#include <RECCES_Mover.hh>

Inheritance diagram for protocols::recces::RECCES_Mover:

[legend]

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 Strings &	info ()
	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::Real >	weights_

utility::vector1< utility::vector1< float > >	data_

utility::vector1< Histogram >	hist_list_

utility::vector1< core::id::TorsionID >	bb_torsion_ids_

utility::vector1< core::id::TorsionID >	chi_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 ( )

overridedefault

Member Function Documentation

◆ apply()

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References protocols::recces::sampler::initialize_sampler(), options_, params_, run_sampler(), sampler_, and save_data_to_disk().

◆ 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

private

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

private

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

Referenced by run_sampler().

◆ get_name()

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

inlineoverridevirtual

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

private

Referenced by run_sampler().

◆ initialize()

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

private

References data_, hist_list_, protocols::mean_field::max(), protocols::mean_field::min(), options_, and weights_.

Referenced by RECCES_Mover().

◆ 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

private

References core::io::silent::SilentStruct::add_energy(), core::pose::Pose::dump_pdb(), options_, protocols::kinmatch::str(), and core::io::silent::SilentFileData::write_silent_struct().

Referenced by run_sampler().

◆ output_pdb_name()

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

private

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

private

References bb_tor_out_, bb_torsion_ids_, chi_tor_out_, chi_torsion_ids_, and protocols::recces::get_torsions().

Referenced by run_sampler().

◆ prepare_output_torsion_ids()

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

private

References core::chemical::rna::ALPHA, core::id::BB, bb_tor_out_, bb_torsion_ids_, core::chemical::rna::BETA, core::chemical::rna::CHI, chi_tor_out_, chi_torsion_ids_, core::chemical::rna::EPSILON, core::chemical::rna::GAMMA, protocols::moves::Mover::name(), options_, and core::chemical::rna::ZETA.

Referenced by run_sampler().

◆ run_sampler()

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

private

◆ save_data_to_disk()

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

private

References bb_tor_out_, chi_tor_out_, data_, protocols::recces::data_dim(), protocols::recces::get_scoretypes(), hist_list_, options_, protocols::kinmatch::str(), protocols::recces::vector2disk_in1d(), and protocols::recces::vector2disk_in2d().

Referenced by apply().

◆ save_history()

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

private

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 )

inline

References params_.

◆ set_sampler_gaussian_stdev()

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

private

References options_, params_, sampler_, and protocols::recces::set_sampler_gaussian_stdev().

Referenced by run_sampler().

◆ set_scorefxn()

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

inline

References scorefxn_.

Member Data Documentation

◆ bb_tor_out_

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

mutableprivate

Referenced by output_torsions(), prepare_output_torsion_ids(), and save_data_to_disk().

◆ bb_torsion_ids_

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

private

Referenced by output_torsions(), and prepare_output_torsion_ids().

◆ chi_tor_out_

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

private

Referenced by output_torsions(), prepare_output_torsion_ids(), and save_data_to_disk().

◆ chi_torsion_ids_

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

private

Referenced by output_torsions(), and prepare_output_torsion_ids().

◆ data_

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

private

Referenced by initialize(), save_data_to_disk(), and save_history().

◆ hist_list_

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

private

Referenced by initialize(), save_data_to_disk(), and save_history().

◆ options_

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

private

Referenced by apply(), dump_stuff(), final_dump_stuff(), initialize(), more_dump_stuff(), output_pdb_name(), prepare_output_torsion_ids(), run_sampler(), save_data_to_disk(), save_history(), and set_sampler_gaussian_stdev().

◆ params_

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

private

Referenced by apply(), set_parameters(), and set_sampler_gaussian_stdev().

◆ sampler_

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

private

Referenced by apply(), run_sampler(), and set_sampler_gaussian_stdev().

◆ scorefxn_

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

private

Referenced by final_dump_stuff(), run_sampler(), and set_scorefxn().

◆ weights_

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

private

Referenced by initialize(), and run_sampler().

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

src/protocols/recces/RECCES_Mover.hh
src/protocols/recces/RECCES_Mover.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ RECCES_Mover()

◆ ~RECCES_Mover()

Member Function Documentation

◆ apply()

◆ dump_stuff()

◆ final_dump_stuff()

◆ get_name()

◆ increment_accepts()

◆ initialize()

◆ more_dump_stuff()

◆ output_pdb_name()

◆ output_torsions()

◆ prepare_output_torsion_ids()

◆ run_sampler()

◆ save_data_to_disk()

◆ save_history()

◆ set_parameters()

◆ set_sampler_gaussian_stdev()

◆ set_scorefxn()

Member Data Documentation

◆ bb_tor_out_

◆ bb_torsion_ids_

◆ chi_tor_out_

◆ chi_torsion_ids_

◆ data_

◆ hist_list_

◆ options_

◆ params_

◆ sampler_

◆ scorefxn_

◆ weights_