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protocols::hybridization::ChunkTrialMover Class Reference

#include <ChunkTrialMover.hh>

Inheritance diagram for protocols::hybridization::ChunkTrialMover:
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Collaboration diagram for protocols::hybridization::ChunkTrialMover:
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Public Member Functions

 ChunkTrialMover (utility::vector1< core::pose::PoseCOP > const &template_poses, utility::vector1< protocols::loops::Loops > const &template_chunks, Loops ss_chunks_pose, bool random_template=true, AlignOption align_option=all_chunks, Size max_registry_shift=0)
 
void get_alignment_from_template (core::pose::PoseCOP template_pose, std::map< core::Size, core::Size > &seqpos_alignment)
 
void get_alignment_from_chunk_mapping (std::map< core::Size, core::Size > const &chunk_mapping, Loops const template_ss_chunks, Loops const target_ss_chunks, std::map< core::Size, core::Size > &sequence_alignment)
 
void set_template (core::Size const template_number)
 
core::Size template_number ()
 
void pick_random_template ()
 
void pick_random_chunk (core::pose::Pose &pose)
 
Size trial_counter (Size ires)
 
void apply (core::pose::Pose &pose)
 
std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void set_templates_to_ignore (std::set< core::Size > template_indices_in)
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
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...
 
void set_current_tag (std::string const &new_tag)
 
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 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...
 
void type (const std::string &type_in)
 
virtual MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
virtual void parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
std::string get_type () const
 
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...
 
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 bool reinitialize_for_each_job () const
 this function informs 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
 this function informs 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
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Private Attributes

utility::vector1
< core::pose::PoseCOP
template_poses_
 
utility::vector1< Loopstemplate_chunks_
 
bool random_template_
 
AlignOption align_option_
 
InsertChunkMover align_chunk_
 
Size max_registry_shift_input_
 
utility::vector1< std::map
< core::Size, core::Size > > 
sequence_alignments_
 
utility::vector1< Sizemax_registry_shift_
 
Size template_number_
 
Size jump_number_
 
std::set< core::Sizeignore_template_indices_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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,
Loops  ss_chunks_pose,
bool  random_template = true,
AlignOption  align_option = all_chunks,
Size  max_registry_shift = 0 
)

Member Function Documentation

void protocols::hybridization::ChunkTrialMover::apply ( core::pose::Pose pose)
virtual
void protocols::hybridization::ChunkTrialMover::get_alignment_from_chunk_mapping ( std::map< core::Size, core::Size > const &  chunk_mapping,
Loops const  template_ss_chunks,
Loops const  target_ss_chunks,
std::map< core::Size, core::Size > &  sequence_alignment 
)
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
virtual

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

Implements protocols::moves::Mover.

void protocols::hybridization::ChunkTrialMover::pick_random_chunk ( core::pose::Pose pose)
void protocols::hybridization::ChunkTrialMover::pick_random_template ( )
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)
inline
core::Size protocols::hybridization::ChunkTrialMover::template_number ( )
Size protocols::hybridization::ChunkTrialMover::trial_counter ( Size  ires)

Member Data Documentation

InsertChunkMover protocols::hybridization::ChunkTrialMover::align_chunk_
private

Referenced by apply(), and trial_counter().

AlignOption protocols::hybridization::ChunkTrialMover::align_option_
private

Referenced by apply().

std::set< core::Size > protocols::hybridization::ChunkTrialMover::ignore_template_indices_
private

Referenced by apply(), and pick_random_template().

Size protocols::hybridization::ChunkTrialMover::jump_number_
private

Referenced by apply(), and pick_random_chunk().

utility::vector1< Size > protocols::hybridization::ChunkTrialMover::max_registry_shift_
private
Size protocols::hybridization::ChunkTrialMover::max_registry_shift_input_
private
bool protocols::hybridization::ChunkTrialMover::random_template_
private

Referenced by apply().

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

Referenced by apply(), and ChunkTrialMover().

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

Referenced by set_template(), and template_number().

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

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