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protocols::simple_moves::ShakeStructureMover Class Reference

#include <ShakeStructureMover.hh>

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

 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...
 
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...
 

Protected Member Functions

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_for_run (core::pose::Pose &p)
 
virtual void minimize_with_constraints (core::pose::Pose &p, 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)
 
virtual void run_mc (core::pose::Pose &p, core::scoring::ScoreFunction &s, core::Real temperature)
 
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...
 

Private Attributes

core::Real mc_temp
 
bool ramp_fa_rep
 
bool min_cst
 
core::scoring::ScoreFunctionOP scorefxn
 
core::Real ensemble_ca_rmsd_
 
core::Real ensemble_ca_rmsd_tolerance_
 
bool is_properly_initialized
 
core::Real harmonic_ca_cst_std_dev
 
bool scorefunction_initialized
 
bool sc_min_only
 
int nrounds
 
double cst_weight
 
bool skip_low_temp_phase
 
core::scoring::ScoreFunctionOP min_scorefxn
 
bool testing_phase
 

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...
 

Constructor & Destructor Documentation

protocols::simple_moves::ShakeStructureMover::ShakeStructureMover ( )
protocols::simple_moves::ShakeStructureMover::ShakeStructureMover ( core::scoring::ScoreFunctionOP  s)
protocols::simple_moves::ShakeStructureMover::ShakeStructureMover ( core::scoring::ScoreFunctionOP  s,
core::Real  temperature 
)
protocols::simple_moves::ShakeStructureMover::ShakeStructureMover ( core::scoring::ScoreFunctionOP  s,
core::Real  ens_diversity,
core::Real  ens_div_tolerance 
)
protocols::simple_moves::ShakeStructureMover::~ShakeStructureMover ( )
overridedefault

Member Function Documentation

void protocols::simple_moves::ShakeStructureMover::apply ( core::pose::Pose )
overridevirtual
void protocols::simple_moves::ShakeStructureMover::create_ensemble ( core::pose::Pose p,
core::scoring::ScoreFunction s 
)
protected

References mc_temp, and run_mc().

Referenced by apply().

core::Real protocols::simple_moves::ShakeStructureMover::get_ensemble_ca_rmsd ( )
core::Real protocols::simple_moves::ShakeStructureMover::get_ensemble_diversity ( )

References ensemble_ca_rmsd_.

core::Real protocols::simple_moves::ShakeStructureMover::get_harmonic_ca_cst_std_dev ( )
core::Real protocols::simple_moves::ShakeStructureMover::get_mc_temperature ( )
bool protocols::simple_moves::ShakeStructureMover::get_min_cst ( )
core::scoring::ScoreFunctionOP protocols::simple_moves::ShakeStructureMover::get_min_scorefunction ( )
bool protocols::simple_moves::ShakeStructureMover::get_minimize_with_cst ( )

References min_cst.

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

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

Implements protocols::moves::Mover.

Reimplemented in protocols::symmetry::SymShakeStructureMover.

core::Size protocols::simple_moves::ShakeStructureMover::get_nrounds ( )
bool protocols::simple_moves::ShakeStructureMover::get_ramp_fa_rep ( )
core::Real protocols::simple_moves::ShakeStructureMover::get_rmsd_target_tolerance ( )
bool protocols::simple_moves::ShakeStructureMover::get_sc_min ( )
core::scoring::ScoreFunctionOP protocols::simple_moves::ShakeStructureMover::get_scorefunction ( )
bool protocols::simple_moves::ShakeStructureMover::get_scorefunction_initialized ( )
bool protocols::simple_moves::ShakeStructureMover::get_skip_low_temp_phase ( )
bool protocols::simple_moves::ShakeStructureMover::get_testing_phase ( )
void protocols::simple_moves::ShakeStructureMover::minimize_with_constraints ( core::pose::Pose p,
core::scoring::ScoreFunction s 
)
protectedvirtual
void protocols::simple_moves::ShakeStructureMover::reduce_fa_rep ( float  fraction_fa_rep,
core::scoring::ScoreFunction s 
)
protected
void protocols::simple_moves::ShakeStructureMover::run_mc ( core::pose::Pose p,
core::scoring::ScoreFunction s,
core::Real  temperature 
)
protectedvirtual
void protocols::simple_moves::ShakeStructureMover::set_ensemble_diversity ( core::Real  ca_rmsd)
void protocols::simple_moves::ShakeStructureMover::set_is_properly_initialized ( bool  truefalse)
protected
void protocols::simple_moves::ShakeStructureMover::set_mc_temp ( core::Real  temperature)
protected
void protocols::simple_moves::ShakeStructureMover::set_mc_temperature ( core::Real  temp)

