Rosetta Protocols  2014.35
Public Member Functions | Private Attributes | List of all members
protocols::jd2::AtomTreeDiffJobInputter Class Reference

#include <AtomTreeDiffJobInputter.hh>

Public Member Functions

 AtomTreeDiffJobInputter ()
 
virtual ~AtomTreeDiffJobInputter ()
 
virtual void pose_from_job (core::pose::Pose &pose, 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. This implementation uses pose_from_pdb More...
 
virtual void fill_jobs (Jobs &jobs)
 this function determines what jobs exist from -in::file::silent and -in::file::tags. More...
 
virtual
JobInputterInputSource::Enum 
input_source () const
 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
virtual ~JobInputter ()
 

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 ( )
virtual

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 ( Jobs jobs)
virtual
JobInputterInputSource::Enum protocols::jd2::AtomTreeDiffJobInputter::input_source ( ) const
virtual

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 
)
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 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(), protocols::jd2::Job::inner_job(), protocols::jd2::Job::input_tag(), basic::options::OptionKeys::in::file::native, basic::options::option, core::import_pose::pose_from_pdb(), protocols::jd2::tr, user, and utility_exit_with_message.

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: