protocols::stepwise::modeler::rna::sugar Namespace Reference

Classes
class	SugarInstantiateMover
class	SugarModeling
class	SugarVirtualizeMover
class	VirtualSugarJustInTimeInstantiator
class	VirtualSugarSampler
class	VirtualSugarSamplerFromStringList

Typedefs
typedef utility::pointer::shared_ptr< SugarInstantiateMover >	SugarInstantiateMoverOP
typedef utility::pointer::shared_ptr< SugarInstantiateMover const >	SugarInstantiateMoverCOP
typedef utility::pointer::shared_ptr< SugarModeling >	SugarModelingOP
typedef utility::pointer::shared_ptr< SugarModeling const >	SugarModelingCOP
typedef utility::pointer::shared_ptr< SugarVirtualizeMover >	SugarVirtualizeMoverOP
typedef utility::pointer::shared_ptr< SugarVirtualizeMover const >	SugarVirtualizeMoverCOP
typedef utility::pointer::shared_ptr< VirtualSugarJustInTimeInstantiator >	VirtualSugarJustInTimeInstantiatorOP
typedef utility::pointer::shared_ptr< VirtualSugarJustInTimeInstantiator const >	VirtualSugarJustInTimeInstantiatorCOP
typedef utility::pointer::shared_ptr< VirtualSugarSamplerFromStringList >	VirtualSugarSamplerFromStringListOP
typedef utility::pointer::shared_ptr< VirtualSugarSamplerFromStringList const >	VirtualSugarSamplerFromStringListCOP

Functions
void	minimize_all_sampled_floating_bases (core::pose::Pose &, utility::vector1< SugarModeling > const &modeling_list, utility::vector1< PoseOP > &pose_data_list, core::scoring::ScoreFunctionCOP const &scorefxn, working_parameters::StepWiseWorkingParametersCOP const &working_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< core::Size > &bulge_residues_to_virtualize)
void	modeler_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< core::Size, core::Size > const	get_reference_res_for_each_virtual_sugar (pose::Pose const &pose, bool const check_for_non_jump, core::Size const moving_suite)
std::map< core::Size, core::Size > const	get_reference_res_for_each_virtual_sugar_without_fold_tree (pose::Pose const &pose, core::Size const moving_suite)
Size	look_for_non_jump_reference_to_previous (core::Size const virtual_sugar_res, pose::Pose const &pose, core::Size const moving_suite)
Size	look_for_non_jump_reference_to_next (core::Size const virtual_sugar_res, pose::Pose const &pose, core::Size const moving_suite)
utility::vector1< core::Size >	get_possible_reference_res_list_from_pose_without_fold_tree (core::Size const virtual_sugar_res, pose::Pose const &pose, core::Size const moving_suite)
std::map< core::Size, core::Size > const	get_reference_res_for_each_virtual_sugar_based_on_fold_tree (pose::Pose const &pose)
Size	get_reference_res_for_virtual_sugar_based_on_fold_tree (pose::Pose const &pose, core::Size const n)
Size	look_for_jumps (core::Size const n, pose::Pose const &pose, bool const force_upstream)
Size	look_for_jumps_to_previous (core::Size const virtual_sugar_res, pose::Pose const &pose, bool const force_upstream)
Size	look_for_jumps_to_next (core::Size const virtual_sugar_res, pose::Pose const &pose, bool const force_upstream)
sampler::copy_dofs::ResidueAlternativeSetOP	convert_sugar_modeling_to_residue_alternative_set (SugarModeling const &sugar_modeling)
VirtualSugarJustInTimeInstantiatorOP	instantiate_any_virtual_sugars (pose::Pose &pose, working_parameters::StepWiseWorkingParametersCOP working_parameters, core::scoring::ScoreFunctionCOP scorefxn, options::StepWiseModelerOptionsCOP options)
void	minimize_all_sampled_floating_bases (core::pose::Pose &viewer_pose, utility::vector1< SugarModeling > const &modeling_list, utility::vector1< core::pose::PoseOP > &pose_data_list, core::scoring::ScoreFunctionCOP const &modeler_scorefxn, working_parameters::StepWiseWorkingParametersCOP const &working_parameters, bool const virtual_sugar_is_from_prior_step=true)
void	modeler_starting_pose_data_list (utility::vector1< core::pose::PoseOP > &starting_pose_data_list, utility::vector1< SugarModeling > const &SugarModeling_list, core::pose::Pose const &pose)
bool	is_sugar_virtual (pose::Pose const &pose, core::Size const &n)

Typedef Documentation

SugarInstantiateMoverCOP

typedef utility::pointer::shared_ptr< SugarInstantiateMover const > protocols::stepwise::modeler::rna::sugar::SugarInstantiateMoverCOP

