Namespaces
	legacy

Classes
class	StepWiseRNA_VirtualSugarJustInTimeInstantiator

class	StepWiseRNA_VirtualSugarSampler

class	StepWiseRNA_VirtualSugarSamplerFromStringList

class	SugarInstantiateMover

class	SugarModeling

class	SugarVirtualizeMover

Typedefs
typedef utility::pointer::owning_ptr < StepWiseRNA_VirtualSugarJustInTimeInstantiator >	StepWiseRNA_VirtualSugarJustInTimeInstantiatorOP

typedef utility::pointer::owning_ptr < StepWiseRNA_VirtualSugarJustInTimeInstantiator const >	StepWiseRNA_VirtualSugarJustInTimeInstantiatorCOP

typedef utility::pointer::owning_ptr < StepWiseRNA_VirtualSugarSamplerFromStringList >	StepWiseRNA_VirtualSugarSamplerFromStringListOP

typedef utility::pointer::owning_ptr < StepWiseRNA_VirtualSugarSamplerFromStringList const >	StepWiseRNA_VirtualSugarSamplerFromStringListCOP

typedef utility::pointer::owning_ptr < StepWiseRNA_VirtualSugarUtil >	StepWiseRNA_VirtualSugarUtilOP

typedef utility::pointer::owning_ptr < StepWiseRNA_VirtualSugarUtil const >	StepWiseRNA_VirtualSugarUtilCOP

typedef utility::pointer::owning_ptr < SugarInstantiateMover >	SugarInstantiateMoverOP

typedef utility::pointer::owning_ptr < SugarInstantiateMover const >	SugarInstantiateMoverCOP

typedef utility::pointer::owning_ptr < SugarModeling >	SugarModelingOP

typedef utility::pointer::owning_ptr < SugarModeling const >	SugarModelingCOP

typedef utility::pointer::owning_ptr < SugarVirtualizeMover >	SugarVirtualizeMoverOP

typedef utility::pointer::owning_ptr < SugarVirtualizeMover const >	SugarVirtualizeMoverCOP

Functions
bool	is_sugar_virtual (pose::Pose const &pose, Size const &n)

void	minimize_all_sampled_floating_bases (core::pose::Pose &viewer_pose, utility::vector1< SugarModeling > const &modeling_list, utility::vector1< PoseOP > &pose_data_list, core::scoring::ScoreFunctionOP const &scorefxn, StepWiseRNA_JobParametersCOP const &job_parameters_, bool const virtual_sugar_is_from_prior_step_)

bool	is_sugar_virtual (core::pose::Pose const &pose, core::Size const sugar_res, core::Size const bulge_res)

bool	is_sugar_virtual (core::pose::Pose const &pose, core::Size const sugar_res, core::Size const bulge_res, utility::vector1< Size > &bulge_residues_to_virtualize)

void	sampling_starting_pose_data_list (utility::vector1< PoseOP > &starting_pose_data_list, utility::vector1< SugarModeling > const &sugar_modeling_list, core::pose::Pose const &pose)

std::map< core::Size, core::Size >	get_res_map (SugarModeling const &sugar_modeling)

void	copy_bulge_res_and_sugar_torsion (SugarModeling const &sugar_modeling, core::pose::Pose &pose, core::pose::Pose const &template_pose, bool instantiate_sugar)

std::map< Size, Size > const	get_reference_res_for_each_virtual_sugar (pose::Pose const &pose, bool const check_for_non_jump, Size const moving_suite)

std::map< Size, Size > const	get_reference_res_for_each_virtual_sugar_without_fold_tree (pose::Pose const &pose, Size const moving_suite)

Size	look_for_non_jump_reference_to_previous (Size const virtual_sugar_res, pose::Pose const &pose, Size const moving_suite)

Size	look_for_non_jump_reference_to_next (Size const virtual_sugar_res, pose::Pose const &pose, Size const moving_suite)

utility::vector1< Size >	get_possible_reference_res_list_from_pose_without_fold_tree (Size const virtual_sugar_res, pose::Pose const &pose, Size const moving_suite)

std::map< Size, Size > const	get_reference_res_for_each_virtual_sugar_based_on_fold_tree (pose::Pose const &pose)

Size	look_for_jumps (Size const n, pose::Pose const &pose, bool const force_upstream)

Size	look_for_jumps_to_previous (Size const virtual_sugar_res, pose::Pose const &pose, bool const force_upstream)

Size	look_for_jumps_to_next (Size const virtual_sugar_res, pose::Pose const &pose, bool const force_upstream)

rotamer_sampler::copy_dofs::ResidueAlternativeSetOP	convert_sugar_modeling_to_residue_alternative_set (SugarModeling const &sugar_modeling)

