#include <StepWiseRNA_ResidueSampler.hh>

Public Member Functions
	StepWiseRNA_ResidueSampler (StepWiseRNA_JobParametersCOP &job_parameters_)

	~StepWiseRNA_ResidueSampler ()

virtual void	apply (core::pose::Pose &pose_to_visualize)

virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...

void	set_scorefxn (core::scoring::ScoreFunctionOP const &scorefxn)

utility::vector1 < core::pose::PoseOP > &	get_pose_list ()

void	output_pose_list (std::string const final_sampler_output_silent_file) const

void	set_base_centroid_checker (checker::RNA_BaseCentroidCheckerOP &checker)

void	set_user_input_VDW_bin_checker (checker::RNA_VDW_BinCheckerOP const &user_input_VDW_bin_checker)

void	set_options (StepWiseRNA_ModelerOptionsCOP options)

void	set_sampling_silent_file (std::string const &setting)

std::string	sampling_silent_file () const

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

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...

void	set_current_tag (std::string const &new_tag)

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	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...

void	type (const std::string &type_in)

virtual MoverOP	clone () const
	Return a clone of the Mover object. More...

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

std::string	get_type () const

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...

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 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...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

Private Member Functions
void	initialize_scorefunctions ()

void	check_res_not_bulged ()

void	unified_sampling (core::pose::Pose &pose)

void	legacy_sampling (core::pose::Pose &pose)

void	standard_sampling (core::pose::Pose &pose)

void	floating_base_sampling (core::pose::Pose &pose)

bool	instantiate_any_virtual_sugars (core::pose::Pose &pose)

void	output_options ()

Private Attributes
StepWiseRNA_JobParametersCOP	job_parameters_

utility::vector1< pose::PoseOP >	pose_list_

core::scoring::ScoreFunctionOP	scorefxn_

StepWiseRNA_ModelerOptionsCOP	options_

checker::RNA_BaseCentroidCheckerOP	base_centroid_checker_

checker::RNA_VDW_BinCheckerOP	user_input_VDW_bin_checker_

sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOP	virtual_sugar_just_in_time_instantiator_

std::string	sampling_silent_file_

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 protocols::filters::Filters_map	Filters_map

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::sampling::rna::StepWiseRNA_ResidueSampler::StepWiseRNA_ResidueSampler ( StepWiseRNA_JobParametersCOP & job_parameters_ )

References job_parameters_, scoring, and protocols::moves::Mover::set_native_pose().

protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::~StepWiseRNA_ResidueSampler ( )

Member Function Documentation

void protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::apply ( core::pose::Pose & pose_to_visualize )

virtual

Implements protocols::moves::Mover.

References instantiate_any_virtual_sugars(), legacy_sampling(), options_, output_options(), protocols::stepwise::sampling::rna::output_title_text(), protocols::TR, and unified_sampling().

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::do_residue_sampling().

void protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::check_res_not_bulged ( )

private

void protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::floating_base_sampling ( core::pose::Pose & pose )

private

References protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::apply(), base_centroid_checker_, core::pose::Pose::clone(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::get_pose_list(), job_parameters_, options_, pose_list_, runtime_assert, sampling_silent_file_, scorefxn_, protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::set_anchor_sugar_modeling(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::set_base_centroid_checker(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::set_options(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::set_scorefxn(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::set_silent_file(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::set_user_input_VDW_bin_checker(), user_input_VDW_bin_checker_, and virtual_sugar_just_in_time_instantiator_.

Referenced by legacy_sampling().

std::string protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

utility::vector1< PoseOP > & protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::get_pose_list ( )

References pose_list_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::do_residue_sampling().

void protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::initialize_scorefunctions ( )

private

bool protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::instantiate_any_virtual_sugars ( core::pose::Pose & pose )

private

References job_parameters_, options_, scorefxn_, and virtual_sugar_just_in_time_instantiator_.

