#include <VirtualSugarSampler.hh>

Inheritance diagram for protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler:

[legend]

Public Member Functions
	VirtualSugarSampler (working_parameters::StepWiseWorkingParametersCOP &working_parameters, SugarModeling &sugar_modeling)

	~VirtualSugarSampler () override

void	apply (core::pose::Pose &pose_to_visualize) override
	Main Method. More...

void	apply (utility::vector1< core::pose::PoseOP > &pose_list, core::pose::Pose &pose_to_visualize) override

std::string	get_name () const override
	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_do_screens (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::ScoreFunctionCOP scorefxn)

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

	~MoverForPoseList () override

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

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

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)

void	reinstantiate_backbone_at_moving_res (core::pose::Pose &pose, core::Size const rebuild_res, core::Size const five_prime_chain_break_res)

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)

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
working_parameters::StepWiseWorkingParametersCOP	working_parameters_

SugarModeling &	sugar_modeling_

std::string	tag_

bool	use_phenix_geo_

bool	keep_base_fixed_

bool	choose_random_

bool	do_minimize_

bool	do_screens_

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_

core::Size const	max_tries_for_random_sugar_setup_

bool	sugar_setup_success_

core::scoring::ScoreFunctionCOP	scorefxn_

checker::RNA_VDW_BinCheckerOP	VDW_bin_checker_

utility::vector1< core::Size >	distal_partition_res_

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 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

◆ VirtualSugarSampler()

protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::VirtualSugarSampler	(	working_parameters::StepWiseWorkingParametersCOP &	working_parameters,
		SugarModeling &	sugar_modeling
	)

◆ ~VirtualSugarSampler()

protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::~VirtualSugarSampler ( )

overridedefault

Member Function Documentation

◆ apply() [1/2]

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::MoverForPoseList.

References choose_random_, max_tries_for_random_sugar_setup_, protocols::stepwise::modeler::rna::sugar::SugarModeling::moving_res, protocols::stepwise::modeler::rna::sugar::SugarModeling::pose_list, protocols::stepwise::modeler::rna::sugar::SugarModeling::reference_res, sugar_modeling_, sugar_setup_success_, protocols::TR(), and viewer_pose.

Referenced by protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::apply(), and protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::do_sugar_sampling().

◆ apply() [2/2]

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

overridevirtual

Reimplemented from protocols::moves::MoverForPoseList.

References protocols::stepwise::modeler::rna::sugar::SugarModeling::bulge_res, protocols::stepwise::modeler::rna::sugar::SugarModeling::check_compatibility(), do_chain_closure_, do_chain_closure_modeler(), do_screens_, original_constraint_set_, protocols::stepwise::modeler::rna::output_title_text(), reinstantiate_distal_partition(), reinstate_original_constraints(), setup_sugar_conformations(), sugar_modeling_, tag_, core::pose::tag_into_pose(), protocols::TR(), viewer_pose, virtual_sugar_is_from_prior_step_, virtualize_distal_partition(), and working_parameters_.

◆ bulge_chain_closure()

void protocols::stepwise::modeler::rna::sugar::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(), legacy_mode_, and viewer_pose.

Referenced by do_chain_closure_modeler().

◆ bulge_chain_closure_complete()

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

private

References protocols::stepwise::modeler::rna::sugar::SugarModeling::bulge_res, integration_test_mode_, protocols::stepwise::legacy::modeler::protein::output_pose_list(), scorefxn_, sugar_modeling_, use_phenix_geo_, and viewer_pose.

Referenced by bulge_chain_closure().

◆ bulge_chain_closure_legacy()

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

private

Referenced by bulge_chain_closure().

◆ bulge_chain_minimize_legacy()

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

private

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::id::BB, protocols::stepwise::modeler::rna::sugar::SugarModeling::bulge_res, core::chemical::rna::CHI, core::scoring::fa_rep, core::scoring::linear_chainbreak, core::optimization::MinimizerOptions::nblist_auto_update(), protocols::stepwise::legacy::modeler::protein::output_pose_list(), protocols::stepwise::modeler::rna::output_title_text(), core::scoring::rna_sugar_close, core::optimization::AtomTreeMinimizer::run(), core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), sugar_modeling_, protocols::TR(), and viewer_pose.

