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protocols::symmetry::SymShakeStructureMover Class Reference

#include <SymShakeStructureMover.hh>

Inheritance diagram for protocols::symmetry::SymShakeStructureMover:
Inheritance graph
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Public Member Functions

 SymShakeStructureMover ()
 
 SymShakeStructureMover (core::scoring::ScoreFunctionOP s)
 
 SymShakeStructureMover (core::scoring::ScoreFunctionOP s, core::Real temperature)
 
 SymShakeStructureMover (core::scoring::ScoreFunctionOP s, core::Real ens_diversity, core::Real ens_div_tolerance)
 
 ~SymShakeStructureMover () override
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void reduce_fa_rep (float fraction_fa_rep, core::scoring::ScoreFunction &s)
 
void minimize_with_constraints (core::pose::Pose &p, core::scoring::ScoreFunction &s) override
 
void setup_for_run (core::pose::Pose &p) override
 
void run_mc (core::pose::Pose &p, core::scoring::ScoreFunction &s, core::Real temperature) override
 
- Public Member Functions inherited from protocols::simple_moves::ShakeStructureMover
 ShakeStructureMover ()
 
 ShakeStructureMover (core::scoring::ScoreFunctionOP s)
 
 ShakeStructureMover (core::scoring::ScoreFunctionOP s, core::Real temperature)
 
 ShakeStructureMover (core::scoring::ScoreFunctionOP s, core::Real ens_diversity, core::Real ens_div_tolerance)
 
 ~ShakeStructureMover () override
 
void set_skip_low_temp_phase (bool truefalse)
 
void set_mc_temperature (core::Real temp)
 
void set_nrounds (int new_nrounds)
 
void set_ramp_fa_rep (bool truefalse)
 
void set_minimize_with_cst (bool truefalse)
 
void set_scorefunction (core::scoring::ScoreFunctionOP s)
 
void set_ensemble_diversity (core::Real ca_rmsd)
 
void set_rmsd_target_tolerance (core::Real tol)
 
void set_sc_min (bool truefalse)
 
core::Real get_mc_temperature ()
 
bool get_ramp_fa_rep ()
 
bool get_minimize_with_cst ()
 
core::scoring::ScoreFunctionOP get_scorefunction ()
 
core::Real get_ensemble_diversity ()
 
core::Real get_rmsd_target_tolerance ()
 
bool get_sc_min ()
 
core::Real get_harmonic_ca_cst_std_dev ()
 
core::Real get_ensemble_ca_rmsd ()
 
bool get_skip_low_temp_phase ()
 
bool get_min_cst ()
 
bool get_testing_phase ()
 
bool get_scorefunction_initialized ()
 
core::scoring::ScoreFunctionOP get_min_scorefunction ()
 
core::Size get_nrounds ()
 
void apply (core::pose::Pose &p) override
 Main Method. 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...
 

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::simple_moves::ShakeStructureMover
void set_testing_phase (bool truefalse)
 
void set_mc_temp (core::Real temperature)
 
void set_is_properly_initialized (bool truefalse)
 
void set_min_scorefunction (core::scoring::ScoreFunctionOP scfxn)
 
void reduce_fa_rep (float fraction_fa_rep, core::scoring::ScoreFunction &s)
 
virtual void setup_ca_constraints (core::pose::Pose &pose, core::scoring::ScoreFunction &s, float const CA_cutoff, float const cst_tol)
 
core::Real set_temp_based_on_ens_diversity (core::pose::Pose &p, core::scoring::ScoreFunction &s)
 
void setup_movers (protocols::simple_moves::SmallMoverOP gsmall, protocols::simple_moves::ShearMoverOP gshear, core::Real small_H_angle_max, core::Real small_E_angle_max, core::Real small_L_angle_max, core::Real shear_H_angle_max, core::Real shear_E_angle_max, core::Real shear_L_angle_max)
 
void create_ensemble (core::pose::Pose &p, core::scoring::ScoreFunction &s)
 
- 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::symmetry::SymShakeStructureMover::SymShakeStructureMover ( )
protocols::symmetry::SymShakeStructureMover::SymShakeStructureMover ( core::scoring::ScoreFunctionOP  s)
protocols::symmetry::SymShakeStructureMover::SymShakeStructureMover ( core::scoring::ScoreFunctionOP  s,
core::Real  temperature 
)
protocols::symmetry::SymShakeStructureMover::SymShakeStructureMover ( core::scoring::ScoreFunctionOP  s,
core::Real  ens_diversity,
core::Real  ens_div_tolerance 
)
protocols::symmetry::SymShakeStructureMover::~SymShakeStructureMover ( )
overridedefault

Member Function Documentation

std::string protocols::symmetry::SymShakeStructureMover::get_name ( ) const
overridevirtual

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

Reimplemented from protocols::simple_moves::ShakeStructureMover.

void protocols::symmetry::SymShakeStructureMover::minimize_with_constraints ( core::pose::Pose p,
core::scoring::ScoreFunction s 
)
overridevirtual
void protocols::symmetry::SymShakeStructureMover::reduce_fa_rep ( float  fraction_fa_rep,
core::scoring::ScoreFunction s 
)
void protocols::symmetry::SymShakeStructureMover::run_mc ( core::pose::Pose p,
core::scoring::ScoreFunction s,
core::Real  temperature 
)
overridevirtual
void protocols::symmetry::SymShakeStructureMover::setup_for_run ( core::pose::Pose p)
overridevirtual

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