protocols::stepwise::sampling::rna::StepWiseRNA_Modeler Class Reference

#include <StepWiseRNA_Modeler.hh>

Public Member Functions
	StepWiseRNA_Modeler (scoring::ScoreFunctionOP scorefxn)
	StepWiseRNA_Modeler (Size const sample_res, scoring::ScoreFunctionOP scorefxn)
	~StepWiseRNA_Modeler ()
	StepWiseRNA_Modeler (StepWiseRNA_Modeler const &src)
StepWiseRNA_ModelerOP	clone_modeler () const
	clone the conformation More...
StepWiseRNA_Modeler &	operator= (StepWiseRNA_Modeler const &src)
void	set_moving_res_and_reset (Size const moving_res)
virtual void	apply (pose::Pose &pose)
virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...
void	set_job_parameters (StepWiseRNA_JobParametersCOP job_parameters)
void	set_silent_file (std::string const &setting)
Size	get_num_sampled ()
void	set_working_fixed_res (utility::vector1< Size > const &setting)
void	set_working_minimize_res (utility::vector1< Size > const &setting)
void	set_terminal_res (utility::vector1< Size > const &setting)
void	set_calc_rms_res (utility::vector1< Size > const &setting)
void	set_syn_chi_res_list (utility::vector1< core::Size > const &setting)
void	set_skip_sampling (bool const &setting)
void	set_minimizer_extra_minimize_res (utility::vector1< core::Size > const &setting)
StepWiseRNA_JobParametersOP	setup_job_parameters_for_stepwise_with_full_model_info (core::pose::Pose &pose)
void	output_pose (pose::Pose &pose, std::string const &out_tag, std::string const out_silent_file) const
StepWiseRNA_ModelerOptionsCOP	options ()
void	set_options (StepWiseRNA_ModelerOptionsCOP options)
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_variables ()
void	initialize_job_parameters_and_root (pose::Pose &pose)
void	do_residue_sampling (pose::Pose &pose, utility::vector1< PoseOP > &pose_list)
bool	sampling_successful (utility::vector1< PoseOP > &pose_list)
void	do_minimizing (pose::Pose &pose, utility::vector1< PoseOP > &pose_list)
void	add_to_pose_list (utility::vector1< pose::PoseOP > &pose_list, pose::Pose const &pose, std::string const pose_tag) const

Private Attributes
StepWiseRNA_JobParametersCOP	job_parameters_
pose::PoseCOP	native_pose_
scoring::ScoreFunctionOP	scorefxn_
std::string	silent_file_
Size	moving_res_
utility::vector1< Size >	working_fixed_res_
utility::vector1< Size >	working_minimize_res_
utility::vector1< Size >	calc_rms_res_
utility::vector1< Size >	terminal_res_
utility::vector1< core::Size >	minimizer_extra_minimize_res_
utility::vector1< core::Size >	syn_chi_res_list_
StepWiseRNA_ModelerOptionsCOP	options_
Size	num_sampled_
StepWiseRNA_MinimizerOP	stepwise_rna_minimizer_
kinematics::MoveMapOP	minimize_move_map_
checker::RNA_BaseCentroidCheckerOP	base_centroid_checker_
checker::RNA_VDW_BinCheckerOP	user_input_VDW_bin_checker_
toolbox::AllowInsertOP	allow_insert_
utility::vector1< std::string >	VDW_rep_screen_info_

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_Modeler::StepWiseRNA_Modeler

(

scoring::ScoreFunctionOP

scorefxn

)

Referenced by clone_modeler().

protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::StepWiseRNA_Modeler	(	core::Size const	sample_res,
		scoring::ScoreFunctionOP	scorefxn
	)

protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::~StepWiseRNA_Modeler

(

)

protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::StepWiseRNA_Modeler

(

StepWiseRNA_Modeler const &

src

)

Member Function Documentation

void protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::add_to_pose_list ( utility::vector1< pose::PoseOP > &  pose_list, pose::Pose const &  pose, std::string const  pose_tag  ) const

private

References core::pose::Pose::clone(), and tag_into_pose().

