#include <SilentFileJobInputter.hh>

Inheritance diagram for protocols::jd2::SilentFileJobInputter:

Public Member Functions
	SilentFileJobInputter ()

	~SilentFileJobInputter () override

void	pose_from_job (core::pose::Pose &pose, 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...

virtual core::io::silent::SilentStruct const &	struct_from_job (JobOP job)
	this function returns the SilentStruct that belongs to the given job More...

void	fill_jobs (JobsContainer &jobs) override
	this function determines what jobs exist from -in::file::silent and -in::file::tags. More...

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

core::io::silent::SilentFileData const &	silent_file_data () const

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...

Private Attributes
core::io::silent::SilentFileData	sfd_

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

Constructor & Destructor Documentation

protocols::jd2::SilentFileJobInputter::SilentFileJobInputter ( )

References protocols::jd2::tr().

protocols::jd2::SilentFileJobInputter::~SilentFileJobInputter ( )

overridedefault

Member Function Documentation

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

overridevirtual

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

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

Implements protocols::jd2::JobInputter.

References protocols::jd2::JobsContainer::clear(), core::sequence::end, protocols::jd2::JobsContainer::push_back(), and protocols::jd2::tr().

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

overridevirtual

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

Returns: Always SILENT_FILE.

Implements protocols::jd2::JobInputter.

References protocols::jd2::JobInputterInputSource::SILENT_FILE.

void protocols::jd2::SilentFileJobInputter::pose_from_job	(	core::pose::Pose &	pose,
		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(), core::pose::symmetry::is_symmetric(), core::pose::symmetry::make_asymmetric_pose(), core::pose::tag_into_pose(), and protocols::jd2::tr().

core::io::silent::SilentFileData const& protocols::jd2::SilentFileJobInputter::silent_file_data ( ) const

inline

References sfd_.

core::io::silent::SilentStruct const & protocols::jd2::SilentFileJobInputter::struct_from_job ( JobOP job )

virtual

this function returns the SilentStruct that belongs to the given job