#include <StepWiseRNA_VirtualSugarSampler.hh>

Public Member Functions
	StepWiseRNA_VirtualSugarSampler (StepWiseRNA_JobParametersCOP &job_parameters, SugarModeling &sugar_modeling)

	~StepWiseRNA_VirtualSugarSampler ()

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

virtual void	apply (utility::vector1< core::pose::PoseOP > &pose_list, 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_tag (std::string const &setting)

void	set_use_phenix_geo (bool const &setting)

void	set_legacy_mode (bool const &setting)

void	set_choose_random (bool const &setting)

void	set_keep_base_fixed (bool const &setting)

void	set_do_minimize (bool const &setting)

void	set_integration_test_mode (bool const &setting)

void	set_virtual_sugar_is_from_prior_step (bool const &setting)

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

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

	~MoverForPoseList ()

virtual void	apply (utility::vector1< core::pose::PoseOP > &pose_list)

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	setup_sugar_conformations (utility::vector1< core::pose::PoseOP > &pose_list, core::pose::Pose &pose)

void	minimize_sugar (core::pose::Pose &pose_with_sugar)

void	get_sugar_setup_scorefxns (core::scoring::ScoreFunctionOP &sugar_scorefxn, core::scoring::ScoreFunctionOP &sugar_scorefxn_without_ch_bond, core::scoring::ScoreFunctionOP &rescaled_sugar_score_fxn_without_ch_bond) const

void	do_chain_closure_sampling (utility::vector1< core::pose::PoseOP > &pose_list, core::pose::Pose &viewer_pose)

void	initialize_pose_variants_for_chain_closure (utility::vector1< core::pose::PoseOP > &pose_list)

void	restore_pose_variants_after_chain_closure (utility::vector1< core::pose::PoseOP > &pose_list)

void	bulge_chain_closure (utility::vector1< core::pose::PoseOP > &pose_list, core::pose::Pose &viewer_pose)

void	bulge_chain_closure_complete (utility::vector1< core::pose::PoseOP > &pose_list, core::pose::Pose &viewer_pose)

void	bulge_chain_closure_legacy (utility::vector1< core::pose::PoseOP > &pose_list, core::pose::Pose &viewer_pose)

void	bulge_chain_minimize_legacy (utility::vector1< core::pose::PoseOP > &pose_list, core::pose::Pose &viewer_pose)

bool	fast_full_atom_VDW_repulsion_screen (core::pose::Pose const &pose, core::Size const res_1, core::Size const res_2, bool const is_prepend)

void	setup_VDW_bin_checker (core::pose::Pose const &input_pose)

void	virtualize_distal_partition (core::pose::Pose &input_pose)

void	reinstantiate_distal_partition (utility::vector1< core::pose::PoseOP > &final_pose_list)

void	reinstantiate_distal_partition (core::pose::Pose &current_pose)

void	reinstate_original_constraints (utility::vector1< core::pose::PoseOP > &pose_list)

Private Attributes
StepWiseRNA_JobParametersCOP	job_parameters_

SugarModeling &	sugar_modeling_

std::string	tag_

bool	use_phenix_geo_

bool	keep_base_fixed_

bool	choose_random_

bool	do_minimize_

bool	integration_test_mode_

bool	virtual_sugar_is_from_prior_step_

bool	legacy_mode_

bool const	do_chain_closure_

bool const	first_minimize_with_fixed_base_

Size const	max_tries_for_random_overall_

Size const	max_tries_for_random_sugar_setup_

bool	sugar_setup_success_

core::scoring::ScoreFunctionOP	scorefxn_

checker::RNA_VDW_BinCheckerOP	VDW_bin_checker_

utility::vector1< core::Size >	distal_partition_pos_

utility::vector1< core::Size >	already_virtualized_res_list_

bool	moving_phosphate_virtualized_

core::pose::PoseOP	pose_with_original_terminal_phosphates_

core::scoring::constraints::ConstraintSetOP	original_constraint_set_

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::sugar::StepWiseRNA_VirtualSugarSampler::StepWiseRNA_VirtualSugarSampler	(	StepWiseRNA_JobParametersCOP &	job_parameters,
		SugarModeling &	sugar_modeling
	)

protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::~StepWiseRNA_VirtualSugarSampler ( )

Member Function Documentation

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

virtual

Implements protocols::moves::MoverForPoseList.