Referenced by do_minimizing(), and do_residue_sampling().

void protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::apply ( pose::Pose &  pose )

virtual

Implements protocols::moves::Mover.

References do_minimizing(), do_residue_sampling(), initialize_job_parameters_and_root(), job_parameters_, and sampling_successful().

StepWiseRNA_ModelerOP protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::clone_modeler

(

)

const

clone the conformation

References StepWiseRNA_Modeler().

void protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::do_minimizing ( pose::Pose &  pose, utility::vector1< PoseOP > &  pose_list  )

private

References add_to_pose_list(), allow_insert_, base_centroid_checker_, const_full_model_info(), protocols::moves::Mover::get_native_pose(), job_parameters_, minimize_move_map_, options_, runtime_assert, scorefxn_, protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_sampler_native_screen_rmsd_cutoff(), silent_file_, stepwise_rna_minimizer_, and user_input_VDW_bin_checker_.

Referenced by apply().

void protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::do_residue_sampling ( pose::Pose &  pose, utility::vector1< PoseOP > &  pose_list  )

private

References add_to_pose_list(), protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::apply(), base_centroid_checker_, protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::get_pose_list(), job_parameters_, moving_res_, options_, protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::output_pose_list(), protocols::stepwise::sampling::rna::print_JobParameters_info(), scorefxn_, protocols::stepwise::sampling::rna::checker::RNA_BaseCentroidChecker::set_allow_base_pair_only_screen(), protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::set_base_centroid_checker(), protocols::stepwise::sampling::rna::checker::RNA_BaseCentroidChecker::set_floating_base(), protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::set_options(), protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::set_sampling_silent_file(), protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::set_scorefxn(), protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::set_user_input_VDW_bin_checker(), protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::setup_using_user_input_VDW_pose(), silent_file_, protocols::TR, user_input_VDW_bin_checker_, and VDW_rep_screen_info_.

Referenced by apply().

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

virtual

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

Implements protocols::moves::Mover.

Size protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::get_num_sampled ( )

inline

void protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::initialize_job_parameters_and_root ( pose::Pose &  pose )

private

References job_parameters_, moving_res_, protocols::stepwise::revise_root_and_moving_res(), and setup_job_parameters_for_stepwise_with_full_model_info().

Referenced by apply().

void protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::initialize_variables ( )

private

StepWiseRNA_Modeler & protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::operator=

(

StepWiseRNA_Modeler const &

src

)

References job_parameters_, minimize_move_map_, moving_res_, native_pose_, num_sampled_, options_, scorefxn_, stepwise_rna_minimizer_, syn_chi_res_list_, terminal_res_, working_fixed_res_, and working_minimize_res_.

StepWiseRNA_ModelerOptionsCOP protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::options

(

)

References options_.

Referenced by set_options().

void protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::output_pose	(	pose::Pose &	pose,
		std::string const &	out_tag,
		std::string const	out_silent_file
	)		const

References stepwise_rna_minimizer_.

bool protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::sampling_successful ( utility::vector1< PoseOP > &  pose_list )

private

References num_sampled_, options_, and protocols::TR.

Referenced by apply().

void protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::set_calc_rms_res ( utility::vector1< Size > const &  setting )

inline

void protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::set_job_parameters

(

StepWiseRNA_JobParametersCOP

job_parameters

)

References job_parameters_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::set_minimizer_extra_minimize_res ( utility::vector1< core::Size > const &  setting )

inline

void protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::set_moving_res_and_reset

(

core::Size const

moving_res

)

References job_parameters_, and moving_res_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::set_options

(

StepWiseRNA_ModelerOptionsCOP

options

)

References options(), and options_.

