#include <ThreadingJobInputter.hh>
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
◆ Alignments
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private |
◆ ExtraResidues
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private |
◆ FileList
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private |
◆ PoseMap
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private |
◆ PoseOPs
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private |
Constructor & Destructor Documentation
◆ ThreadingJobInputter()
| protocols::comparative_modeling::ThreadingJobInputter::ThreadingJobInputter | ( | ) |
References core::scoring::alignment, alignments_, core::io::silent::SilentFileData::begin(), core::io::silent::SilentFileData::end(), extra_residues_, input_source_, core::import_pose::PDB_file, protocols::jd2::JobInputterInputSource::PDB_FILE, core::import_pose::poseOPs_from_files(), 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().
Member Function Documentation
◆ fill_jobs()
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overridevirtual |
this function determines what jobs exist
this function determines what jobs
Implements protocols::jd2::JobInputter.
References alignments_, protocols::jd2::JobsContainer::back(), protocols::jd2::JobsContainer::clear(), extra_residues_, protocols::jd2::JobInputter::get_nstruct(), protocols::jd2::JobsContainer::push_back(), template_poses_, and protocols::comparative_modeling::tr().
◆ input_source()
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overridevirtual |
Return the type of input source that the ThreadingJobInputter is currently using for template structures.
Implements protocols::jd2::JobInputter.
References input_source_.
◆ num_templates()
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private |
Returns the number of templates in <template_poses_>
References template_poses_.
◆ pose_from_job()
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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_
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private |
Referenced by fill_jobs(), and ThreadingJobInputter().
◆ extra_residues_
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private |
Referenced by fill_jobs(), and ThreadingJobInputter().
◆ input_source_
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private |
Referenced by input_source(), and ThreadingJobInputter().
◆ template_poses_
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private |
Referenced by fill_jobs(), num_templates(), and ThreadingJobInputter().
The documentation for this class was generated from the following files:
- src/protocols/comparative_modeling/ThreadingJobInputter.hh
- src/protocols/comparative_modeling/ThreadingJobInputter.cc