Typedef Documentation

typedef utility::pointer::owning_ptr< StepWiseRNA_VirtualSugarJustInTimeInstantiator const > protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiatorCOP

typedef utility::pointer::owning_ptr< StepWiseRNA_VirtualSugarJustInTimeInstantiator > protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOP

typedef utility::pointer::owning_ptr< StepWiseRNA_VirtualSugarSamplerFromStringList const > protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringListCOP

typedef utility::pointer::owning_ptr< StepWiseRNA_VirtualSugarSamplerFromStringList > protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringListOP

typedef utility::pointer::owning_ptr< StepWiseRNA_VirtualSugarUtil const > protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarUtilCOP

typedef utility::pointer::owning_ptr< StepWiseRNA_VirtualSugarUtil > protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarUtilOP

typedef utility::pointer::owning_ptr< SugarInstantiateMover const > protocols::stepwise::sampling::rna::sugar::SugarInstantiateMoverCOP

typedef utility::pointer::owning_ptr< SugarInstantiateMover > protocols::stepwise::sampling::rna::sugar::SugarInstantiateMoverOP

typedef utility::pointer::owning_ptr< SugarModeling const > protocols::stepwise::sampling::rna::sugar::SugarModelingCOP

typedef utility::pointer::owning_ptr< SugarModeling > protocols::stepwise::sampling::rna::sugar::SugarModelingOP

typedef utility::pointer::owning_ptr< SugarVirtualizeMover const > protocols::stepwise::sampling::rna::sugar::SugarVirtualizeMoverCOP

typedef utility::pointer::owning_ptr< SugarVirtualizeMover > protocols::stepwise::sampling::rna::sugar::SugarVirtualizeMoverOP

Function Documentation

rotamer_sampler::copy_dofs::ResidueAlternativeSetOP protocols::stepwise::sampling::rna::sugar::convert_sugar_modeling_to_residue_alternative_set ( SugarModeling const & sugar_modeling )

References get_res_map(), protocols::stepwise::sampling::rna::sugar::SugarModeling::moving_res, and protocols::stepwise::sampling::rna::sugar::SugarModeling::pose_list.

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::get_sugar_modeling_set().

void protocols::stepwise::sampling::rna::sugar::copy_bulge_res_and_sugar_torsion	(	SugarModeling const &	sugar_modeling,
		core::pose::Pose &	pose,
		core::pose::Pose const &	template_pose,
		bool	instantiate_sugar
	)

References copy_dofs_match_atom_names(), get_res_map(), core::conformation::Residue::has_variant_type(), protocols::stepwise::sampling::rna::sugar::SugarModeling::moving_res, core::pose::Pose::residue(), and runtime_assert.

Referenced by protocols::stepwise::screener::AnchorSugarScreener::check_screen(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_poses_and_stubs_and_checkers(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::initialize_poses_and_stubs_and_checkers(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::instantiate_sugar(), protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::instantiate_sugar(), sampling_starting_pose_data_list(), and protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::screen_anchor_sugar_conformation().

utility::vector1< Size > protocols::stepwise::sampling::rna::sugar::get_possible_reference_res_list_from_pose_without_fold_tree	(	Size const	virtual_sugar_res,
		pose::Pose const &	pose,
		Size const	moving_suite
	)

References core::pose::Pose::fold_tree(), look_for_jumps_to_next(), look_for_jumps_to_previous(), look_for_non_jump_reference_to_next(), look_for_non_jump_reference_to_previous(), and protocols::TR.

Referenced by get_reference_res_for_each_virtual_sugar_without_fold_tree().

std::map< Size, Size > const protocols::stepwise::sampling::rna::sugar::get_reference_res_for_each_virtual_sugar	(	pose::Pose const &	pose,
		bool const	check_for_non_jump,
		Size const	moving_suite
	)

References get_reference_res_for_each_virtual_sugar_based_on_fold_tree(), and get_reference_res_for_each_virtual_sugar_without_fold_tree().

std::map< Size, Size > const protocols::stepwise::sampling::rna::sugar::get_reference_res_for_each_virtual_sugar_based_on_fold_tree ( pose::Pose const & pose )

References core::conformation::Residue::has_variant_type(), look_for_jumps(), core::pose::Pose::residue(), runtime_assert, and core::pose::Pose::total_residue().

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

std::map< Size, Size > const protocols::stepwise::sampling::rna::sugar::get_reference_res_for_each_virtual_sugar_without_fold_tree	(	pose::Pose const &	pose,
		Size const	moving_suite
	)

References get_possible_reference_res_list_from_pose_without_fold_tree(), core::conformation::Residue::has_variant_type(), core::pose::Pose::residue(), runtime_assert, size(), core::pose::Pose::total_residue(), protocols::TR, and virtual_sugar_res.