References choose_random_, max_tries_for_random_sugar_setup_, protocols::stepwise::sampling::rna::sugar::SugarModeling::moving_res, protocols::stepwise::sampling::rna::sugar::SugarModeling::pose_list, protocols::stepwise::sampling::rna::sugar::SugarModeling::reference_res, sugar_modeling_, sugar_setup_success_, and protocols::TR.

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList::apply(), protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::do_sugar_sampling(), and protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::do_sugar_sampling().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::apply	(	utility::vector1< core::pose::PoseOP > &	pose_list,
		core::pose::Pose &	pose_to_visualize
	)

virtual

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::bulge_chain_closure	(	utility::vector1< core::pose::PoseOP > &	pose_list,
		core::pose::Pose &	viewer_pose
	)

private

References bulge_chain_closure_complete(), bulge_chain_closure_legacy(), bulge_chain_minimize_legacy(), and legacy_mode_.

Referenced by do_chain_closure_sampling().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::bulge_chain_closure_complete	(	utility::vector1< core::pose::PoseOP > &	pose_list,
		core::pose::Pose &	viewer_pose
	)

private

References protocols::stepwise::sampling::rna::sugar::SugarModeling::bulge_res, core::pose::Pose::clone(), integration_test_mode_, options, scorefxn_, protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_integration_test_mode(), protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_kic_sampling_if_relevant(), protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_num_pose_minimize(), protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_use_phenix_geo(), sugar_modeling_, and use_phenix_geo_.

Referenced by bulge_chain_closure().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::bulge_chain_closure_legacy	(	utility::vector1< core::pose::PoseOP > &	pose_list,
		core::pose::Pose &	viewer_pose
	)

private

References protocols::stepwise::sampling::rna::add_harmonic_chain_break_constraint(), ANY_CHI, ANY_PUCKER, assign_pucker(), protocols::stepwise::sampling::rna::sugar::SugarModeling::bulge_res, protocols::stepwise::sampling::rna::sugar::SugarModeling::bulge_suite, fast_full_atom_VDW_repulsion_screen(), protocols::stepwise::sampling::rna::sugar::SugarModeling::five_prime_chain_break, integration_test_mode_, protocols::stepwise::sampling::rna::sugar::SugarModeling::is_prepend, legacy_mode_, protocols::stepwise::sampling::rna::sugar::SugarModeling::moving_res, NO_CHI, protocols::stepwise::sampling::rna::output_title_text(), sugar_modeling_, protocols::TR, use_phenix_geo_, VDW_bin_checker_, and protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen().

Referenced by bulge_chain_closure().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::bulge_chain_minimize_legacy	(	utility::vector1< core::pose::PoseOP > &	pose_list,
		core::pose::Pose &	viewer_pose
	)

private

References angle_constraint, atom_pair_constraint, protocols::stepwise::sampling::rna::sugar::SugarModeling::bulge_res, core::pose::Pose::clone(), fa_rep, linear_chainbreak, minimizer, core::optimization::MinimizerOptions::nblist_auto_update(), options, protocols::stepwise::sampling::rna::output_title_text(), rna_sugar_close, core::kinematics::MoveMap::set_bb(), sugar_modeling_, and protocols::TR.

Referenced by bulge_chain_closure().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::do_chain_closure_sampling	(	utility::vector1< core::pose::PoseOP > &	pose_list,
		core::pose::Pose &	viewer_pose
	)

private

References bulge_chain_closure(), initialize_pose_variants_for_chain_closure(), and restore_pose_variants_after_chain_closure().

