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Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
protocols::comparative_modeling::ThreadingJob Class Reference

#include <ThreadingJob.hh>

Inheritance diagram for protocols::comparative_modeling::ThreadingJob:
Inheritance graph
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Public Member Functions

 ThreadingJob (core::pose::PoseCOP template_pdb, core::sequence::SequenceAlignmentCOP alignment, std::string const &input_tag, core::Size nstruct_max)
 ctor. Note that it takes only the input tag and max nstruct, pose instantiation is deferred until the pose is needed More...
 
core::sequence::SequenceAlignment
const & 
alignment () const
 the alignment for this Job More...
 
std::string alignment_id () const
 convenience : alignment id More...
 
protocols::loops::Loops loops (core::Size nres) const
 returns the "standard" loop definition (as conservative as possible) More...
 
utility::vector1< core::Size >
const & 
extra_residues_to_steal () const
 returns list of extra residues to steal More...
 
void extra_residues_to_steal (utility::vector1< core::Size > const &res)
 
- Public Member Functions inherited from protocols::jd2::InnerJob
 InnerJob (std::string const &input_tag, core::Size nstruct_max)
 ctor. Note that it takes only the input tag and max nstruct, pose instantiation is deferred until the pose is needed More...
 
 InnerJob (core::pose::PoseCOP, std::string const &input_tag, core::Size nstruct_max)
 ctor. Note that it takes only the input tag and max nstruct, pose instantiation is deferred until the pose is needed More...
 
 InnerJob (InnerJob const &src)
 Copy constructor. More...
 
 ~InnerJob () override
 
InnerJobOP clone () const
 Return an owning pointer to a copy of this object. More...
 
bool operator== (InnerJob const &other) const
 Mutual comparison of this inner job to the other inner job so that if either one thinks it's not the same as the other, then it returns false. Invokes the same() function on both this and other. More...
 
bool operator!= (InnerJob const &other) const
 
virtual bool same (InnerJob const &other) const
 returns true if this is the same as other; does not call other.same() More...
 
virtual void show (std::ostream &out) const
 
std::string const & input_tag () const
 return the input tag (a string of space separated PDB filenames) More...
 
std::string const & optional_output_name () const
 returns a job name controlled by the mover. Must be turned with the optional_output_name out flag. This flag is typically used in conjuction with a mover More...
 
void optional_output_name (std::string output_name)
 sets a job name controlled by the mover More...
 
core::Size nstruct_max () const
 
core::pose::PoseCOP get_pose () const
 return a COP to the input pose DO NOT USE OUTSIDE OF JD2 NAMESPACE More...
 
void set_bad (bool value=true)
 
bool bad () const
 

Static Public Member Functions

static ThreadingJob const * current_job ()
 Convenience function to get the current ThreadingJob from JD2 Will return a nullptr if we can't get a ThreadingJob from JD2. More...
 

Private Attributes

core::sequence::SequenceAlignmentCOP alignment_
 
core::sequence::SequenceAlignmentCOP fasta2template_
 
core::Size nres_template_
 
utility::vector1< core::Sizeextra_residues_to_steal_
 

Additional Inherited Members

- Protected Member Functions inherited from protocols::jd2::InnerJob
void set_pose (core::pose::PoseCOP pose)
 set the input pose. this function is deliberately heavily protected. Parser uses it to re-load the pose after adding constraints. JobInputter is its primary client (using it to load poses). JobDistributor uses it to set the PoseCOP to NULL when done with the input. More...
 

Detailed Description

The InnerThreadingJob class is responsible for knowing input requirements for a given job - how many nstruct, and what the input is. InnerThreadingJobs are relatively heavy; there is no need to duplicate a series of InnerThreadingJobs for each index into nstruct. The companion ThreadingJob class handles the nstruct index and has a pointer to an InnerThreadingJob (which is shared across many ThreadingJobs). InnerThreadingJob also holds a PoseOP to maintain the unmodified input pose for that job.

Constructor & Destructor Documentation

protocols::comparative_modeling::ThreadingJob::ThreadingJob ( core::pose::PoseCOP  template_pdb,
core::sequence::SequenceAlignmentCOP  alignment,
std::string const &  input_tag,
core::Size  nstruct_max 
)

ctor. Note that it takes only the input tag and max nstruct, pose instantiation is deferred until the pose is needed

References alignment(), alignment_, fasta2template_, and nres_template_.

Member Function Documentation

core::sequence::SequenceAlignment const& protocols::comparative_modeling::ThreadingJob::alignment ( ) const
inline

the alignment for this Job

References alignment_.

Referenced by alignment_id(), and ThreadingJob().

std::string protocols::comparative_modeling::ThreadingJob::alignment_id ( ) const
inline

convenience : alignment id

References alignment(), and core::sequence::SequenceAlignment::alignment_id().

protocols::comparative_modeling::ThreadingJob const * protocols::comparative_modeling::ThreadingJob::current_job ( )
static

Convenience function to get the current ThreadingJob from JD2 Will return a nullptr if we can't get a ThreadingJob from JD2.

utility::vector1< core::Size > const & protocols::comparative_modeling::ThreadingJob::extra_residues_to_steal ( ) const

returns list of extra residues to steal

References extra_residues_to_steal_.

void protocols::comparative_modeling::ThreadingJob::extra_residues_to_steal ( utility::vector1< core::Size > const &  res)
protocols::loops::Loops protocols::comparative_modeling::ThreadingJob::loops ( core::Size  nres) const

returns the "standard" loop definition (as conservative as possible)

References alignment_, extra_residues_to_steal_, fasta2template_, protocols::comparative_modeling::loops_from_transitive_alignments(), and nres_template_.

Member Data Documentation

core::sequence::SequenceAlignmentCOP protocols::comparative_modeling::ThreadingJob::alignment_
private

Referenced by alignment(), loops(), and ThreadingJob().

utility::vector1< core::Size > protocols::comparative_modeling::ThreadingJob::extra_residues_to_steal_
private

Referenced by extra_residues_to_steal(), and loops().

core::sequence::SequenceAlignmentCOP protocols::comparative_modeling::ThreadingJob::fasta2template_
private

Referenced by loops(), and ThreadingJob().

core::Size protocols::comparative_modeling::ThreadingJob::nres_template_
private

Referenced by loops(), and ThreadingJob().


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