protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection Class Reference

#include <StepWiseRNA_PoseSelection.hh>

Public Member Functions
	StepWiseRNA_PoseSelection (StepWiseRNA_JobParametersCOP &job_parameters, core::scoring::ScoreFunctionCOP scorefxn, StepWiseRNA_CountStruct &count_data=local_count_data)
	~StepWiseRNA_PoseSelection ()
void	initialize_sampling_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 (StepWiseRNA_CountStruct &setting)

Private Attributes
StepWiseRNA_JobParametersCOP	job_parameters_
core::scoring::ScoreFunctionOP	sampling_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_
StepWiseRNA_CountStruct &	count_data_
utility::vector1< pose::PoseOP >	pose_list_

Constructor & Destructor Documentation

protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::StepWiseRNA_PoseSelection	(	StepWiseRNA_JobParametersCOP &	job_parameters,
		core::scoring::ScoreFunctionCOP	scorefxn,
		StepWiseRNA_CountStruct &	count_data = local_count_data
	)

References initialize_sampling_scorefxn().

protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::~StepWiseRNA_PoseSelection

(

)

Member Function Documentation

void protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::cluster_pose_list

(

)

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

Referenced by finalize(), and pose_selection_by_full_score().

void protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::finalize

(

bool const

do_clustering = true

)

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

Referenced by protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::apply(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::apply(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler::apply(), protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler::apply(), and protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::apply().

void protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::initialize_sampling_scorefxn

(

core::scoring::ScoreFunctionCOP &

scorefxn

)

References protocols::stepwise::sampling::rna::get_sampling_scorefxn(), and sampling_scorefxn_.

Referenced by StepWiseRNA_PoseSelection().

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

(

)

References pose_list_.

Referenced by protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::apply(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::apply(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler::apply(), protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler::apply(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::apply(), and set_pose_list().

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

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

Referenced by protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::apply(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::apply(), and protocols::stepwise::screener::PoseSelectionScreener::check_screen().

void protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::set_cluster_rmsd

(

core::Real const &

setting

)

References cluster_rmsd_, and protocols::TR.

Referenced by protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::initialize_poses_and_checkers(), protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler::initialize_poses_and_checkers(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_poses_and_stubs_and_checkers(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler::initialize_poses_and_stubs_and_checkers(), and protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::initialize_poses_and_stubs_and_checkers().

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

inline

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

inline

Referenced by protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::initialize_poses_and_checkers(), protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler::initialize_poses_and_checkers(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_poses_and_stubs_and_checkers(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler::initialize_poses_and_stubs_and_checkers(), and protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::initialize_poses_and_stubs_and_checkers().

void protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::set_num_pose_kept

(

core::Size const &

num_pose_kept

)

References num_pose_kept_.

Referenced by protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::initialize_poses_and_checkers(), protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler::initialize_poses_and_checkers(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_poses_and_stubs_and_checkers(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler::initialize_poses_and_stubs_and_checkers(), and protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::initialize_poses_and_stubs_and_checkers().

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

inline

Referenced by protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::initialize_poses_and_checkers(), protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler::initialize_poses_and_checkers(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_poses_and_stubs_and_checkers(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler::initialize_poses_and_stubs_and_checkers(), and protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::initialize_poses_and_stubs_and_checkers().

void protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::set_pose_list

(

utility::vector1< pose::PoseOP > &

pose_list

)

References pose_list(), and pose_list_.

Referenced by protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::initialize_poses_and_checkers(), protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler::initialize_poses_and_checkers(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_poses_and_stubs_and_checkers(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler::initialize_poses_and_stubs_and_checkers(), and protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::initialize_poses_and_stubs_and_checkers().

void protocols::stepwise::sampling::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::sampling::rna::StepWiseRNA_PoseSelection::cluster_rmsd_

private

Referenced by cluster_pose_list(), and set_cluster_rmsd().

StepWiseRNA_CountStruct& protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::count_data_

private

Referenced by pose_selection_by_full_score().

core::Real protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::current_score_cutoff_

private

Referenced by cluster_pose_list(), and update_pose_list().

bool protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::distinguish_pucker_

private

Referenced by cluster_pose_list().

StepWiseRNA_JobParametersCOP protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::job_parameters_

private

Referenced by cluster_pose_list().

Size const protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::multiplier_

private

Referenced by pose_selection_by_full_score().

Size protocols::stepwise::sampling::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::sampling::rna::StepWiseRNA_PoseSelection::PBP_clustering_at_chain_closure_

private

Referenced by cluster_pose_list().

utility::vector1< pose::PoseOP > protocols::stepwise::sampling::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().

core::scoring::ScoreFunctionOP protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::sampling_scorefxn_

private

Referenced by initialize_sampling_scorefxn().

bool protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::verbose_

private

Referenced by cluster_pose_list(), and update_pose_list().

---

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

• symlinks/rosetta/src/protocols/stepwise/sampling/rna/StepWiseRNA_PoseSelection.hh
• symlinks/rosetta/src/protocols/stepwise/sampling/rna/StepWiseRNA_PoseSelection.cc