#include <ThreadingJobInputter.hh>

Inheritance diagram for protocols::comparative_modeling::ThreadingJobInputter:

Collaboration diagram for protocols::comparative_modeling::ThreadingJobInputter:

Public Member Functions
	ThreadingJobInputter ()

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. More...

virtual void	fill_jobs (protocols::jd2::Jobs &jobs)
	this function determines what jobs exist More...

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

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

Private Types
typedef utility::vector1 < core::sequence::SequenceAlignment >	Alignments

typedef utility::vector1 < core::pose::PoseOP >	PoseOPs

typedef std::map< std::string, PoseOPs >	PoseMap

typedef utility::vector1 < std::string >	FileList

typedef std::map< std::string, utility::vector1< core::Size > >	ExtraResidues

Private Member Functions
size_t	num_templates () const
	Returns the number of templates in <template_poses_> More...

Private Attributes
Alignments	alignments_

PoseMap	template_poses_

ExtraResidues	extra_residues_

protocols::jd2::JobInputterInputSource::Enum	input_source_

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

Definition at line 38 of file ThreadingJobInputter.hh.

Member Typedef Documentation

typedef utility::vector1< core::sequence::SequenceAlignment > protocols::comparative_modeling::ThreadingJobInputter::Alignments

private

Definition at line 39 of file ThreadingJobInputter.hh.

typedef std::map< std::string, utility::vector1< core::Size > > protocols::comparative_modeling::ThreadingJobInputter::ExtraResidues

private

Definition at line 43 of file ThreadingJobInputter.hh.

typedef utility::vector1< std::string > protocols::comparative_modeling::ThreadingJobInputter::FileList

private

Definition at line 42 of file ThreadingJobInputter.hh.

typedef std::map< std::string, PoseOPs > protocols::comparative_modeling::ThreadingJobInputter::PoseMap

private

Definition at line 41 of file ThreadingJobInputter.hh.

typedef utility::vector1< core::pose::PoseOP > protocols::comparative_modeling::ThreadingJobInputter::PoseOPs

private

Definition at line 40 of file ThreadingJobInputter.hh.

Constructor & Destructor Documentation

protocols::comparative_modeling::ThreadingJobInputter::ThreadingJobInputter ( )

Definition at line 92 of file ThreadingJobInputter.cc.

References alignments_, core::io::silent::SilentFileData::begin(), core::io::silent::SilentFileData::end(), extra_residues_, input_source_, protocols::jd2::JobInputterInputSource::PDB_FILE, core::import_pose::poseOPs_from_pdbs(), core::sequence::read_aln(), protocols::comparative_modeling::read_extra_residues(), core::io::silent::SilentFileData::read_file(), protocols::jd2::JobInputterInputSource::SILENT_FILE, template_poses_, and protocols::comparative_modeling::tr().

Referenced by protocols::comparative_modeling::ThreadingJobInputterCreator::create_JobInputter().

Member Function Documentation

void protocols::comparative_modeling::ThreadingJobInputter::fill_jobs ( protocols::jd2::Jobs & jobs)

virtual

this function determines what jobs exist

this function determines what jobs

Implements protocols::jd2::JobInputter.

Definition at line 232 of file ThreadingJobInputter.cc.

References alignments_, extra_residues_, protocols::jd2::JobInputter::get_nstruct(), template_poses_, and protocols::comparative_modeling::tr().

protocols::jd2::JobInputterInputSource::Enum protocols::comparative_modeling::ThreadingJobInputter::input_source ( ) const

virtual

Return the type of input source that the ThreadingJobInputter is currently using for template structures.

Implements protocols::jd2::JobInputter.

Definition at line 318 of file ThreadingJobInputter.cc.

References input_source_.

size_t protocols::comparative_modeling::ThreadingJobInputter::num_templates ( ) const

private

Returns the number of templates in <template_poses_>

Definition at line 322 of file ThreadingJobInputter.cc.

References template_poses_.

void protocols::comparative_modeling::ThreadingJobInputter::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 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 155 of file ThreadingJobInputter.cc.

References core::sequence::alignment_into_pose(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::comparative_modeling::ThreadingMover::build_loops(), core::chemical::FA_STANDARD, core::chemical::ChemicalManager::get_instance(), core::pose::make_pose_from_sequence(), protocols::comparative_modeling::ThreadingMover::randomize_loop_coords(), core::sequence::read_fasta_file(), protocols::comparative_modeling::ThreadingMover::repack_query(), core::pose::Pose::total_residue(), and protocols::comparative_modeling::tr().