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protocols::hybridization::InsertChunkMover Class Reference

#include <InsertChunkMover.hh>

Inheritance diagram for protocols::hybridization::InsertChunkMover:
Inheritance graph
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Public Member Functions

 InsertChunkMover ()
 
 ~InsertChunkMover () override
 
void init ()
 
void set_bb_xyz_aligned (core::pose::Pose &pose)
 
bool success ()
 
void set_template (core::pose::PoseCOP template_pose, core::Size template_id, std::map< core::Size, core::Size > const &sequence_alignment)
 
void set_aligned_chunk (core::pose::Pose const &pose, core::Size const jump_number, bool anchor_insert_only_in)
 
bool get_local_sequence_mapping (core::pose::Pose &pose, int registry_shift=0, core::Size MAX_TRIAL=100)
 
void check_overlap (core::pose::Pose &pose)
 
void set_registry_shift (int registry_shift)
 
core::Size trial_counter (core::Size ires)
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- 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 bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Private Attributes

core::pose::PoseCOP template_pose_
 
core::Size template_id_
 
std::map< core::Size, core::Sizesequence_alignment_
 
int registry_shift_
 
bool anchor_insert_only_
 
core::Size jump_number_
 
core::Size seqpos_start_
 
core::Size seqpos_stop_
 
core::Size seqpos_aligned_start_
 
core::Size seqpos_aligned_stop_
 
bool success_
 
bool align_to_ss_only_
 
bool copy_ss_torsion_only_
 
char secstruct_
 
std::map< core::Size, core::Sizesequence_alignment_local_
 
core::id::AtomID_Map
< core::id::AtomID
atom_map_
 
utility::vector1< core::Sizealign_trial_counter_
 

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::InsertChunkMover::InsertChunkMover ( )
protocols::hybridization::InsertChunkMover::~InsertChunkMover ( )
overridedefault

Member Function Documentation

void protocols::hybridization::InsertChunkMover::apply ( core::pose::Pose )
overridevirtual
void protocols::hybridization::InsertChunkMover::check_overlap ( core::pose::Pose pose)
bool protocols::hybridization::InsertChunkMover::get_local_sequence_mapping ( core::pose::Pose pose,
int  registry_shift = 0,
core::Size  MAX_TRIAL = 100 
)
std::string protocols::hybridization::InsertChunkMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

void protocols::hybridization::InsertChunkMover::init ( void  )
void protocols::hybridization::InsertChunkMover::set_aligned_chunk ( core::pose::Pose const &  pose,
core::Size const  jump_number,
bool  anchor_insert_only_in 
)
void protocols::hybridization::InsertChunkMover::set_bb_xyz_aligned ( core::pose::Pose pose)
void protocols::hybridization::InsertChunkMover::set_registry_shift ( int  registry_shift)
void protocols::hybridization::InsertChunkMover::set_template ( core::pose::PoseCOP  template_pose,
core::Size  template_id,
std::map< core::Size, core::Size > const &  sequence_alignment 
)
bool protocols::hybridization::InsertChunkMover::success ( )
inline
Size protocols::hybridization::InsertChunkMover::trial_counter ( core::Size  ires)

Member Data Documentation

bool protocols::hybridization::InsertChunkMover::align_to_ss_only_
private
utility::vector1<core::Size> protocols::hybridization::InsertChunkMover::align_trial_counter_
private
bool protocols::hybridization::InsertChunkMover::anchor_insert_only_
private
core::id::AtomID_Map< core::id::AtomID > protocols::hybridization::InsertChunkMover::atom_map_
private
bool protocols::hybridization::InsertChunkMover::copy_ss_torsion_only_
private
core::Size protocols::hybridization::InsertChunkMover::jump_number_
private
int protocols::hybridization::InsertChunkMover::registry_shift_
private
char protocols::hybridization::InsertChunkMover::secstruct_
private
core::Size protocols::hybridization::InsertChunkMover::seqpos_aligned_start_
private
core::Size protocols::hybridization::InsertChunkMover::seqpos_aligned_stop_
private
core::Size protocols::hybridization::InsertChunkMover::seqpos_start_
private
core::Size protocols::hybridization::InsertChunkMover::seqpos_stop_
private
std::map<core::Size, core::Size> protocols::hybridization::InsertChunkMover::sequence_alignment_
private
std::map<core::Size, core::Size> protocols::hybridization::InsertChunkMover::sequence_alignment_local_
private
bool protocols::hybridization::InsertChunkMover::success_
private

Referenced by success().

core::Size protocols::hybridization::InsertChunkMover::template_id_
private
core::pose::PoseCOP protocols::hybridization::InsertChunkMover::template_pose_
private

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