Referenced by set_skip_sampling().

void protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::set_silent_file ( std::string const &  setting )

inline

void protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::set_skip_sampling

(

bool const &

setting

)

References options_, set_options(), and protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_skip_sampling().

void protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::set_syn_chi_res_list ( utility::vector1< core::Size > const &  setting )

inline

void protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::set_terminal_res ( utility::vector1< Size > const &  setting )

inline

void protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::set_working_fixed_res ( utility::vector1< Size > const &  setting )

inline

void protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::set_working_minimize_res ( utility::vector1< Size > const &  setting )

inline

StepWiseRNA_JobParametersOP protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::setup_job_parameters_for_stepwise_with_full_model_info

(

core::pose::Pose &

pose

)

References allow_insert_, calc_rms_res_, const_full_model_info(), protocols::moves::Mover::get_native_pose(), minimize_move_map_, moving_res_, protocols::stepwise::sampling::rna::setup_job_parameters_for_swa(), syn_chi_res_list_, terminal_res_, working_fixed_res_, and working_minimize_res_.

Referenced by initialize_job_parameters_and_root().

Member Data Documentation

toolbox::AllowInsertOP protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::allow_insert_

private

Referenced by do_minimizing(), and setup_job_parameters_for_stepwise_with_full_model_info().

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

private

Referenced by do_minimizing(), and do_residue_sampling().

utility::vector1< Size > protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::calc_rms_res_

private

Referenced by setup_job_parameters_for_stepwise_with_full_model_info().

StepWiseRNA_JobParametersCOP protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::job_parameters_

private

Referenced by apply(), do_minimizing(), do_residue_sampling(), initialize_job_parameters_and_root(), operator=(), set_job_parameters(), and set_moving_res_and_reset().

kinematics::MoveMapOP protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::minimize_move_map_

private

Referenced by do_minimizing(), operator=(), and setup_job_parameters_for_stepwise_with_full_model_info().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::minimizer_extra_minimize_res_

private

Size protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::moving_res_

private

Referenced by do_residue_sampling(), initialize_job_parameters_and_root(), operator=(), set_moving_res_and_reset(), and setup_job_parameters_for_stepwise_with_full_model_info().

pose::PoseCOP protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::native_pose_

private

Referenced by operator=().

Size protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::num_sampled_

private

Referenced by operator=(), and sampling_successful().

StepWiseRNA_ModelerOptionsCOP protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::options_

private

Referenced by do_minimizing(), do_residue_sampling(), operator=(), options(), sampling_successful(), set_options(), and set_skip_sampling().

scoring::ScoreFunctionOP protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::scorefxn_

private

Referenced by do_minimizing(), do_residue_sampling(), and operator=().

std::string protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::silent_file_

private

Referenced by do_minimizing(), and do_residue_sampling().

StepWiseRNA_MinimizerOP protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::stepwise_rna_minimizer_

private

Referenced by do_minimizing(), operator=(), and output_pose().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::syn_chi_res_list_

private

Referenced by operator=(), and setup_job_parameters_for_stepwise_with_full_model_info().

utility::vector1< Size > protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::terminal_res_

private

Referenced by operator=(), and setup_job_parameters_for_stepwise_with_full_model_info().

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

private

Referenced by do_minimizing(), and do_residue_sampling().

utility::vector1< std::string > protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::VDW_rep_screen_info_

private

Referenced by do_residue_sampling().

utility::vector1< Size > protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::working_fixed_res_

private

Referenced by operator=(), and setup_job_parameters_for_stepwise_with_full_model_info().

utility::vector1< Size > protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::working_minimize_res_

private

Referenced by operator=(), and setup_job_parameters_for_stepwise_with_full_model_info().

---

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

• symlinks/rosetta/src/protocols/stepwise/sampling/rna/StepWiseRNA_Modeler.hh
• symlinks/rosetta/src/protocols/stepwise/sampling/rna/StepWiseRNA_Modeler.cc