Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Attributes | List of all members
protocols::jd2::AtomTreeDiffJobInputter Class Reference

#include <AtomTreeDiffJobInputter.hh>

Inheritance diagram for protocols::jd2::AtomTreeDiffJobInputter:
Inheritance graph
[legend]

Public Member Functions

 AtomTreeDiffJobInputter ()
 
 ~AtomTreeDiffJobInputter () 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...
 
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 AtomTreeDiffJobInputter is currently using. More...
 
core::pose::PoseOPs const & all_ref_poses () const
 Utility function to allow mutatable (!) access to the reference poses of the undelying AtomTreeDiff object. Use with caution. 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 Attributes

core::import_pose::atom_tree_diffs::AtomTreeDiff atom_tree_diff_
 

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 AtomTree files.

Constructor & Destructor Documentation

protocols::jd2::AtomTreeDiffJobInputter::AtomTreeDiffJobInputter ( )

References protocols::jd2::tr().

protocols::jd2::AtomTreeDiffJobInputter::~AtomTreeDiffJobInputter ( )
overridedefault

Member Function Documentation

utility::vector1< core::pose::PoseOP > const & protocols::jd2::AtomTreeDiffJobInputter::all_ref_poses ( ) const

Utility function to allow mutatable (!) access to the reference poses of the undelying AtomTreeDiff object. Use with caution.

This exists to allow setup on stored reference poses for properties that don't get saved/restored in PDB format, like covalent constraints for enzyme design.

void protocols::jd2::AtomTreeDiffJobInputter::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 -in:file:atom_tree_diff

Implements protocols::jd2::JobInputter.

References protocols::jd2::JobsContainer::clear(), protocols::jd2::JobsContainer::push_back(), protocols::hybridization::score, and protocols::jd2::tr().

JobInputterInputSource::Enum protocols::jd2::AtomTreeDiffJobInputter::input_source ( ) const
overridevirtual

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

Returns
Always ATOM_TREE_FILE.

Implements protocols::jd2::JobInputter.

References protocols::jd2::JobInputterInputSource::ATOM_TREE_FILE.

void protocols::jd2::AtomTreeDiffJobInputter::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::import_pose::PDB_file, core::import_pose::pose_from_file(), and protocols::jd2::tr().

Member Data Documentation

core::import_pose::atom_tree_diffs::AtomTreeDiff protocols::jd2::AtomTreeDiffJobInputter::atom_tree_diff_
private

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