#include <LargeNstructJobInputter.hh>

Inheritance diagram for protocols::jd2::LargeNstructJobInputter:

[legend]

Public Member Functions
	LargeNstructJobInputter ()

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. More...

void	fill_jobs (protocols::jd2::JobsContainer &jobs) override
	This function determines what jobs exist. More...

void	update_jobs_list (JobsContainerOP jobs) override
	This function is only called by certain JobInputters to update the jobs list after it has already been created. More...

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

bool	updates_jobs_list () const override
	Does this type of JobInputter update the jobs list? 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...

Private Member Functions
void	populate_next_n_jobs (protocols::jd2::JobsContainer &jobs, core::Size const first_job_index, core::Size const number_of_jobs_to_add, core::Size const total_jobs)
	Private function to add N jobs to the list of jobs. More...

Additional Inherited Members
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...

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 an implementation of JobInputter for cases where it's not possible to list all jobs at once.

Constructor & Destructor Documentation

◆ LargeNstructJobInputter()

protocols::jd2::LargeNstructJobInputter::LargeNstructJobInputter ( )

References protocols::jd2::tr().

Member Function Documentation

◆ fill_jobs()

void protocols::jd2::LargeNstructJobInputter::fill_jobs ( protocols::jd2::JobsContainer & jobs )

overridevirtual

This function determines what jobs exist.

Unlike the GenericJobInputter, this version only ever has a subset of total jobs in memory at any given time.

this function determines what jobs exist. Note that if the value of the -jd2:max_nstruct_in_memory flag is less than the value specified with the -nstruct flag, this ONLY sets up the first max_nstruct_in_memory jobs.

Implements protocols::jd2::JobInputter.

References protocols::jd2::JobsContainer::clear(), protocols::jd2::JobInputter::get_nstruct(), protocols::jd2::JobInputter::get_self_ptr(), populate_next_n_jobs(), protocols::jd2::JobsContainer::set_job_inputter(), protocols::jd2::JobsContainer::set_total_jobs(), and protocols::jd2::tr().

◆ input_source()

protocols::jd2::JobInputterInputSource::Enum protocols::jd2::LargeNstructJobInputter::input_source ( ) const

overridevirtual

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

Returns: Always POSE.

Implements protocols::jd2::JobInputter.

References protocols::jd2::JobInputterInputSource::POSE.

◆ populate_next_n_jobs()

void protocols::jd2::LargeNstructJobInputter::populate_next_n_jobs	(	protocols::jd2::JobsContainer &	jobs,
		core::Size const	first_job_index,
		core::Size const	number_of_jobs_to_add,
		core::Size const	total_jobs
	)

private

Private function to add N jobs to the list of jobs.

References protocols::jd2::JobsContainer::push_back().

Referenced by fill_jobs(), and update_jobs_list().

◆ pose_from_job()

void protocols::jd2::LargeNstructJobInputter::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 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::chemical::CENTROID, core::pose::symmetry::is_symmetric(), core::pose::symmetry::make_asymmetric_pose(), core::pose::make_pose_from_sequence(), core::sequence::read_fasta_file_str(), and protocols::jd2::tr().