Referenced by apply().

bool protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::fast_full_atom_VDW_repulsion_screen	(	core::pose::Pose const &	pose,
		core::Size const	res_1,
		core::Size const	res_2,
		bool const	is_prepend
	)

private

References core::conformation::Residue::atom_type(), core::conformation::Residue::is_virtual(), core::chemical::AtomType::lj_radius(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by bulge_chain_closure_legacy().

std::string protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::get_sugar_setup_scorefxns	(	core::scoring::ScoreFunctionOP &	sugar_scorefxn,
		core::scoring::ScoreFunctionOP &	sugar_scorefxn_without_ch_bond,
		core::scoring::ScoreFunctionOP &	rescaled_sugar_score_fxn_without_ch_bond
	)		const

private

References angle_constraint, atom_pair_constraint, ch_bond, core::scoring::ScoreFunction::clone(), coordinate_constraint, linear_chainbreak, protocols::stepwise::sampling::rna::rescale_scorefxn(), scorefxn_, and protocols::TR.

Referenced by minimize_sugar().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::initialize_pose_variants_for_chain_closure ( utility::vector1< core::pose::PoseOP > & pose_list )

private

References protocols::stepwise::sampling::rna::sugar::SugarModeling::bulge_res, protocols::stepwise::sampling::rna::sugar::SugarModeling::five_prime_chain_break, legacy_mode_, protocols::stepwise::sampling::rna::remove_virtual_rna_residue_variant_type(), protocols::stepwise::sampling::rna::setup_chain_break_variants(), and sugar_modeling_.

Referenced by do_chain_closure_sampling().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::minimize_sugar ( core::pose::Pose & pose_with_sugar )

private

References core::kinematics::FoldTree::downstream_jump_residue(), first_minimize_with_fixed_base_, core::pose::Pose::fold_tree(), get_sugar_setup_scorefxns(), keep_base_fixed_, core::optimization::MinimizerOptions::min_type(), core::optimization::MinimizerOptions::minimize_tolerance(), protocols::stepwise::sampling::rna::minimize_with_constraints(), minimizer, protocols::stepwise::sampling::rna::sugar::SugarModeling::moving_res, core::optimization::MinimizerOptions::nblist_auto_update(), core::kinematics::FoldTree::num_jump(), runtime_assert, core::kinematics::MoveMap::set_bb(), sugar_modeling_, protocols::TR, and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by setup_sugar_conformations().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::reinstantiate_distal_partition ( utility::vector1< core::pose::PoseOP > & final_pose_list )

private

References virtual_sugar_is_from_prior_step_.

Referenced by apply().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::reinstantiate_distal_partition ( core::pose::Pose & current_pose )

private

References already_virtualized_res_list_, protocols::stepwise::sampling::rna::phosphate::copy_over_phosphate_variants(), distal_partition_pos_, utility::vector1< T, class >::has_value(), moving_phosphate_virtualized_, protocols::stepwise::sampling::rna::sugar::SugarModeling::moving_res, pose_with_original_terminal_phosphates_, and sugar_modeling_.

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::reinstate_original_constraints ( utility::vector1< core::pose::PoseOP > & pose_list )

private

References original_constraint_set_.

Referenced by apply().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::restore_pose_variants_after_chain_closure ( utility::vector1< core::pose::PoseOP > & pose_list )

private

References protocols::stepwise::sampling::rna::apply_virtual_rna_residue_variant_type(), protocols::stepwise::sampling::rna::sugar::SugarModeling::bulge_res, protocols::stepwise::sampling::rna::sugar::SugarModeling::five_prime_chain_break, protocols::stepwise::sampling::rna::get_sampling_scorefxn(), protocols::stepwise::sampling::rna::remove_chain_break_variants(), scorefxn_, and sugar_modeling_.

Referenced by do_chain_closure_sampling().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::set_choose_random ( bool const & setting )

inline

References choose_random_.

