Rosetta 3.4
Public Member Functions | Static Public Member Functions
protocols::features::DatabaseJobInputter Class Reference

#include <DatabaseJobInputter.hh>

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List of all members.

Public Member Functions

 DatabaseJobInputter ()
virtual ~DatabaseJobInputter ()
void load_options_from_option_system ()
 load options from option sytem
void set_database_fname (std::string const &database_fname)
 Set database file name.
std::string get_database_fname () const
 Get database file name.
core::scoring::ScoreFunctionOP get_scorefunction ()
 Get score function.
void set_scorefunction (core::scoring::ScoreFunctionOP scorefunction)
 Set score function.
void set_tags (utility::vector1< std::string > const &tags)
 Set input tags. If none are specified, use all tags.
void set_tags_from_sql (utility::vector1< std::string > const &sql)
 set input tags using a database SELECT command
void get_tags (utility::vector1< std::string > &tags)
 Get input tags.
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
virtual void fill_jobs (protocols::jd2::Jobs &jobs)
 this function determines what jobs exist from -in::file::silent and
virtual
protocols::jd2::JobInputterInputSource::Enum 
input_source () const
 Return the type of input source that the DatabaseJobInputter is currently using.

Static Public Member Functions

static void register_options ()

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 ( ) [virtual]

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.

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

std::string protocols::features::DatabaseJobInputter::get_database_fname ( ) const

Get database file name.

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

Get score function.

void protocols::features::DatabaseJobInputter::get_tags ( utility::vector1< std::string > &  tags)

Get input tags.

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.

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

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

load options from option sytem

References set_database_fname(), set_tags(), and set_tags_from_sql().

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.

References core::pose::Pose::clear(), core::pose::initialize_disulfide_bonds(), core::conformation::symmetry::is_symmetric(), core::pose::symmetry::make_asymmetric_pose(), and protocols::features::tr().

void protocols::features::DatabaseJobInputter::register_options ( ) [static]
void protocols::features::DatabaseJobInputter::set_database_fname ( std::string const &  database_fname)

Set database file name.

Referenced by load_options_from_option_system().

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

Set score function.

void protocols::features::DatabaseJobInputter::set_tags ( utility::vector1< std::string > const &  tags)

Set input tags. If none are specified, use all tags.

The specified tags indicate which structures should be used. If no tags are specified, then all tags will be used. Tags are short strings that uniquely identify a structure. WARNING: As of Jan '11, gives a pose there are several places one my look for such a string identifier: If the pose has a PDBInfo object: pose.pdb_info()->name() tag_from_pose(pose) <=> pose.data().get(JOBDIST_OUTPUT_TAG) JobDistributor::get_instance()->current_job()->input_tag()

The last two will work, and the first will work when pdb info stored with the structures in the database.

Referenced by load_options_from_option_system().

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

set input tags using a database SELECT command

Referenced by load_options_from_option_system().


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