protocols::comparative_modeling::ThreadingJob Class Reference

#include <ThreadingJob.hh>

Inheritance diagram for protocols::comparative_modeling::ThreadingJob:

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::Size >	extra_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

)

References extra_residues_to_steal_.

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().

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

• src/protocols/comparative_modeling/ThreadingJob.hh
• src/protocols/comparative_modeling/ThreadingJob.cc