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protocols::stepwise::monte_carlo::mover::StepWiseMasterMover Class Reference

Central mover of stepwise Monte Carlo protocols, handing work off to special move types. More...

#include <StepWiseMasterMover.hh>

Inheritance diagram for protocols::stepwise::monte_carlo::mover::StepWiseMasterMover:
Inheritance graph
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Public Member Functions

 StepWiseMasterMover (core::scoring::ScoreFunctionCOP scorefxn, protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptionsCOP options)
 
 ~StepWiseMasterMover () override
 
void apply (Pose &) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
 StepWiseMasterMover (StepWiseMasterMover const &src)
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
void apply (core::pose::Pose &pose, StepWiseMove const &stepwise_move, bool const figure_out_all_possible_moves=true)
 
void do_the_move (StepWiseMove const &move, core::pose::Pose &pose)
 
bool apply_legacy (Pose &)
 
void initialize (core::scoring::ScoreFunctionCOP scorefxn, protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptionsCOP options)
 
void initialize_pose_if_empty (core::pose::Pose &pose)
 
void set_minimize_single_res (bool const minimize_single_res)
 
bool do_test_move (StepWiseMove const &move, core::pose::Pose &pose)
 
void preminimize_pose (core::pose::Pose &pose)
 
void set_options (protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptionsCOP options)
 
void set_scorefxn (core::scoring::ScoreFunctionCOP scorefxn)
 
std::string move_type_string () const
 
bool success () const
 
core::Real const & proposal_density_ratio () const
 
void resample_full_model (core::pose::Pose const &start_pose, core::pose::Pose &output_pose, bool const checkpointing_breadcrumbs)
 
void resample_full_model (core::pose::Pose const &start_pose, core::pose::Pose &output_pose, bool const checkpointing_breadcrumbs, utility::vector1< core::Size > const &residues_to_resample, core::Size const resample_round, core::Size const nstruct)
 
void build_full_model (core::pose::Pose const &start_pose, core::pose::Pose &full_model_pose, bool const &choose_random=false)
 
void set_submotif_library (monte_carlo::submotif::SubMotifLibraryCOP setting)
 
StepWiseMoveSelectorCOP stepwise_move_selector () const
 
- 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 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...
 

Private Member Functions

void initialize ()
 
bool test_all_moves (core::pose::Pose &pose)
 
void test_all_moves_recursively (core::pose::Pose &pose)
 
utility::vector1< StepWiseMovemoves_for_pose (core::pose::Pose const &start_pose, utility::vector1< core::Size > const &residues_to_rebuild)
 

Private Attributes

bool minimize_single_res_
 
core::scoring::ScoreFunctionCOP scorefxn_
 
protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptionsCOP options_
 
modeler::StepWiseModelerOP stepwise_modeler_
 
DeleteMoverOP delete_mover_
 
AddMoverOP add_mover_
 
FromScratchMoverOP from_scratch_mover_
 
AddOrDeleteMoverOP add_or_delete_mover_
 
ResampleMoverOP resample_mover_
 
VaryLoopLengthMoverOP vary_loop_length_mover_
 
monte_carlo::submotif::SubMotifLibraryCOP submotif_library_
 
StepWiseMoveSelectorOP stepwise_move_selector_
 
bool success_
 
std::string move_type_string_
 
core::Real proposal_density_ratio_
 
core::Size num_tested_moves_
 

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...
 

Detailed Description

Central mover of stepwise Monte Carlo protocols, handing work off to special move types.

It's worth noting that one function that for historical reasons is a method of this class is capable of spawning threads. Notably, that method is not called by this Mover's apply function (rather, it calls this Mover's apply function!) and so you don't have to worry. If you are studying this class as an archetypical example of a Mover, for one thing, don't do that because it isn't; for another thing, don't multithread your apply function as a misguided inference from how this Mover has a multithreaded function that's not apply.