Referenced by bulge_chain_closure().

◆ do_chain_closure_modeler()

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::do_chain_closure_modeler	(	utility::vector1< core::pose::PoseOP > &	pose_list,
		core::pose::Pose &	viewer_pose
	)

private

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

Referenced by apply().

◆ fast_full_atom_VDW_repulsion_screen()

bool protocols::stepwise::modeler::rna::sugar::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().

◆ get_name()

std::string protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ get_sugar_setup_scorefxns()

void protocols::stepwise::modeler::rna::sugar::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 core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::ch_bond, core::scoring::coordinate_constraint, core::scoring::linear_chainbreak, protocols::stepwise::modeler::rna::rescale_scorefxn(), scorefxn_, and protocols::TR().

Referenced by minimize_sugar().

◆ initialize_pose_variants_for_chain_closure()

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

private

References core::pose::add_variant_type_to_pose_residue(), protocols::stepwise::modeler::rna::sugar::SugarModeling::bulge_res, protocols::stepwise::modeler::rna::sugar::SugarModeling::five_prime_chain_break, legacy_mode_, reinstantiate_backbone_at_moving_res(), core::pose::rna::remove_virtual_rna_residue_variant_type(), protocols::stepwise::modeler::rna::setup_chain_break_variants(), sugar_modeling_, core::chemical::VIRTUAL_PHOSPHATE, and core::chemical::VIRTUAL_RNA_RESIDUE.

Referenced by do_chain_closure_modeler().

◆ minimize_sugar()

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::minimize_sugar ( core::pose::Pose & pose_with_sugar )

private

References core::chemical::rna::CHI, 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::modeler::rna::minimize_with_constraints(), protocols::stepwise::modeler::rna::sugar::SugarModeling::moving_res, core::optimization::MinimizerOptions::nblist_auto_update(), core::optimization::AtomTreeMinimizer::run(), core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), sugar_modeling_, protocols::TR(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by setup_sugar_conformations().

◆ reinstantiate_backbone_at_moving_res()

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::reinstantiate_backbone_at_moving_res	(	core::pose::Pose &	pose,
		core::Size const	rebuild_res,
		core::Size const	five_prime_chain_break_res
	)

private

References core::pose::remove_variant_type_from_pose_residue(), core::chemical::VIRTUAL_O2PRIME_HYDROGEN, core::chemical::VIRTUAL_PHOSPHATE, and core::chemical::VIRTUAL_RIBOSE.

Referenced by initialize_pose_variants_for_chain_closure().

◆ reinstantiate_distal_partition() [1/2]

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::reinstantiate_distal_partition ( core::pose::Pose & current_pose )

private

References already_virtualized_res_list_, protocols::stepwise::modeler::rna::phosphate::copy_over_phosphate_variants(), distal_partition_res_, moving_phosphate_virtualized_, protocols::stepwise::modeler::rna::sugar::SugarModeling::moving_res, pose_with_original_terminal_phosphates_, core::pose::remove_variant_type_from_pose_residue(), sugar_modeling_, core::chemical::VIRTUAL_PHOSPHATE, and core::chemical::VIRTUAL_RNA_RESIDUE.

◆ reinstantiate_distal_partition() [2/2]

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

private

References virtual_sugar_is_from_prior_step_.

Referenced by apply().

◆ reinstate_original_constraints()

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

private

References original_constraint_set_.

Referenced by apply().

◆ restore_pose_variants_after_chain_closure()

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

private

References core::pose::rna::apply_virtual_rna_residue_variant_type(), protocols::stepwise::modeler::rna::sugar::SugarModeling::bulge_res, protocols::stepwise::modeler::rna::sugar::SugarModeling::five_prime_chain_break, protocols::stepwise::modeler::rna::get_modeler_scorefxn(), protocols::stepwise::modeler::rna::remove_chain_break_variants(), core::pose::remove_variant_type_from_pose_residue(), scorefxn_, sugar_modeling_, and core::chemical::VIRTUAL_PHOSPHATE.

Referenced by do_chain_closure_modeler().

◆ set_choose_random()

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_choose_random ( bool const & setting )

inline

References choose_random_.

Referenced by protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::apply(), and protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::do_sugar_sampling().

