Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::recces::RECCES_Mover Class Reference

#include <RECCES_Mover.hh>

Inheritance diagram for protocols::recces::RECCES_Mover:
Inheritance graph

Public Member Functions

 RECCES_Mover (options::RECCES_OptionsCOP options)
 ~RECCES_Mover () override
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...
void set_scorefxn (core::scoring::ScoreFunctionCOP scorefxn)
void set_parameters (params::RECCES_ParametersCOP params)
- 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 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

void initialize ()
void run_sampler (core::pose::Pose &pose)
void increment_accepts (core::Size &n_accept_total, std::map< std::string, core::Size > &num_accepts, sampler::MC_LoopCOP loop_sampler) const
void save_history (core::Size const &curr_counts, utility::vector1< float > const &scores, core::Size const &temp_id)
void dump_stuff (core::Size const &n, core::pose::Pose const &pose, utility::vector1< core::Real > const &scores, core::pose::Pose &min_pose, core::Real &min_score, core::Size &curr_dump) const
void more_dump_stuff (core::pose::Pose const &pose, core::Size const &n, core::Real const &temperature) const
void final_dump_stuff (core::pose::Pose &pose, core::pose::Pose &min_pose) const
void save_data_to_disk () const
void set_sampler_gaussian_stdev (core::Real const &temperature, core::pose::Pose const &pose)
void prepare_output_torsion_ids ()
std::string output_pdb_name (std::string const &tag) const
void output_torsions (core::pose::Pose const &pose, core::Size const &curr_counts) const

Private Attributes

core::scoring::ScoreFunctionCOP scorefxn_
options::RECCES_OptionsCOP options_
params::RECCES_ParametersCOP params_
sampler::MC_CombOP sampler_
utility::vector1< core::Realweights_
utility::vector1< utility::vector1< float > > data_
utility::vector1< Histogramhist_list_
utility::vector1< core::id::TorsionIDbb_torsion_ids_
utility::vector1< core::id::TorsionIDchi_torsion_ids_
std::ofstream bb_tor_out_
std::ofstream chi_tor_out_

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

◆ RECCES_Mover()

protocols::recces::RECCES_Mover::RECCES_Mover ( options::RECCES_OptionsCOP  options)

References initialize().

◆ ~RECCES_Mover()

protocols::recces::RECCES_Mover::~RECCES_Mover ( )

Member Function Documentation

◆ apply()

void protocols::recces::RECCES_Mover::apply ( core::pose::Pose )

◆ dump_stuff()

void protocols::recces::RECCES_Mover::dump_stuff ( core::Size const &  n,
core::pose::Pose const &  pose,
utility::vector1< core::Real > const &  scores,
core::pose::Pose min_pose,
core::Real min_score,
core::Size curr_dump 
) const

References core::pose::Pose::dump_pdb(), and options_.

Referenced by run_sampler().

◆ final_dump_stuff()

void protocols::recces::RECCES_Mover::final_dump_stuff ( core::pose::Pose pose,
core::pose::Pose min_pose 
) const

◆ get_name()

std::string protocols::recces::RECCES_Mover::get_name ( ) const

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

Implements protocols::moves::Mover.

◆ increment_accepts()

void protocols::recces::RECCES_Mover::increment_accepts ( core::Size n_accept_total,
std::map< std::string, core::Size > &  num_accepts,
sampler::MC_LoopCOP  loop_sampler 
) const

Referenced by run_sampler().

◆ initialize()

void protocols::recces::RECCES_Mover::initialize ( )

◆ more_dump_stuff()

void protocols::recces::RECCES_Mover::more_dump_stuff ( core::pose::Pose const &  pose,
core::Size const &  n,
core::Real const &  temperature 
) const

◆ output_pdb_name()

std::string protocols::recces::RECCES_Mover::output_pdb_name ( std::string const &  tag) const

References options_.

Referenced by final_dump_stuff(), and run_sampler().

◆ output_torsions()

void protocols::recces::RECCES_Mover::output_torsions ( core::pose::Pose const &  pose,
core::Size const &  curr_counts 
) const

◆ prepare_output_torsion_ids()

void protocols::recces::RECCES_Mover::prepare_output_torsion_ids ( )

◆ run_sampler()

void protocols::recces::RECCES_Mover::run_sampler ( core::pose::Pose pose)

◆ save_data_to_disk()

void protocols::recces::RECCES_Mover::save_data_to_disk ( ) const

◆ save_history()

void protocols::recces::RECCES_Mover::save_history ( core::Size const &  curr_counts,
utility::vector1< float > const &  scores,
core::Size const &  temp_id 

curr_counts is a running count of number of times the pose has been the same.

References data_, protocols::recces::fill_data(), hist_list_, and options_.

Referenced by run_sampler().

◆ set_parameters()

void protocols::recces::RECCES_Mover::set_parameters ( params::RECCES_ParametersCOP  params)

References params_.

◆ set_sampler_gaussian_stdev()

void protocols::recces::RECCES_Mover::set_sampler_gaussian_stdev ( core::Real const &  temperature,
core::pose::Pose const &  pose 

◆ set_scorefxn()

void protocols::recces::RECCES_Mover::set_scorefxn ( core::scoring::ScoreFunctionCOP  scorefxn)

References scorefxn_.

Member Data Documentation

◆ bb_tor_out_

std::ofstream protocols::recces::RECCES_Mover::bb_tor_out_

◆ bb_torsion_ids_

utility::vector1< core::id::TorsionID > protocols::recces::RECCES_Mover::bb_torsion_ids_

◆ chi_tor_out_

std::ofstream protocols::recces::RECCES_Mover::chi_tor_out_

◆ chi_torsion_ids_

utility::vector1< core::id::TorsionID > protocols::recces::RECCES_Mover::chi_torsion_ids_

◆ data_

utility::vector1<utility::vector1< float > > protocols::recces::RECCES_Mover::data_

◆ hist_list_

utility::vector1< Histogram > protocols::recces::RECCES_Mover::hist_list_

◆ options_

options::RECCES_OptionsCOP protocols::recces::RECCES_Mover::options_

◆ params_

params::RECCES_ParametersCOP protocols::recces::RECCES_Mover::params_

◆ sampler_

sampler::MC_CombOP protocols::recces::RECCES_Mover::sampler_

◆ scorefxn_

core::scoring::ScoreFunctionCOP protocols::recces::RECCES_Mover::scorefxn_

◆ weights_

utility::vector1< core::Real > protocols::recces::RECCES_Mover::weights_

Referenced by initialize(), and run_sampler().

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