Constructor & Destructor Documentation

protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::StepWiseMasterMover ( core::scoring::ScoreFunctionCOP  scorefxn,
protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptionsCOP  options 
)

References initialize().

protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::~StepWiseMasterMover ( )
overridedefault
protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::StepWiseMasterMover ( StepWiseMasterMover const &  src)

References initialize(), options_, and scorefxn_.

Member Function Documentation

void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::apply ( Pose )
overridevirtual
void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::apply ( core::pose::Pose pose,
StepWiseMove const &  stepwise_move,
bool const  figure_out_all_possible_moves = true 
)
bool protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::apply_legacy ( pose::Pose pose)
void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::build_full_model ( core::pose::Pose const &  start_pose,
core::pose::Pose full_model_pose,
bool const &  choose_random = false 
)
protocols::moves::MoverOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::clone ( ) const
overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

bool protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::do_test_move ( StepWiseMove const &  move,
core::pose::Pose pose 
)
void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::do_the_move ( StepWiseMove const &  move,
core::pose::Pose pose 
)
std::string protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::get_name ( ) const
inlineoverridevirtual

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

Implements protocols::moves::Mover.

void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::initialize ( core::scoring::ScoreFunctionCOP  scorefxn,
protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptionsCOP  options 
)

References initialize(), options_, and scorefxn_.

void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::initialize ( )
private
void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::initialize_pose_if_empty ( core::pose::Pose pose)
std::string protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::move_type_string ( ) const
inline

References move_type_string_.

Referenced by build_full_model().

utility::vector1< StepWiseMove > protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose ( core::pose::Pose const &  start_pose,
utility::vector1< core::Size > const &  residues_to_rebuild 
)
private
void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::preminimize_pose ( core::pose::Pose pose)
core::Real const& protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::proposal_density_ratio ( ) const
inline
void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::resample_full_model ( core::pose::Pose const &  start_pose,
core::pose::Pose output_pose,
bool const  checkpointing_breadcrumbs 
)
void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::resample_full_model ( core::pose::Pose const &  start_pose,
core::pose::Pose output_pose,
bool const  checkpointing_breadcrumbs,
utility::vector1< core::Size > const &  residues_to_resample,
core::Size const  resample_round,
core::Size const  nstruct 
)
void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::set_minimize_single_res ( bool const  minimize_single_res)
void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::set_options ( protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptionsCOP  options)

References initialize(), and options_.

void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::set_scorefxn ( core::scoring::ScoreFunctionCOP  scorefxn)
inline

References scorefxn_.

void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::set_submotif_library ( monte_carlo::submotif::SubMotifLibraryCOP  setting)
inline

References submotif_library_.

StepWiseMoveSelectorCOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::stepwise_move_selector ( ) const
inline
bool protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::success ( ) const
inline

References success_.

bool protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::test_all_moves ( core::pose::Pose pose)
private
void protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::test_all_moves_recursively ( core::pose::Pose pose)
private

Member Data Documentation

AddMoverOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::add_mover_
private
AddOrDeleteMoverOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::add_or_delete_mover_
private
DeleteMoverOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::delete_mover_
private

Referenced by initialize().

FromScratchMoverOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::from_scratch_mover_
private

Referenced by initialize().

bool protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::minimize_single_res_
private
std::string protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::move_type_string_
private
core::Size protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::num_tested_moves_
private
protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptionsCOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::options_
private
core::Real protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::proposal_density_ratio_
private
ResampleMoverOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::resample_mover_
private
core::scoring::ScoreFunctionCOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::scorefxn_
private
modeler::StepWiseModelerOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::stepwise_modeler_
private

Referenced by initialize(), and preminimize_pose().

StepWiseMoveSelectorOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::stepwise_move_selector_
private
monte_carlo::submotif::SubMotifLibraryCOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::submotif_library_
private

Referenced by initialize(), and set_submotif_library().

bool protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::success_
private
VaryLoopLengthMoverOP protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::vary_loop_length_mover_
private

Referenced by do_the_move(), and initialize().


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