Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Types | Private Member Functions | Private Attributes | List of all members
protocols::comparative_modeling::ThreadingJobInputter Class Reference

#include <ThreadingJobInputter.hh>

Inheritance diagram for protocols::comparative_modeling::ThreadingJobInputter:
Inheritance graph
[legend]

Public Member Functions

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

Member Typedef Documentation

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

Constructor & Destructor Documentation

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

Member Function Documentation

void protocols::comparative_modeling::ThreadingJobInputter::fill_jobs ( protocols::jd2::JobsContainer jobs)
overridevirtual
protocols::jd2::JobInputterInputSource::Enum protocols::comparative_modeling::ThreadingJobInputter::input_source ( ) const
overridevirtual

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

Implements protocols::jd2::JobInputter.

References input_source_.

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

Returns the number of templates in <template_poses_>

References template_poses_.

void protocols::comparative_modeling::ThreadingJobInputter::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::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::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::size(), and protocols::comparative_modeling::tr().

Member Data Documentation

Alignments protocols::comparative_modeling::ThreadingJobInputter::alignments_
private

Referenced by fill_jobs(), and ThreadingJobInputter().

ExtraResidues protocols::comparative_modeling::ThreadingJobInputter::extra_residues_
private

Referenced by fill_jobs(), and ThreadingJobInputter().

protocols::jd2::JobInputterInputSource::Enum protocols::comparative_modeling::ThreadingJobInputter::input_source_
private
PoseMap protocols::comparative_modeling::ThreadingJobInputter::template_poses_
private

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