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protocols::hybridization::ChunkTrialMover Class Reference

#include <ChunkTrialMover.hh>

Inheritance diagram for protocols::hybridization::ChunkTrialMover:
Inheritance graph

Public Member Functions

 ChunkTrialMover (utility::vector1< core::pose::PoseCOP > const &template_poses, utility::vector1< protocols::loops::Loops > const &template_chunks, bool random_template=true, AlignOption align_option=all_chunks, utility::vector1< bool > residue_sample_template=utility::vector1< bool >())
void get_alignment_from_template (core::pose::PoseCOP template_pose, std::map< core::Size, core::Size > &seqpos_alignment)
void apply (core::pose::Pose &pose) override
 Main Method. More...
void set_template (core::Size const template_number)
void set_max_registry_shift (core::Size max_registry_shift_in)
core::Size template_number ()
void pick_random_template ()
void pick_random_chunk (core::pose::Pose &pose)
core::Size trial_counter (core::Size ires)
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
bool has_valid_moves ()
void set_templates_to_ignore (std::set< core::Size > template_indices_in)
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
virtual MoverOP create ()
MoverCOP get_self_ptr () const
MoverOP get_self_ptr ()
MoverCAP get_self_weak_ptr () const
MoverAP get_self_weak_ptr ()
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
virtual void test_move (Pose &pose)
 : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
virtual MoverOP clone () const
 Return a clone of the Mover object. More...
virtual bool reinitialize_for_each_job () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
virtual bool reinitialize_for_new_input () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
MoverStatus get_last_move_status () const
 end parser interface, start Job Distributor interface///////////// More...
void reset_status ()
 resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
virtual core::pose::PoseOP get_additional_output ()
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
void set_type (std::string const &setting)
 Set the 'type' string. More...
std::string get_type () const
void type (const std::string &type_in)
 Set the 'type' string. More...
std::string const & type () const
 Get the set 'type' string. More...
virtual void set_input_pose (PoseCOP pose)
 setter for poses contained for rms More...
virtual void set_native_pose (PoseCOP pose)
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
PoseCOP get_input_pose () const
PoseCOP get_native_pose () const
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const
virtual void set_current_tag (std::string const &new_tag)
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
virtual core::Real last_proposal_density_ratio ()
virtual void clear_info ()
 Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
virtual Stringsinfo ()
 non-const accessor More...
virtual Strings const & info () const
 const accessor More...
virtual void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Attributes

< core::pose::PoseCOP
< protocols::loops::Loops
bool random_template_
bool has_valid_moves_
AlignOption align_option_
InsertChunkMover align_chunk_
utility::vector1< std::map
< core::Size, core::Size > > 
utility::vector1< core::Sizeresidue_covered_by_template_
core::Size template_number_
core::Size jump_number_
core::Size highest_tmpl_resnum_
std::set< core::Sizeignore_template_indices_
utility::vector1< boolsampling_chunk_
core::Size max_registry_shift_global_

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
typedef core::pose::Pose Pose
typedef core::pose::PoseCOP PoseCOP
typedef std::list< std::string > Strings
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
static void register_options ()
 Overload this static method if you access options within the mover. More...
- Protected Member Functions inherited from protocols::moves::Mover
void set_last_move_status (MoverStatus status)
 nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Constructor & Destructor Documentation

protocols::hybridization::ChunkTrialMover::ChunkTrialMover ( utility::vector1< core::pose::PoseCOP > const &  template_poses,
utility::vector1< protocols::loops::Loops > const &  template_chunks,
bool  random_template = true,
AlignOption  align_option = all_chunks,
utility::vector1< bool residue_sample_template = utility::vector1<bool>() 

Member Function Documentation

void protocols::hybridization::ChunkTrialMover::apply ( core::pose::Pose )
void protocols::hybridization::ChunkTrialMover::get_alignment_from_template ( core::pose::PoseCOP  template_pose,
std::map< core::Size, core::Size > &  seqpos_alignment 
std::string protocols::hybridization::ChunkTrialMover::get_name ( ) const

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

bool protocols::hybridization::ChunkTrialMover::has_valid_moves ( )
void protocols::hybridization::ChunkTrialMover::pick_random_chunk ( core::pose::Pose pose)
void protocols::hybridization::ChunkTrialMover::pick_random_template ( )
void protocols::hybridization::ChunkTrialMover::set_max_registry_shift ( core::Size  max_registry_shift_in)
void protocols::hybridization::ChunkTrialMover::set_template ( core::Size const  template_number)
void protocols::hybridization::ChunkTrialMover::set_templates_to_ignore ( std::set< core::Size template_indices_in)
core::Size protocols::hybridization::ChunkTrialMover::template_number ( )
Size protocols::hybridization::ChunkTrialMover::trial_counter ( core::Size  ires)

Member Data Documentation

InsertChunkMover protocols::hybridization::ChunkTrialMover::align_chunk_

Referenced by apply(), and trial_counter().

AlignOption protocols::hybridization::ChunkTrialMover::align_option_

Referenced by apply().

bool protocols::hybridization::ChunkTrialMover::has_valid_moves_

Referenced by ChunkTrialMover(), and has_valid_moves().

core::Size protocols::hybridization::ChunkTrialMover::highest_tmpl_resnum_
std::set< core::Size > protocols::hybridization::ChunkTrialMover::ignore_template_indices_
core::Size protocols::hybridization::ChunkTrialMover::jump_number_

Referenced by apply(), and pick_random_chunk().

core::Size protocols::hybridization::ChunkTrialMover::max_registry_shift_global_

Referenced by apply(), and set_max_registry_shift().

bool protocols::hybridization::ChunkTrialMover::random_template_

Referenced by apply().

utility::vector1< core::Size > protocols::hybridization::ChunkTrialMover::residue_covered_by_template_

Referenced by apply(), and ChunkTrialMover().

utility::vector1<bool> protocols::hybridization::ChunkTrialMover::sampling_chunk_
utility::vector1< std::map <core::Size, core::Size> > protocols::hybridization::ChunkTrialMover::sequence_alignments_

Referenced by apply(), and ChunkTrialMover().

utility::vector1< protocols::loops::Loops > protocols::hybridization::ChunkTrialMover::template_chunks_
core::Size protocols::hybridization::ChunkTrialMover::template_number_

Referenced by set_template(), and template_number().

utility::vector1< core::pose::PoseCOP > protocols::hybridization::ChunkTrialMover::template_poses_

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