References mc_temp.

void protocols::simple_moves::ShakeStructureMover::set_min_scorefunction ( core::scoring::ScoreFunctionOP  scfxn)
protected
void protocols::simple_moves::ShakeStructureMover::set_minimize_with_cst ( bool  truefalse)

References min_cst.

void protocols::simple_moves::ShakeStructureMover::set_nrounds ( int  new_nrounds)

References nrounds.

void protocols::simple_moves::ShakeStructureMover::set_ramp_fa_rep ( bool  truefalse)

References ramp_fa_rep.

void protocols::simple_moves::ShakeStructureMover::set_rmsd_target_tolerance ( core::Real  tol)
void protocols::simple_moves::ShakeStructureMover::set_sc_min ( bool  truefalse)

References min_cst, and sc_min_only.

void protocols::simple_moves::ShakeStructureMover::set_scorefunction ( core::scoring::ScoreFunctionOP  s)
void protocols::simple_moves::ShakeStructureMover::set_skip_low_temp_phase ( bool  truefalse)

References skip_low_temp_phase.

core::Real protocols::simple_moves::ShakeStructureMover::set_temp_based_on_ens_diversity ( core::pose::Pose p,
core::scoring::ScoreFunction s 
)
protected
void protocols::simple_moves::ShakeStructureMover::set_testing_phase ( bool  truefalse)
protected
void protocols::simple_moves::ShakeStructureMover::setup_ca_constraints ( core::pose::Pose pose,
core::scoring::ScoreFunction s,
float const  CA_cutoff,
float const  cst_tol 
)
protectedvirtual
void protocols::simple_moves::ShakeStructureMover::setup_for_run ( core::pose::Pose p)
protectedvirtual
void protocols::simple_moves::ShakeStructureMover::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 
)
protected

Member Data Documentation

double protocols::simple_moves::ShakeStructureMover::cst_weight
private

Referenced by setup_ca_constraints().

core::Real protocols::simple_moves::ShakeStructureMover::ensemble_ca_rmsd_
private
core::Real protocols::simple_moves::ShakeStructureMover::ensemble_ca_rmsd_tolerance_
private
core::Real protocols::simple_moves::ShakeStructureMover::harmonic_ca_cst_std_dev
private
bool protocols::simple_moves::ShakeStructureMover::is_properly_initialized
private
core::Real protocols::simple_moves::ShakeStructureMover::mc_temp
private
bool protocols::simple_moves::ShakeStructureMover::min_cst
private
core::scoring::ScoreFunctionOP protocols::simple_moves::ShakeStructureMover::min_scorefxn
private
int protocols::simple_moves::ShakeStructureMover::nrounds
private

Referenced by get_nrounds(), run_mc(), and set_nrounds().

bool protocols::simple_moves::ShakeStructureMover::ramp_fa_rep
private
bool protocols::simple_moves::ShakeStructureMover::sc_min_only
private
bool protocols::simple_moves::ShakeStructureMover::scorefunction_initialized
private
core::scoring::ScoreFunctionOP protocols::simple_moves::ShakeStructureMover::scorefxn
private
bool protocols::simple_moves::ShakeStructureMover::skip_low_temp_phase
private
bool protocols::simple_moves::ShakeStructureMover::testing_phase
private

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