::fill_jobs ( protocols::jd2::JobsContainer jobs)
overridevirtual

this function determines what jobs exist from -in::file::silent and -in::file::tags.

this function determines what jobs exist

Implements protocols::jd2::JobInputter.

References protocols::jd2::JobsContainer::clear(), database_name_, database_pq_schema_, protocols::jd2::JobInputter::get_nstruct(), protocols::jd2::JobsContainer::push_back(), tag_structures_, core::id::to_string(), and protocols::features::tr().

string protocols::features::DatabaseJobInputter::get_database_name ( ) const

Get database name.

References database_name_.

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

Get database postreSQL schema.

References database_pq_schema_.

ScoreFunctionOP protocols::features::DatabaseJobInputter::get_scorefunction ( )

Get score function.

References scfxn_.

protocols::jd2::JobInputterInputSource::Enum protocols::features::DatabaseJobInputter::input_source ( ) const
overridevirtual

Return the type of input source that the DatabaseJobInputter is currently using.

Returns
Always DATABASE.

Implements protocols::jd2::JobInputter.

References protocols::jd2::JobInputterInputSource::DATABASE.

void protocols::features::DatabaseJobInputter::load_options_from_option_system ( )
void protocols::features::DatabaseJobInputter::pose_from_job ( core::pose::Pose pose,
protocols::jd2::JobOP  job 
)
overridevirtual

this function is responsible for filling the pose reference with the pose indicated by the job. The Job object (within its InnerJob) contains a PoseCOP. This function needs to either fill the pose reference from the InnerJob or, on first demand of a pose from that InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill the reference. This implementation uses pose_from_pdb

This function will first see if the pose already exists in the Job. If not, it will read it into the pose reference, and hand a COP cloned from that pose to the Job. If the pose pre-exists it just copies the COP's pose into it.

Implements protocols::jd2::JobInputter.

References core::pose::Pose::clear(), database_name_, database_pq_schema_, core::pose::initialize_disulfide_bonds(), core::conformation::symmetry::is_symmetric(), core::pose::symmetry::make_asymmetric_pose(), protein_silent_report_, tag_residues_, tag_structures_, and protocols::features::tr().

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

Set database name.

References database_name_.

Referenced by load_options_from_option_system().

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

Set database postreSQL schema.

References database_pq_schema_.

Referenced by load_options_from_option_system().

void protocols::features::DatabaseJobInputter::set_scorefunction ( core::scoring::ScoreFunctionOP  scorefunction)

Set score function.

References scfxn_.

void protocols::features::DatabaseJobInputter::set_struct_ids_from_sql ( utility::vector1< std::string > const &  sql)

set input tags using a database SELECT command

The specified struct_ids indicate which structures should be used. If no ids are specified, then all will be used. Unless a tag column is specified in the SQL statement, the job name (and consequently, the file output name) will be an integer representation of the struct_id. If a tag column is given, then the file name will be the tag associated with the given row.

References database_name_, database_pq_schema_, tag_residues_, tag_structures_, and core::id::to_string().

Referenced by load_options_from_option_system().

void protocols::features::DatabaseJobInputter::set_struct_ids_from_strings ( utility::vector1< std::string > const &  struct_id_strings)

set struct_ids from a list of strings of integer representations

References tag_structures_.

Referenced by load_options_from_option_system().

Member Data Documentation

std::string protocols::features::DatabaseJobInputter::database_name_
private
std::string protocols::features::DatabaseJobInputter::database_pq_schema_
private
protocols::features::ProteinSilentReportOP protocols::features::DatabaseJobInputter::protein_silent_report_
private

Referenced by pose_from_job().

core::scoring::ScoreFunctionOP protocols::features::DatabaseJobInputter::scfxn_
private
std::map< std::string, std::set< core::Size > > protocols::features::DatabaseJobInputter::tag_residues_
private
std::map< std::string, StructureID > protocols::features::DatabaseJobInputter::tag_structures_
private

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