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protocols::simple_moves::symmetry::SymShakeStructureMover Class Reference

#include <SymShakeStructureMover.hh>

Inheritance diagram for protocols::simple_moves::symmetry::SymShakeStructureMover:
Inheritance graph
Collaboration diagram for protocols::simple_moves::symmetry::SymShakeStructureMover:
Collaboration graph

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)
virtual ~SymShakeStructureMover ()
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
core::scoring::symmetry::SymmetricScoreFunction reduce_fa_rep (float fraction_fa_rep, core::scoring::ScoreFunction &s)
void minimize_with_constraints (core::pose::Pose &p, core::scoring::ScoreFunction &s)
void setup_for_run (core::pose::Pose &p)
void run_mc (core::pose::Pose &p, core::scoring::ScoreFunction &s, core::Real temperature)
- 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)
virtual ~ShakeStructureMover ()
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::ScoreFunction &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)
- 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

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 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::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)
core::scoring::ScoreFunction 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)

Constructor & Destructor Documentation

protocols::simple_moves::symmetry::SymShakeStructureMover::SymShakeStructureMover ( )
protocols::simple_moves::symmetry::SymShakeStructureMover::SymShakeStructureMover ( core::scoring::ScoreFunctionOP  s)
protocols::simple_moves::symmetry::SymShakeStructureMover::SymShakeStructureMover ( core::scoring::ScoreFunctionOP  s,
core::Real  temperature 
protocols::simple_moves::symmetry::SymShakeStructureMover::SymShakeStructureMover ( core::scoring::ScoreFunctionOP  s,
core::Real  ens_diversity,
core::Real  ens_div_tolerance 
protocols::simple_moves::symmetry::SymShakeStructureMover::~SymShakeStructureMover ( )

Member Function Documentation

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

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

Reimplemented from protocols::simple_moves::ShakeStructureMover.

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

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