Referenced by get_reference_res_for_each_virtual_sugar(), and protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::update_fold_tree_at_virtual_sugars().

std::map< core::Size, core::Size > protocols::stepwise::sampling::rna::sugar::get_res_map ( SugarModeling const & sugar_modeling )

References protocols::stepwise::sampling::rna::sugar::SugarModeling::bulge_res, protocols::stepwise::sampling::rna::sugar::SugarModeling::moving_res, and protocols::stepwise::sampling::rna::sugar::SugarModeling::reference_res.

Referenced by convert_sugar_modeling_to_residue_alternative_set(), and copy_bulge_res_and_sugar_torsion().

bool protocols::stepwise::sampling::rna::sugar::is_sugar_virtual	(	core::pose::Pose const &	pose,
		core::Size const	sugar_res,
		core::Size const	bulge_res
	)

References is_sugar_virtual().

bool protocols::stepwise::sampling::rna::sugar::is_sugar_virtual	(	core::pose::Pose const &	pose,
		core::Size const	sugar_res,
		core::Size const	bulge_res,
		utility::vector1< Size > &	bulge_residues_to_virtualize
	)

References core::conformation::Residue::has_variant_type(), nres, core::pose::Pose::residue(), runtime_assert, core::pose::Pose::total_residue(), protocols::TR, and utility_exit_with_message.

bool protocols::stepwise::sampling::rna::sugar::is_sugar_virtual	(	pose::Pose const &	pose,
		Size const &	n
	)

References core::conformation::Residue::has_variant_type(), and core::pose::Pose::residue().

Referenced by is_sugar_virtual(), and protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::setup_sugar_modeling().

Size protocols::stepwise::sampling::rna::sugar::look_for_jumps	(	Size const	n,
		pose::Pose const &	pose,
		bool const	force_upstream
	)

References look_for_jumps_to_next(), look_for_jumps_to_previous(), and runtime_assert.

Referenced by get_reference_res_for_each_virtual_sugar_based_on_fold_tree().

Size protocols::stepwise::sampling::rna::sugar::look_for_jumps_to_next	(	Size const	virtual_sugar_res,
		pose::Pose const &	pose,
		bool const	force_upstream
	)

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::jump_nr(), jump_nr, core::pose::Pose::total_residue(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by get_possible_reference_res_list_from_pose_without_fold_tree(), and look_for_jumps().

Size protocols::stepwise::sampling::rna::sugar::look_for_jumps_to_previous	(	Size const	virtual_sugar_res,
		pose::Pose const &	pose,
		bool const	force_upstream
	)

References core::pose::Pose::fold_tree(), jump_nr, core::kinematics::FoldTree::jump_nr(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by get_possible_reference_res_list_from_pose_without_fold_tree(), and look_for_jumps().

Size protocols::stepwise::sampling::rna::sugar::look_for_non_jump_reference_to_next	(	Size const	virtual_sugar_res,
		pose::Pose const &	pose,
		Size const	moving_suite
	)

References core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by get_possible_reference_res_list_from_pose_without_fold_tree().

Size protocols::stepwise::sampling::rna::sugar::look_for_non_jump_reference_to_previous	(	Size const	virtual_sugar_res,
		pose::Pose const &	pose,
		Size const	moving_suite
	)

References core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), and core::pose::Pose::residue().

Referenced by get_possible_reference_res_list_from_pose_without_fold_tree().

void protocols::stepwise::sampling::rna::sugar::minimize_all_sampled_floating_bases	(	core::pose::Pose &	viewer_pose,
		utility::vector1< SugarModeling > const &	modeling_list,
		utility::vector1< PoseOP > &	pose_data_list,
		core::scoring::ScoreFunctionOP const &	scorefxn,
		StepWiseRNA_JobParametersCOP const &	job_parameters_,
		bool const	virtual_sugar_is_from_prior_step_
	)

References protocols::stepwise::sampling::rna::sugar::SugarModeling::bulge_res, protocols::stepwise::sampling::rna::get_sampling_scorefxn(), utility::vector1< T, class >::has_value(), core::conformation::Residue::has_variant_type(), minimizer, core::optimization::MinimizerOptions::nblist_auto_update(), options, protocols::stepwise::sampling::rna::output_title_text(), core::pose::Pose::residue(), core::kinematics::MoveMap::set_bb(), and protocols::TR.

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

void protocols::stepwise::sampling::rna::sugar::sampling_starting_pose_data_list	(	utility::vector1< PoseOP > &	starting_pose_data_list,
		utility::vector1< SugarModeling > const &	sugar_modeling_list,
		core::pose::Pose const &	pose
	)

References core::pose::Pose::clone(), copy_bulge_res_and_sugar_torsion(), protocols::stepwise::sampling::rna::sugar::SugarModeling::moving_res, protocols::stepwise::sampling::rna::sugar::SugarModeling::pose_list, tag_from_pose(), and tag_into_pose().

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

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Functions

Typedef Documentation

Function Documentation