Referenced by apply().

void protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::legacy_sampling ( core::pose::Pose & pose )

private

References floating_base_sampling(), job_parameters_, and standard_sampling().

Referenced by apply().

void protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::output_options ( )

private

References base_centroid_checker_, job_parameters_, options_, protocols::stepwise::sampling::rna::output_boolean(), protocols::stepwise::sampling::rna::output_seq_num_list(), and protocols::TR.

Referenced by apply().

void protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::output_pose_list ( std::string const final_sampler_output_silent_file ) const

References protocols::moves::Mover::get_native_pose(), job_parameters_, options_, protocols::stepwise::sampling::rna::output_data(), pose_list_, runtime_assert, and tag_from_pose().

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::do_residue_sampling().

std::string protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::sampling_silent_file ( ) const

inline

void protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::set_base_centroid_checker ( checker::RNA_BaseCentroidCheckerOP & checker )

References base_centroid_checker_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::do_residue_sampling().

void protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::set_options ( StepWiseRNA_ModelerOptionsCOP options )

References protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::choose_random(), protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::integration_test_mode(), options_, protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_cluster_rmsd(), protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_sampler_native_rmsd_screen(), protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_sampler_native_screen_rmsd_cutoff(), and protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_sampler_num_pose_kept().

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::do_residue_sampling().

void protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::set_sampling_silent_file ( std::string const & setting )

inline

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::do_residue_sampling().

void protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::set_scorefxn ( core::scoring::ScoreFunctionOP const & scorefxn )

References scorefxn_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::do_residue_sampling().

void protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::set_user_input_VDW_bin_checker ( checker::RNA_VDW_BinCheckerOP const & user_input_VDW_bin_checker )

References user_input_VDW_bin_checker_.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::do_residue_sampling().

void protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::standard_sampling ( core::pose::Pose & pose )

private

Referenced by legacy_sampling().

void protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::unified_sampling ( core::pose::Pose & pose )

private

Referenced by apply().

Member Data Documentation

checker::RNA_BaseCentroidCheckerOP protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::base_centroid_checker_

private

Referenced by floating_base_sampling(), output_options(), set_base_centroid_checker(), standard_sampling(), and unified_sampling().

StepWiseRNA_JobParametersCOP protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::job_parameters_

private

Referenced by floating_base_sampling(), instantiate_any_virtual_sugars(), legacy_sampling(), output_options(), output_pose_list(), standard_sampling(), StepWiseRNA_ResidueSampler(), and unified_sampling().

StepWiseRNA_ModelerOptionsCOP protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::options_

private

Referenced by apply(), floating_base_sampling(), instantiate_any_virtual_sugars(), output_options(), output_pose_list(), set_options(), standard_sampling(), and unified_sampling().

utility::vector1< pose::PoseOP > protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::pose_list_

private

Referenced by floating_base_sampling(), get_pose_list(), output_pose_list(), standard_sampling(), and unified_sampling().

std::string protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::sampling_silent_file_

private

Referenced by floating_base_sampling(), standard_sampling(), and unified_sampling().

core::scoring::ScoreFunctionOP protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::scorefxn_

private

Referenced by floating_base_sampling(), instantiate_any_virtual_sugars(), set_scorefxn(), standard_sampling(), and unified_sampling().

checker::RNA_VDW_BinCheckerOP protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::user_input_VDW_bin_checker_

private

Referenced by floating_base_sampling(), set_user_input_VDW_bin_checker(), standard_sampling(), and unified_sampling().

sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOP protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::virtual_sugar_just_in_time_instantiator_

private

Referenced by floating_base_sampling(), instantiate_any_virtual_sugars(), standard_sampling(), and unified_sampling().

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

symlinks/rosetta/src/protocols/stepwise/sampling/rna/StepWiseRNA_ResidueSampler.hh
symlinks/rosetta/src/protocols/stepwise/sampling/rna/StepWiseRNA_ResidueSampler.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation