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

#include <PDBJobInputter.hh>

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

Public Member Functions

 PDBJobInputter ()
 
 ~PDBJobInputter () 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 -s/-l More...
 
JobInputterInputSource::Enum input_source () const override
 Return the type of input source that the PDBJobInputter is currently using. 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...
 

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 PDB files.

Constructor & Destructor Documentation

protocols::jd2::PDBJobInputter::PDBJobInputter ( )

References protocols::jd2::TR().

protocols::jd2::PDBJobInputter::~PDBJobInputter ( )
overridedefault

Member Function Documentation

void protocols::jd2::PDBJobInputter::fill_jobs ( JobsContainer jobs)
overridevirtual

this function determines what jobs exist from -s/-l

this function determines what jobs exist from -s/-l

Implements protocols::jd2::JobInputter.

References protocols::jd2::JobsContainer::clear(), protocols::jd2::JobsContainer::push_back(), and protocols::jd2::TR().

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

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

Returns
Always PDB_FILE.

Implements protocols::jd2::JobInputter.

References protocols::jd2::JobInputterInputSource::PDB_FILE.

void protocols::jd2::PDBJobInputter::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.

Reimplemented in protocols::protein_interface_design::ParserJobInputter.

References core::util::auto_setup_all_metal_constraints(), core::chemical::FULL_ATOM_t, core::import_pose::initialize_pose_and_other_poses_from_command_line(), core::import_pose::pose_from_file(), core::pose::Pose::residue_type_set_for_pose(), and protocols::jd2::TR().


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