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protocols::stepwise::monte_carlo::StepWiseMonteCarlo Class Reference

#include <StepWiseMonteCarlo.hh>

Inheritance diagram for protocols::stepwise::monte_carlo::StepWiseMonteCarlo:
Inheritance graph
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Public Member Functions

 StepWiseMonteCarlo (core::scoring::ScoreFunctionCOP scorefxn)
 
 ~StepWiseMonteCarlo () override
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void apply (core::pose::Pose &pose) override
 Apply the loop-rebuild protocol to the input pose. More...
 
void set_native_pose (core::pose::PoseCOP pose) override
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
 
void set_align_pose (core::pose::PoseCOP pose)
 
void set_options (options::StepWiseMonteCarloOptionsCOP options)
 
options::StepWiseMonteCarloOptionsCOP options () const
 
void set_model_tag (std::string const &setting)
 
std::string model_tag () const
 
void set_out_path (std::string const &setting)
 
std::string out_path () const
 
void set_move (mover::StepWiseMove const &setting)
 
mover::StepWiseMove move () const
 
void set_submotif_library (monte_carlo::submotif::SubMotifLibraryCOP setting)
 
mover::StepWiseMasterMoverCOP master_mover () const
 
void output_checkpoint_file (core::pose::Pose const &pose, core::pose::Pose const &low, core::Size const k) const
 
void remove_checkpoint_file () const
 
bool checkpoint_file_exists () const
 
core::pose::Pose pose_from_checkpoint_file () const
 
core::pose::Pose pose_from_checkpoint_file_low () const
 
void set_out_file_prefix (std::string const &setting)
 
- 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...
 
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...
 

Private Member Functions

void initialize ()
 
void initialize_scorefunction ()
 
void initialize_for_movie (core::pose::Pose const &pose)
 
void do_main_loop (core::pose::Pose &pose)
 
void output_movie (core::pose::Pose const &pose, core::Size const k, std::string const &tag, std::string const &movie_file)
 
core::Real display_progress (core::pose::Pose &pose, core::Size const cycle_num)
 
core::Real show_scores (core::pose::Pose &pose, std::string const &tag)
 
std::string checkpoint_file_name () const
 Helper that contains the formula for naming checkpoint files. More...
 
std::string checkpoint_file_name_low () const
 Helper that contains the formula for naming checkpoint files. More...
 
void anneal_missing (protocols::moves::MonteCarloOP monte_carlo)
 

Private Attributes

core::scoring::ScoreFunctionCOP scorefxn_input_
 
core::scoring::ScoreFunctionOP scorefxn_
 
options::StepWiseMonteCarloOptionsCOP options_
 
mover::StepWiseMasterMoverOP master_mover_
 
core::pose::PoseCOP align_pose_ = nullptr
 
core::Real const max_missing_weight_
 
core::Real missing_weight_interval_
 
core::Real missing_weight_
 
std::string model_tag_
 
std::string out_path_
 
std::string out_file_prefix_
 
std::string movie_file_trial_
 
std::string movie_file_accepted_
 
mover::StepWiseMove move_
 
std::clock_t start_time_
 

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

protocols::stepwise::monte_carlo::StepWiseMonteCarlo::StepWiseMonteCarlo ( core::scoring::ScoreFunctionCOP  scorefxn)
protocols::stepwise::monte_carlo::StepWiseMonteCarlo::~StepWiseMonteCarlo ( )
overridedefault

Member Function Documentation

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::anneal_missing ( protocols::moves::MonteCarloOP  monte_carlo)
private
void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::apply ( core::pose::Pose pose)
overridevirtual
bool protocols::stepwise::monte_carlo::StepWiseMonteCarlo::checkpoint_file_exists ( ) const
std::string protocols::stepwise::monte_carlo::StepWiseMonteCarlo::checkpoint_file_name ( ) const
private

Helper that contains the formula for naming checkpoint files.

References out_file_prefix_, and out_path_.

Referenced by checkpoint_file_exists(), output_checkpoint_file(), pose_from_checkpoint_file(), and remove_checkpoint_file().

std::string protocols::stepwise::monte_carlo::StepWiseMonteCarlo::checkpoint_file_name_low ( ) const
private

Helper that contains the formula for naming checkpoint files.

References out_file_prefix_, and out_path_.

Referenced by output_checkpoint_file(), pose_from_checkpoint_file_low(), and remove_checkpoint_file().

Real protocols::stepwise::monte_carlo::StepWiseMonteCarlo::display_progress ( core::pose::Pose pose,
core::Size const  cycle_num 
)
private
void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::do_main_loop ( core::pose::Pose pose)
private
std::string protocols::stepwise::monte_carlo::StepWiseMonteCarlo::get_name ( ) const
inlineoverridevirtual

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

Implements protocols::moves::Mover.

