protocols::comparative_modeling::ThreadingJob Class Reference

#include <ThreadingJob.hh>

Inheritance diagram for protocols::comparative_modeling::ThreadingJob:

Collaboration 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...
virtual	~InnerJob ()
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...
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

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.

Definition at line 43 of file ThreadingJob.hh.

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

Definition at line 38 of file ThreadingJob.cc.

References alignment(), alignment_, fasta2template_, nres_template_, and protocols::comparative_modeling::tr().

Member Function Documentation

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

inline

the alignment for this Job

Definition at line 55 of file ThreadingJob.hh.

References alignment_.

Referenced by alignment_id(), and ThreadingJob().

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

inline

convenience : alignment id

Definition at line 60 of file ThreadingJob.hh.

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

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

(

)

const

returns list of extra residues to steal

Definition at line 116 of file ThreadingJob.cc.

References extra_residues_to_steal_.

void protocols::comparative_modeling::ThreadingJob::extra_residues_to_steal

(

utility::vector1< core::Size > const &

res)

Definition at line 120 of file ThreadingJob.cc.

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)

Definition at line 95 of file ThreadingJob.cc.

References alignment_, protocols::loops::Loops::begin(), protocols::loops::Loops::end(), 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

Definition at line 78 of file ThreadingJob.hh.

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

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

private

Definition at line 83 of file ThreadingJob.hh.

Referenced by extra_residues_to_steal(), and loops().

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

private

Definition at line 79 of file ThreadingJob.hh.

Referenced by loops(), and ThreadingJob().

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

private

Definition at line 80 of file ThreadingJob.hh.

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