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protocols::jd2::LargeNstructJobInputter Class Reference

#include <LargeNstructJobInputter.hh>

Inheritance diagram for protocols::jd2::LargeNstructJobInputter:
Inheritance graph
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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

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

References protocols::jd2::tr().

Member Function Documentation

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().

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.

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().

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().

void protocols::jd2::LargeNstructJobInputter::update_jobs_list ( JobsContainerOP  jobs)
overridevirtual

This function is only called by certain JobInputters to update the jobs list after it has already been created.

An example case would be the LargeNstructJobInputter, which uses this function to load additional jobs after the first N have started to come back.

Reimplemented from protocols::jd2::JobInputter.

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

bool protocols::jd2::LargeNstructJobInputter::updates_jobs_list ( ) const
inlineoverridevirtual

Does this type of JobInputter update the jobs list?

False by default. Override this function in derived classes to make it true. The LargeNstructJobInputter overrides this, and returns true.

Reimplemented from protocols::jd2::JobInputter.


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