#include <DatabaseJobInputter.hh>

Inheritance diagram for protocols::features::DatabaseJobInputter:

Collaboration diagram for protocols::features::DatabaseJobInputter:

Public Member Functions
	DatabaseJobInputter ()

virtual	~DatabaseJobInputter ()

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 hex-uuid representations More...

void	set_struct_ids_from_sql (utility::vector1< std::string > const &sql)
	set input tags using a database SELECT command More...

virtual void	pose_from_job (core::pose::Pose &pose, protocols::jd2::JobOP job)
	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...

virtual void	fill_jobs (protocols::jd2::Jobs &jobs)
	this function determines what jobs exist from -in::file::silent and -in::file::tags. More...

virtual protocols::jd2::JobInputterInputSource::Enum	input_source () const
	Return the type of input source that the DatabaseJobInputter is currently using. More...

Public Member Functions inherited from protocols::jd2::JobInputter
virtual	~JobInputter ()

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_

core::Size	input_protocol_id_

std::map< std::string, boost::uuids::uuid >	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.

Definition at line 46 of file DatabaseJobInputter.hh.

Constructor & Destructor Documentation

protocols::features::DatabaseJobInputter::DatabaseJobInputter ( )

Definition at line 81 of file DatabaseJobInputter.cc.

References load_options_from_option_system(), and protocols::features::tr().

Referenced by protocols::features::DatabaseJobInputterCreator::create_JobInputter().

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

virtual

Definition at line 90 of file DatabaseJobInputter.cc.

Member Function Documentation

void protocols::features::DatabaseJobInputter::fill_jobs ( protocols::jd2::Jobs & jobs)

virtual

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

this function determines what jobs exist

Implements protocols::jd2::JobInputter.

Definition at line 321 of file DatabaseJobInputter.cc.

References database_name_, database_pq_schema_, protocols::jd2::JobInputter::get_nstruct(), tag_structures_, and protocols::features::tr().

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

Get database name.

Definition at line 152 of file DatabaseJobInputter.cc.

References database_name_.

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

Get database postreSQL schema.

Definition at line 170 of file DatabaseJobInputter.cc.

References database_pq_schema_.

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

Get score function.

Definition at line 177 of file DatabaseJobInputter.cc.

References scfxn_.

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

virtual

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

Returns: Always DATABASE.

Implements protocols::jd2::JobInputter.

Definition at line 396 of file DatabaseJobInputter.cc.

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

void protocols::features::DatabaseJobInputter::load_options_from_option_system ( )

load options from option sytem

Definition at line 94 of file DatabaseJobInputter.cc.

References set_database_name(), set_database_pq_schema(), set_struct_ids_from_sql(), and set_struct_ids_from_strings().

Referenced by DatabaseJobInputter().

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

virtual

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.

Definition at line 282 of file DatabaseJobInputter.cc.

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

Definition at line 129 of file DatabaseJobInputter.cc.

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

Set database name.

Definition at line 145 of file DatabaseJobInputter.cc.

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.

Definition at line 163 of file DatabaseJobInputter.cc.

References database_pq_schema_.

Referenced by load_options_from_option_system().

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

Set score function.

Definition at line 183 of file DatabaseJobInputter.cc.

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 ASCII hexadecimal representation of the struct_id (a boost UUID). If a tag column is given, then the file name will be the tag associated with the given row.

Definition at line 214 of file DatabaseJobInputter.cc.

References database_name_, database_pq_schema_, tag_residues_, and tag_structures_.

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 hex-uuid representations

Definition at line 188 of file DatabaseJobInputter.cc.

References tag_structures_.

Referenced by load_options_from_option_system().