◆ set_do_minimize()

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_do_minimize ( bool const & setting )

inline

References do_minimize_.

Referenced by protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::do_sugar_sampling().

◆ set_do_screens()

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_do_screens ( bool const & setting )

inline

References do_screens_.

Referenced by protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::do_sugar_sampling().

◆ set_integration_test_mode()

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_integration_test_mode ( bool const & setting )

inline

References integration_test_mode_.

Referenced by protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::apply(), and protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::do_sugar_sampling().

◆ set_keep_base_fixed()

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_keep_base_fixed ( bool const & setting )

inline

References keep_base_fixed_.

Referenced by protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::do_sugar_sampling().

◆ set_legacy_mode()

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_legacy_mode ( bool const & setting )

inline

References legacy_mode_.

Referenced by protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::apply(), and protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::do_sugar_sampling().

◆ set_scorefxn()

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_scorefxn ( core::scoring::ScoreFunctionCOP scorefxn )

References scorefxn_.

Referenced by protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::apply(), and protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::do_sugar_sampling().

◆ set_tag()

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_tag ( std::string const & setting )

inline

References tag_.

Referenced by protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::apply(), and protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::do_sugar_sampling().

◆ set_use_phenix_geo()

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_use_phenix_geo ( bool const & setting )

inline

References use_phenix_geo_.

Referenced by protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::apply(), and protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::do_sugar_sampling().

◆ set_virtual_sugar_is_from_prior_step()

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::set_virtual_sugar_is_from_prior_step ( bool const & setting )

inline

References virtual_sugar_is_from_prior_step_.

Referenced by protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::apply().

◆ setup_sugar_conformations()

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

private

References protocols::stepwise::modeler::rna::add_fade_chain_break_constraint_across_gap(), protocols::stepwise::modeler::rna::add_harmonic_chain_break_constraint(), choose_random_, core::pose::Pose::clone(), do_chain_closure_, do_minimize_, do_screens_, core::pose::full_model_info::figure_out_chain_numbers_from_full_model_info(), protocols::stepwise::modeler::rna::sugar::SugarModeling::five_prime_chain_break, core::pose::full_model_info::get_res_list_from_full_model_info(), protocols::stepwise::modeler::rna::sugar::SugarModeling::is_prepend, legacy_mode_, max_tries_for_random_sugar_setup_, minimize_sugar(), protocols::stepwise::modeler::rna::sugar::SugarModeling::moving_res, protocols::stepwise::modeler::rna::sugar::SugarModeling::moving_res_base_state, protocols::stepwise::modeler::rna::sugar::SugarModeling::moving_res_pucker_state, protocols::stepwise::modeler::rna::output_title_text(), protocols::stepwise::modeler::rna::sugar::SugarModeling::reference_res, core::pose::remove_variant_type_from_pose_residue(), scorefxn_, protocols::stepwise::modeler::rna::setup_chain_break_variants(), sugar_modeling_, sugar_setup_success_, core::pose::tag_from_pose(), core::pose::tag_into_pose(), protocols::TR(), use_phenix_geo_, core::chemical::VIRTUAL_RIBOSE, and working_parameters_.

Referenced by apply().

◆ setup_VDW_bin_checker()

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::setup_VDW_bin_checker ( core::pose::Pose const & input_pose )

private

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

◆ virtualize_distal_partition()

void protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::virtualize_distal_partition ( core::pose::Pose & input_pose )

private

Member Data Documentation

◆ already_virtualized_res_list_

utility::vector1< core::Size > protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::already_virtualized_res_list_

private

Referenced by reinstantiate_distal_partition(), and virtualize_distal_partition().

◆ choose_random_

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::choose_random_

private

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

◆ distal_partition_res_

utility::vector1< core::Size > protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::distal_partition_res_

private

Referenced by reinstantiate_distal_partition(), and virtualize_distal_partition().

◆ do_chain_closure_

bool const protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::do_chain_closure_

private

Referenced by apply(), and setup_sugar_conformations().

◆ do_minimize_

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::do_minimize_

private

Referenced by set_do_minimize(), and setup_sugar_conformations().

◆ do_screens_

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::do_screens_

private

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

◆ first_minimize_with_fixed_base_

bool const protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::first_minimize_with_fixed_base_

private

Referenced by minimize_sugar().