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::initialize ( )
private
void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::initialize_for_movie ( core::pose::Pose const &  pose)
private
void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::initialize_scorefunction ( )
private
mover::StepWiseMasterMoverCOP protocols::stepwise::monte_carlo::StepWiseMonteCarlo::master_mover ( ) const
inline

References master_mover_.

std::string protocols::stepwise::monte_carlo::StepWiseMonteCarlo::model_tag ( ) const
inline

References model_tag_.

mover::StepWiseMove protocols::stepwise::monte_carlo::StepWiseMonteCarlo::move ( ) const
inline

References move_.

options::StepWiseMonteCarloOptionsCOP protocols::stepwise::monte_carlo::StepWiseMonteCarlo::options ( ) const
inline

References options_.

Referenced by set_options().

std::string protocols::stepwise::monte_carlo::StepWiseMonteCarlo::out_path ( ) const
inline

References out_path_.

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::output_checkpoint_file ( core::pose::Pose const &  pose,
core::pose::Pose const &  low,
core::Size const  k 
) const
void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::output_movie ( core::pose::Pose const &  pose,
core::Size const  k,
std::string const &  tag,
std::string const &  movie_file 
)
private
core::pose::Pose protocols::stepwise::monte_carlo::StepWiseMonteCarlo::pose_from_checkpoint_file ( ) const

References checkpoint_file_exists(), and checkpoint_file_name().

Referenced by apply().

core::pose::Pose protocols::stepwise::monte_carlo::StepWiseMonteCarlo::pose_from_checkpoint_file_low ( ) const
void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::remove_checkpoint_file ( ) const
void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::set_align_pose ( core::pose::PoseCOP  pose)
inline

References align_pose_.

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::set_model_tag ( std::string const &  setting)
inline

References model_tag_.

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::set_move ( mover::StepWiseMove const &  setting)
inline

References move_.

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::set_native_pose ( core::pose::PoseCOP  pose)
overridevirtual

setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe

Reimplemented from protocols::moves::Mover.

References master_mover_.

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::set_options ( options::StepWiseMonteCarloOptionsCOP  options)

References master_mover_, options(), and options_.

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::set_out_file_prefix ( std::string const &  setting)
inline

References out_file_prefix_.

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::set_out_path ( std::string const &  setting)
inline

References out_path_.

void protocols::stepwise::monte_carlo::StepWiseMonteCarlo::set_submotif_library ( monte_carlo::submotif::SubMotifLibraryCOP  setting)

References master_mover_.

Real protocols::stepwise::monte_carlo::StepWiseMonteCarlo::show_scores ( core::pose::Pose pose,
std::string const &  tag 
)
private

Member Data Documentation

core::pose::PoseCOP protocols::stepwise::monte_carlo::StepWiseMonteCarlo::align_pose_ = nullptr
private

Referenced by initialize(), and set_align_pose().

mover::StepWiseMasterMoverOP protocols::stepwise::monte_carlo::StepWiseMonteCarlo::master_mover_
private
core::Real const protocols::stepwise::monte_carlo::StepWiseMonteCarlo::max_missing_weight_
private
core::Real protocols::stepwise::monte_carlo::StepWiseMonteCarlo::missing_weight_
private
core::Real protocols::stepwise::monte_carlo::StepWiseMonteCarlo::missing_weight_interval_
private
std::string protocols::stepwise::monte_carlo::StepWiseMonteCarlo::model_tag_
private
mover::StepWiseMove protocols::stepwise::monte_carlo::StepWiseMonteCarlo::move_
private

Referenced by apply(), move(), and set_move().

std::string protocols::stepwise::monte_carlo::StepWiseMonteCarlo::movie_file_accepted_
private
std::string protocols::stepwise::monte_carlo::StepWiseMonteCarlo::movie_file_trial_
private
options::StepWiseMonteCarloOptionsCOP protocols::stepwise::monte_carlo::StepWiseMonteCarlo::options_
private
std::string protocols::stepwise::monte_carlo::StepWiseMonteCarlo::out_file_prefix_
private
std::string protocols::stepwise::monte_carlo::StepWiseMonteCarlo::out_path_
private
core::scoring::ScoreFunctionOP protocols::stepwise::monte_carlo::StepWiseMonteCarlo::scorefxn_
private
core::scoring::ScoreFunctionCOP protocols::stepwise::monte_carlo::StepWiseMonteCarlo::scorefxn_input_
private
std::clock_t protocols::stepwise::monte_carlo::StepWiseMonteCarlo::start_time_
private

Referenced by do_main_loop(), and initialize().


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