SugarInstantiateMoverOP

typedef utility::pointer::shared_ptr< SugarInstantiateMover > protocols::stepwise::modeler::rna::sugar::SugarInstantiateMoverOP

SugarModelingCOP

typedef utility::pointer::shared_ptr< SugarModeling const > protocols::stepwise::modeler::rna::sugar::SugarModelingCOP

SugarModelingOP

typedef utility::pointer::shared_ptr< SugarModeling > protocols::stepwise::modeler::rna::sugar::SugarModelingOP

SugarVirtualizeMoverCOP

typedef utility::pointer::shared_ptr< SugarVirtualizeMover const > protocols::stepwise::modeler::rna::sugar::SugarVirtualizeMoverCOP

SugarVirtualizeMoverOP

typedef utility::pointer::shared_ptr< SugarVirtualizeMover > protocols::stepwise::modeler::rna::sugar::SugarVirtualizeMoverOP

VirtualSugarJustInTimeInstantiatorCOP

typedef utility::pointer::shared_ptr< VirtualSugarJustInTimeInstantiator const > protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiatorCOP

VirtualSugarJustInTimeInstantiatorOP

typedef utility::pointer::shared_ptr< VirtualSugarJustInTimeInstantiator > protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiatorOP

VirtualSugarSamplerFromStringListCOP

typedef utility::pointer::shared_ptr< VirtualSugarSamplerFromStringList const > protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringListCOP

VirtualSugarSamplerFromStringListOP

typedef utility::pointer::shared_ptr< VirtualSugarSamplerFromStringList > protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringListOP

Function Documentation

convert_sugar_modeling_to_residue_alternative_set()

sampler::copy_dofs::ResidueAlternativeSetOP protocols::stepwise::modeler::rna::sugar::convert_sugar_modeling_to_residue_alternative_set

(

SugarModeling const &

sugar_modeling

)

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

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

copy_bulge_res_and_sugar_torsion()

void protocols::stepwise::modeler::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 core::pose::copydofs::copy_dofs_match_atom_names(), protocols::stepwise::modeler::get_res_map(), core::conformation::Residue::has_variant_type(), protocols::stepwise::modeler::rna::sugar::SugarModeling::moving_res, core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), and core::chemical::VIRTUAL_RIBOSE.

Referenced by protocols::stepwise::screener::AnchorSugarScreener::check_screen(), protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::instantiate_sugar(), and modeler_starting_pose_data_list().

get_possible_reference_res_list_from_pose_without_fold_tree()

utility::vector1< core::Size > protocols::stepwise::modeler::rna::sugar::get_possible_reference_res_list_from_pose_without_fold_tree	(	core::Size const	virtual_sugar_res,
		pose::Pose const &	pose,
		core::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 core::pose::TR().

Referenced by get_reference_res_for_each_virtual_sugar_without_fold_tree().

get_reference_res_for_each_virtual_sugar()

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

get_reference_res_for_each_virtual_sugar_based_on_fold_tree()

std::map< core::Size, core::Size > const protocols::stepwise::modeler::rna::sugar::get_reference_res_for_each_virtual_sugar_based_on_fold_tree

(

pose::Pose const &

pose

)

References get_reference_res_for_virtual_sugar_based_on_fold_tree(), core::conformation::Residue::has_variant_type(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::chemical::VIRTUAL_RIBOSE.

Referenced by get_reference_res_for_each_virtual_sugar().

get_reference_res_for_each_virtual_sugar_without_fold_tree()

std::map< core::Size, core::Size > const protocols::stepwise::modeler::rna::sugar::get_reference_res_for_each_virtual_sugar_without_fold_tree	(	pose::Pose const &	pose,
		core::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(), core::pose::Pose::size(), core::pose::TR(), and core::chemical::VIRTUAL_RIBOSE.

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

get_reference_res_for_virtual_sugar_based_on_fold_tree()

core::Size protocols::stepwise::modeler::rna::sugar::get_reference_res_for_virtual_sugar_based_on_fold_tree	(	pose::Pose const &	pose,
		core::Size const	n
	)

References look_for_jumps().

Referenced by get_reference_res_for_each_virtual_sugar_based_on_fold_tree(), and protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::setup_sugar_modeling().

get_res_map()

std::map< core::Size, core::Size > protocols::stepwise::modeler::rna::sugar::get_res_map

(

SugarModeling const &

sugar_modeling

)

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

instantiate_any_virtual_sugars()

VirtualSugarJustInTimeInstantiatorOP protocols::stepwise::modeler::rna::sugar::instantiate_any_virtual_sugars	(	pose::Pose &	pose,
		working_parameters::StepWiseWorkingParametersCOP	working_parameters,
		core::scoring::ScoreFunctionCOP	scorefxn,
		options::StepWiseModelerOptionsCOP	options
	)

Referenced by protocols::stepwise::modeler::StepWiseConnectionSampler::presample_virtual_sugars().

is_sugar_virtual() [1/3]

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

References is_sugar_virtual().

