protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection Class Reference

#include <StepWiseRNA_PoseSelection.hh>

Public Member Functions
	StepWiseRNA_PoseSelection (protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP &working_parameters, core::scoring::ScoreFunctionCOP scorefxn, protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct &count_data=local_count_data)
	~StepWiseRNA_PoseSelection ()
void	initialize_modeler_scorefxn (core::scoring::ScoreFunctionCOP &scorefxn)
Real	pose_selection_by_full_score (pose::Pose &current_pose, std::string const &tag)
void	cluster_pose_list ()
void	set_num_pose_kept (core::Size const &num_pose_kept)
void	set_cluster_rmsd (core::Real const &setting)
void	set_distinguish_pucker (bool const &setting)
void	set_PBP_clustering_at_chain_closure (bool const &setting)
void	update_pose_list (std::string const &tag, pose::Pose const &current_pose, Real const &current_score)
utility::vector1< pose::PoseOP >	pose_list ()
void	set_pose_list (utility::vector1< pose::PoseOP > &pose_list)
void	finalize (bool const do_clustering=true)
void	set_count_data (protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct &setting)

Private Attributes
protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP	working_parameters_
core::scoring::ScoreFunctionOP	modeler_scorefxn_
Size	num_pose_kept_
Size const	multiplier_
core::Real	cluster_rmsd_
bool	PBP_clustering_at_chain_closure_
bool	distinguish_pucker_
core::Real	current_score_cutoff_
bool	verbose_
protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct &	count_data_
utility::vector1< pose::PoseOP >	pose_list_

Constructor & Destructor Documentation

protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::StepWiseRNA_PoseSelection	(	protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP &	working_parameters,
		core::scoring::ScoreFunctionCOP	scorefxn,
		protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct &	count_data = local_count_data
	)

References initialize_modeler_scorefxn().

protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::~StepWiseRNA_PoseSelection

(

)

Member Function Documentation

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::cluster_pose_list

(

)

References cluster_rmsd_, current_score_cutoff_, distinguish_pucker_, protocols::stepwise::legacy::modeler::rna::get_residue_pucker_state(), protocols::stepwise::legacy::modeler::rna::is_same_sugar_pucker(), num_pose_kept_, output_boolean(), PBP_clustering_at_chain_closure_, protocols::stepwise::modeler::rna::phosphate_base_phosphate_rmsd(), pose_list_, protocols::stepwise::modeler::rna::print_sugar_pucker_state(), rmsd, protocols::stepwise::modeler::rna::suite_rmsd(), tag_from_pose(), total_energy_from_pose(), protocols::TR, verbose_, and working_parameters_.

Referenced by finalize(), and pose_selection_by_full_score().

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::finalize

(

bool const

do_clustering = true

)

References cluster_pose_list(), num_pose_kept_, pose_list_, and sort_pose_by_score().

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::initialize_modeler_scorefxn

(

core::scoring::ScoreFunctionCOP &

scorefxn

)

References protocols::stepwise::modeler::rna::get_modeler_scorefxn(), and modeler_scorefxn_.

Referenced by StepWiseRNA_PoseSelection().

utility::vector1< pose::PoseOP > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::pose_list

(

)

References pose_list_.

Referenced by set_pose_list().

Real protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::pose_selection_by_full_score	(	pose::Pose &	current_pose,
		std::string const &	tag
	)

References cluster_pose_list(), count_data_, protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct::full_score_count, multiplier_, num_pose_kept_, pose_list_, sort_pose_by_score(), protocols::TR, and update_pose_list().

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::set_cluster_rmsd

(

core::Real const &

setting

)

References cluster_rmsd_, and protocols::TR.

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::set_count_data ( protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct &  setting )

inline

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::set_distinguish_pucker ( bool const &  setting )

inline

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::set_num_pose_kept

(

core::Size const &

num_pose_kept

)

References num_pose_kept_.

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::set_PBP_clustering_at_chain_closure ( bool const &  setting )

inline

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::set_pose_list

(

utility::vector1< pose::PoseOP > &

pose_list

)

References pose_list(), and pose_list_.

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::update_pose_list	(	std::string const &	tag,
		pose::Pose const &	current_pose,
		Real const &	current_score
	)

References core::pose::Pose::clone(), current_score_cutoff_, pose_list_, protocols::TR, and verbose_.

Referenced by pose_selection_by_full_score().

Member Data Documentation

core::Real protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::cluster_rmsd_

private

Referenced by cluster_pose_list(), and set_cluster_rmsd().

protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct& protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::count_data_

private

Referenced by pose_selection_by_full_score().

core::Real protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::current_score_cutoff_

private

Referenced by cluster_pose_list(), and update_pose_list().

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::distinguish_pucker_

private

Referenced by cluster_pose_list().

core::scoring::ScoreFunctionOP protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::modeler_scorefxn_

private

Referenced by initialize_modeler_scorefxn().

Size const protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::multiplier_

private

Referenced by pose_selection_by_full_score().

Size protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::num_pose_kept_

private

Referenced by cluster_pose_list(), finalize(), pose_selection_by_full_score(), and set_num_pose_kept().

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::PBP_clustering_at_chain_closure_

private

Referenced by cluster_pose_list().

utility::vector1< pose::PoseOP > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::pose_list_

private

Referenced by cluster_pose_list(), finalize(), pose_list(), pose_selection_by_full_score(), set_pose_list(), and update_pose_list().

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::verbose_

private

Referenced by cluster_pose_list(), and update_pose_list().

protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::working_parameters_

private

Referenced by cluster_pose_list().

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

• src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_PoseSelection.hh
• src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_PoseSelection.cc