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protocols::simple_moves::TailsScoreMover Class Reference

#include <TailsScoreMover.hh>

Inheritance diagram for protocols::simple_moves::TailsScoreMover:
Inheritance graph
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Public Member Functions

 TailsScoreMover ()
 empty constructor fills values with the values read in from the commandline More...
 
 TailsScoreMover (core::scoring::ScoreFunctionOP scorefxn_in)
 
void apply (core::pose::Pose &pose) override
 Simply score a pdb. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::simple_moves::ScoreMover
 ScoreMover ()
 empty constructor fills values with the values read in from the commandline More...
 
 ~ScoreMover () override
 
 ScoreMover (std::string const &, std::string const &patch="")
 constructor More...
 
 ScoreMover (ScoreFunctionOP)
 constructor More...
 
moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
void parse_my_tag (TagCOP, basic::datacache::DataMap &) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
void insert_rms (core::Real rms)
 add an rms to the score_map TODO possibly find a better way to do this? for now, there are too many different rmsd calculation functions to be able to do the actual calculation in the protocols::moves::Mover More...
 
void test_move (Pose &pose) override
 : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
 
void set_verbose (bool value)
 
ScoreFunctionOP score_function () const
 
void set_score_file (std::string scorefile)
 
- 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 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...
 
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
 
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 Member Functions

core::Real score_mode1 (int &out_min_ltail_length, int &out_min_rtail_length, std::ofstream &in_tail_output, core::pose::Pose &pose)
 
core::Real score_mode2 (int &out_min_ltail_length, int &out_min_rtail_length, std::ofstream &in_tail_output, core::pose::Pose &pose)
 
core::Real score_mode3 (int &out_min_ltail_length, int &out_min_rtail_length, std::ofstream &in_tail_output, core::pose::Pose &pose)
 
core::Real visit (core::Real in_current_min, int in_current_min_ltail, int in_current_min_rtail, int in_ltail, int in_rtail, int in_array_of_visits[][200], int &out_min_ltail, int &out_min_rtail, int in_sequence_length, utility::vector1< core::Size > &tail, core::pose::Pose &pose, std::ofstream &area_file)
 
void make_tail (utility::vector1< core::Size > &tail, int in_ltaillength, int in_rtaillength, int in_sequence_length)
 

Private Attributes

core::Real m_hill_size_
 
int m_number_of_hill_points_
 
bool m_done_all
 

Additional Inherited Members

- Public Types inherited from protocols::simple_moves::ScoreMover
typedef
core::scoring::ScoreFunctionOP 
ScoreFunctionOP
 
- 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::simple_moves::ScoreMover
static void register_options ()
 
static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- 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::simple_moves::TailsScoreMover::TailsScoreMover ( )
inline

empty constructor fills values with the values read in from the commandline

protocols::simple_moves::TailsScoreMover::TailsScoreMover ( core::scoring::ScoreFunctionOP  scorefxn_in)
inline

Member Function Documentation

void protocols::simple_moves::TailsScoreMover::apply ( core::pose::Pose pose)
overridevirtual

Simply score a pdb.

Reimplemented from protocols::simple_moves::ScoreMover.

References core::pose::setPoseExtraScore(), TR(), and core::pack::tt().

std::string protocols::simple_moves::TailsScoreMover::get_name ( ) const
overridevirtual

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

Reimplemented from protocols::simple_moves::ScoreMover.

void protocols::simple_moves::TailsScoreMover::make_tail ( utility::vector1< core::Size > &  tail,
int  in_ltaillength,
int  in_rtaillength,
int  in_sequence_length 
)
private
core::Real protocols::simple_moves::TailsScoreMover::score_mode1 ( int &  out_min_ltail_length,
int &  out_min_rtail_length,
std::ofstream &  in_tail_output,
core::pose::Pose pose 
)
private

References core::pose::Pose::size(), and TR().

core::Real protocols::simple_moves::TailsScoreMover::score_mode2 ( int &  out_min_ltail_length,
int &  out_min_rtail_length,
std::ofstream &  in_tail_output,
core::pose::Pose pose 
)
private
core::Real protocols::simple_moves::TailsScoreMover::score_mode3 ( int &  out_min_ltail_length,
int &  out_min_rtail_length,
std::ofstream &  in_tail_output,
core::pose::Pose pose 
)
private
core::Real protocols::simple_moves::TailsScoreMover::visit ( core::Real  in_current_min,
int  in_current_min_ltail,
int  in_current_min_rtail,
int  in_ltail,
int  in_rtail,
int  in_array_of_visits[][200],
int &  out_min_ltail,
int &  out_min_rtail,
int  in_sequence_length,
utility::vector1< core::Size > &  tail,
core::pose::Pose pose,
std::ofstream &  area_file 
)
private

Member Data Documentation

bool protocols::simple_moves::TailsScoreMover::m_done_all
private
core::Real protocols::simple_moves::TailsScoreMover::m_hill_size_
private
int protocols::simple_moves::TailsScoreMover::m_number_of_hill_points_
private

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