◆ integration_test_mode_

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::integration_test_mode_

private

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

◆ keep_base_fixed_

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::keep_base_fixed_

private

Referenced by minimize_sugar(), and set_keep_base_fixed().

◆ legacy_mode_

bool protocols::stepwise::modeler::rna::sugar::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().

◆ max_tries_for_random_sugar_setup_

core::Size const protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::max_tries_for_random_sugar_setup_

private

Referenced by apply(), and setup_sugar_conformations().

◆ moving_phosphate_virtualized_

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::moving_phosphate_virtualized_

private

Referenced by reinstantiate_distal_partition(), and virtualize_distal_partition().

◆ original_constraint_set_

core::scoring::constraints::ConstraintSetOP protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::original_constraint_set_

private

Referenced by apply(), and reinstate_original_constraints().

◆ pose_with_original_terminal_phosphates_

core::pose::PoseOP protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::pose_with_original_terminal_phosphates_

private

Referenced by reinstantiate_distal_partition(), and virtualize_distal_partition().

◆ scorefxn_

core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::scorefxn_

private

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

◆ sugar_modeling_

SugarModeling& protocols::stepwise::modeler::rna::sugar::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().

◆ sugar_setup_success_

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::sugar_setup_success_

private

Referenced by apply(), and setup_sugar_conformations().

◆ tag_

std::string protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::tag_

private

Referenced by apply(), and set_tag().

◆ use_phenix_geo_

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::use_phenix_geo_

private

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

◆ VDW_bin_checker_

checker::RNA_VDW_BinCheckerOP protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::VDW_bin_checker_

private

Referenced by bulge_chain_closure_legacy(), and setup_VDW_bin_checker().

◆ virtual_sugar_is_from_prior_step_

bool protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::virtual_sugar_is_from_prior_step_

private

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

◆ working_parameters_

working_parameters::StepWiseWorkingParametersCOP protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::working_parameters_

private

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

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

src/protocols/stepwise/modeler/rna/sugar/VirtualSugarSampler.hh
src/protocols/stepwise/modeler/rna/sugar/VirtualSugarSampler.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ VirtualSugarSampler()

◆ ~VirtualSugarSampler()

Member Function Documentation

◆ apply() [1/2]

◆ apply() [2/2]

◆ bulge_chain_closure()

◆ bulge_chain_closure_complete()

◆ bulge_chain_closure_legacy()

◆ bulge_chain_minimize_legacy()

◆ do_chain_closure_modeler()

◆ fast_full_atom_VDW_repulsion_screen()

◆ get_name()

◆ get_sugar_setup_scorefxns()

◆ initialize_pose_variants_for_chain_closure()

◆ minimize_sugar()

◆ reinstantiate_backbone_at_moving_res()

◆ reinstantiate_distal_partition() [1/2]

◆ reinstantiate_distal_partition() [2/2]

◆ reinstate_original_constraints()

◆ restore_pose_variants_after_chain_closure()

◆ set_choose_random()

◆ set_do_minimize()

◆ set_do_screens()

◆ set_integration_test_mode()

◆ set_keep_base_fixed()

◆ set_legacy_mode()

◆ set_scorefxn()

◆ set_tag()

◆ set_use_phenix_geo()

◆ set_virtual_sugar_is_from_prior_step()

◆ setup_sugar_conformations()

◆ setup_VDW_bin_checker()

◆ virtualize_distal_partition()

Member Data Documentation

◆ already_virtualized_res_list_

◆ choose_random_

◆ distal_partition_res_

◆ do_chain_closure_

◆ do_minimize_

◆ do_screens_

◆ first_minimize_with_fixed_base_

◆ integration_test_mode_

◆ keep_base_fixed_

◆ legacy_mode_

◆ max_tries_for_random_sugar_setup_

◆ moving_phosphate_virtualized_

◆ original_constraint_set_

◆ pose_with_original_terminal_phosphates_

◆ scorefxn_

◆ sugar_modeling_

◆ sugar_setup_success_

◆ tag_

◆ use_phenix_geo_

◆ VDW_bin_checker_

◆ virtual_sugar_is_from_prior_step_

◆ working_parameters_