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

is_sugar_virtual() [2/3]

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

References core::conformation::Residue::has_variant_type(), core::pose::Pose::residue(), core::pose::Pose::size(), core::pose::TR(), core::chemical::VIRTUAL_RIBOSE, and core::chemical::VIRTUAL_RNA_RESIDUE.

Referenced by is_sugar_virtual().

is_sugar_virtual() [3/3]

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

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

look_for_jumps()

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

References core::pose::Pose::annotated_sequence(), core::pose::Pose::fold_tree(), look_for_jumps_to_next(), look_for_jumps_to_previous(), and core::pose::TR().

Referenced by get_reference_res_for_virtual_sugar_based_on_fold_tree().

look_for_jumps_to_next()

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

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

Referenced by get_possible_reference_res_list_from_pose_without_fold_tree(), and look_for_jumps().

look_for_jumps_to_previous()

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

References core::pose::Pose::fold_tree(), 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().

look_for_non_jump_reference_to_next()

core::Size protocols::stepwise::modeler::rna::sugar::look_for_non_jump_reference_to_next	(	core::Size const	virtual_sugar_res,
		pose::Pose const &	pose,
		core::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(), core::pose::Pose::size(), and core::chemical::VIRTUAL_RNA_RESIDUE.

Referenced by get_possible_reference_res_list_from_pose_without_fold_tree().

look_for_non_jump_reference_to_previous()

core::Size protocols::stepwise::modeler::rna::sugar::look_for_non_jump_reference_to_previous	(	core::Size const	virtual_sugar_res,
		pose::Pose const &	pose,
		core::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::chemical::VIRTUAL_RNA_RESIDUE.

Referenced by get_possible_reference_res_list_from_pose_without_fold_tree().

minimize_all_sampled_floating_bases() [1/2]

void protocols::stepwise::modeler::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::ScoreFunctionCOP const &	scorefxn,
		working_parameters::StepWiseWorkingParametersCOP const &	working_parameters_,
		bool const	virtual_sugar_is_from_prior_step_
	)

References core::pose::add_variant_type_to_pose_residue(), core::id::BB, core::id::CHI, protocols::stepwise::modeler::rna::get_modeler_scorefxn(), core::optimization::MinimizerOptions::nblist_auto_update(), protocols::stepwise::modeler::rna::output_title_text(), core::pose::remove_variant_type_from_pose_residue(), core::optimization::AtomTreeMinimizer::run(), core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::pose::TR(), viewer_pose, core::chemical::VIRTUAL_PHOSPHATE, and core::chemical::VIRTUAL_RNA_RESIDUE.

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

minimize_all_sampled_floating_bases() [2/2]

void protocols::stepwise::modeler::rna::sugar::minimize_all_sampled_floating_bases	(	core::pose::Pose &	viewer_pose,
		utility::vector1< SugarModeling > const &	modeling_list,
		utility::vector1< core::pose::PoseOP > &	pose_data_list,
		core::scoring::ScoreFunctionCOP const &	modeler_scorefxn,
		working_parameters::StepWiseWorkingParametersCOP const &	working_parameters,
		bool const	virtual_sugar_is_from_prior_step = true
	)

References core::pose::add_variant_type_to_pose_residue(), core::id::BB, core::id::CHI, protocols::stepwise::modeler::rna::get_modeler_scorefxn(), core::optimization::MinimizerOptions::nblist_auto_update(), protocols::stepwise::modeler::rna::output_title_text(), core::pose::remove_variant_type_from_pose_residue(), core::optimization::AtomTreeMinimizer::run(), core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::pose::TR(), viewer_pose, core::chemical::VIRTUAL_PHOSPHATE, and core::chemical::VIRTUAL_RNA_RESIDUE.

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

modeler_starting_pose_data_list() [1/2]

void protocols::stepwise::modeler::rna::sugar::modeler_starting_pose_data_list	(	utility::vector1< core::pose::PoseOP > &	starting_pose_data_list,
		utility::vector1< SugarModeling > const &	SugarModeling_list,
		core::pose::Pose const &	pose
	)

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

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

modeler_starting_pose_data_list() [2/2]

void protocols::stepwise::modeler::rna::sugar::modeler_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::modeler::rna::sugar::SugarModeling::moving_res, protocols::stepwise::modeler::rna::sugar::SugarModeling::pose_list, core::pose::remove_variant_type_from_pose_residue(), core::pose::tag_from_pose(), core::pose::tag_into_pose(), and core::chemical::VIRTUAL_RIBOSE.

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