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList::apply(), protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::do_sugar_sampling(), and protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::do_sugar_sampling().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::set_do_minimize ( bool const & setting )

inline

References do_minimize_.

Referenced by protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::do_sugar_sampling(), and protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::do_sugar_sampling().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::set_integration_test_mode ( bool const & setting )

inline

References integration_test_mode_.

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList::apply(), protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::do_sugar_sampling(), and protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::do_sugar_sampling().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::set_keep_base_fixed ( bool const & setting )

inline

References keep_base_fixed_.

Referenced by protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::do_sugar_sampling(), and protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::do_sugar_sampling().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::set_legacy_mode ( bool const & setting )

inline

References legacy_mode_.

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList::apply(), protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::do_sugar_sampling(), and protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::do_sugar_sampling().

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

References scorefxn_.

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList::apply(), protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::do_sugar_sampling(), and protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::do_sugar_sampling().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::set_tag ( std::string const & setting )

inline

References tag_.

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList::apply(), protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::do_sugar_sampling(), and protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::do_sugar_sampling().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::set_use_phenix_geo ( bool const & setting )

inline

References use_phenix_geo_.

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList::apply(), protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::do_sugar_sampling(), and protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::do_sugar_sampling().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::set_virtual_sugar_is_from_prior_step ( bool const & setting )

inline

References virtual_sugar_is_from_prior_step_.

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList::apply().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::setup_sugar_conformations	(	utility::vector1< core::pose::PoseOP > &	pose_list,
		core::pose::Pose &	pose
	)

private

References protocols::stepwise::sampling::rna::add_fade_chain_break_constraint_across_gap(), protocols::stepwise::sampling::rna::add_harmonic_chain_break_constraint(), choose_random_, core::pose::Pose::clone(), do_chain_closure_, do_minimize_, figure_out_chains_from_full_model_info(), protocols::stepwise::sampling::rna::sugar::SugarModeling::five_prime_chain_break, get_res_list_from_full_model_info(), protocols::stepwise::sampling::rna::sugar::SugarModeling::is_prepend, job_parameters_, legacy_mode_, max_tries_for_random_sugar_setup_, minimize_sugar(), protocols::stepwise::sampling::rna::sugar::SugarModeling::moving_res, protocols::stepwise::sampling::rna::sugar::SugarModeling::moving_res_base_state, protocols::stepwise::sampling::rna::sugar::SugarModeling::moving_res_pucker_state, protocols::stepwise::sampling::rna::output_title_text(), protocols::stepwise::sampling::rna::sugar::SugarModeling::reference_res, protocols::stepwise::sampling::rna::setup_chain_break_variants(), sugar_modeling_, sugar_setup_success_, tag_from_pose(), tag_into_pose(), protocols::TR, and use_phenix_geo_.

Referenced by apply().

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::setup_VDW_bin_checker ( core::pose::Pose const & input_pose )

private

References protocols::stepwise::sampling::rna::sugar::SugarModeling::bulge_res, protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::create_VDW_screen_bin(), core::chemical::rna::get_rna_base_centroid(), core::chemical::rna::get_rna_base_coordinate_system(), protocols::stepwise::sampling::rna::sugar::SugarModeling::is_prepend, core::kinematics::Stub::M, make_vector1(), protocols::stepwise::sampling::rna::sugar::SugarModeling::moving_res, protocols::stepwise::sampling::rna::sugar::SugarModeling::reference_res, core::pose::Pose::residue(), sugar_modeling_, core::kinematics::Stub::v, and VDW_bin_checker_.

void protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::virtualize_distal_partition ( core::pose::Pose & input_pose )

private

References already_virtualized_res_list_, core::pose::Pose::clone(), distal_partition_pos_, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), job_parameters_, core::kinematics::FoldTree::jump_nr(), moving_phosphate_virtualized_, protocols::stepwise::sampling::rna::sugar::SugarModeling::moving_res, nres, core::kinematics::FoldTree::partition_by_jump(), pose_with_original_terminal_phosphates_, protocols::stepwise::sampling::rna::sugar::SugarModeling::reference_res, protocols::stepwise::sampling::rna::phosphate::remove_terminal_phosphates(), core::pose::Pose::residue(), runtime_assert, and sugar_modeling_.

Referenced by apply().

Member Data Documentation

utility::vector1< core::Size > protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::already_virtualized_res_list_

private

Referenced by reinstantiate_distal_partition(), and virtualize_distal_partition().

bool protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::choose_random_

private

Referenced by apply(), set_choose_random(), and setup_sugar_conformations().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::distal_partition_pos_

private

Referenced by reinstantiate_distal_partition(), and virtualize_distal_partition().

bool const protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::do_chain_closure_

private

Referenced by apply(), and setup_sugar_conformations().

bool protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::do_minimize_

private

Referenced by set_do_minimize(), and setup_sugar_conformations().

bool const protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::first_minimize_with_fixed_base_

private

Referenced by minimize_sugar().

bool protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::integration_test_mode_

private

Referenced by bulge_chain_closure_complete(), bulge_chain_closure_legacy(), and set_integration_test_mode().

StepWiseRNA_JobParametersCOP protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::job_parameters_

private

Referenced by apply(), setup_sugar_conformations(), and virtualize_distal_partition().

bool protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::keep_base_fixed_

private

Referenced by minimize_sugar(), and set_keep_base_fixed().

bool protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::legacy_mode_

private

Referenced by bulge_chain_closure(), bulge_chain_closure_legacy(), initialize_pose_variants_for_chain_closure(), set_legacy_mode(), and setup_sugar_conformations().

Size const protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::max_tries_for_random_overall_

private

Size const protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::max_tries_for_random_sugar_setup_

private

Referenced by apply(), and setup_sugar_conformations().

bool protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::moving_phosphate_virtualized_

private

Referenced by reinstantiate_distal_partition(), and virtualize_distal_partition().

core::scoring::constraints::ConstraintSetOP protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::original_constraint_set_

private

Referenced by apply(), and reinstate_original_constraints().

core::pose::PoseOP protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::pose_with_original_terminal_phosphates_

private

Referenced by reinstantiate_distal_partition(), and virtualize_distal_partition().

core::scoring::ScoreFunctionOP protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::scorefxn_

private

Referenced by bulge_chain_closure_complete(), get_sugar_setup_scorefxns(), restore_pose_variants_after_chain_closure(), and set_scorefxn().

SugarModeling& protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::sugar_modeling_

private

Referenced by apply(), bulge_chain_closure_complete(), bulge_chain_closure_legacy(), bulge_chain_minimize_legacy(), initialize_pose_variants_for_chain_closure(), minimize_sugar(), reinstantiate_distal_partition(), restore_pose_variants_after_chain_closure(), setup_sugar_conformations(), setup_VDW_bin_checker(), and virtualize_distal_partition().

bool protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::sugar_setup_success_

private

Referenced by apply(), and setup_sugar_conformations().

std::string protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::tag_

private

Referenced by apply(), and set_tag().

bool protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::use_phenix_geo_

private

Referenced by bulge_chain_closure_complete(), bulge_chain_closure_legacy(), set_use_phenix_geo(), and setup_sugar_conformations().

checker::RNA_VDW_BinCheckerOP protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::VDW_bin_checker_

private

Referenced by bulge_chain_closure_legacy(), and setup_VDW_bin_checker().

bool protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::virtual_sugar_is_from_prior_step_

private

Referenced by apply(), reinstantiate_distal_partition(), and set_virtual_sugar_is_from_prior_step().

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

symlinks/rosetta/src/protocols/stepwise/sampling/rna/sugar/StepWiseRNA_VirtualSugarSampler.hh
symlinks/rosetta/src/protocols/stepwise/sampling/rna/sugar/StepWiseRNA_VirtualSugarSampler.cc

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