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protocols::stepwise::modeler::align::StepWiseClusterer Class Reference

#include <StepWiseClusterer.hh>

Inheritance diagram for protocols::stepwise::modeler::align::StepWiseClusterer:
Inheritance graph
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Public Member Functions

 StepWiseClusterer ()
 
 StepWiseClusterer (options::StepWiseModelerOptionsCOP options)
 
 ~StepWiseClusterer () override
 
void cluster ()
 
core::Size size () const
 
void set_max_decoys (core::Size const &setting)
 
void set_pose_list (utility::vector1< core::pose::PoseOP > const &setting)
 
utility::vector1
< core::pose::PoseOP
pose_list ()
 
void set_calc_rms_res (utility::vector1< core::Size > const &setting)
 
void set_silent_file (std::string const &setting)
 
void set_do_checks (core::Size const &setting)
 
void set_assume_atom_ids_invariant (core::Size const &setting)
 
void apply (core::pose::Pose const &pose)
 
core::Real cluster_rmsd () const
 

Private Member Functions

void initialize_parameters (core::pose::Pose const &pose)
 
void sort_pose_list ()
 
bool check_screen_and_kick_out_displaced_model (core::pose::Pose const &pose)
 
void kick_out_pose_at_idx (core::Size const n)
 
bool check_for_closeness (core::pose::Pose const &pose1, core::pose::Pose const &pose2)
 

Private Attributes

utility::vector1
< core::pose::PoseOP
pose_list_
 
utility::vector1< core::Sizecalc_rms_res_
 
core::Size max_decoys_
 
core::Real rmsd_
 
core::Real cluster_rmsd_
 
core::Real score_diff_cut_
 
bool do_checks_
 
bool assume_atom_ids_invariant_
 
bool initialized_
 
core::Size count_
 
core::Real cluster_size_
 
bool output_cluster_size_
 
std::string silent_file_
 
StepWisePoseAlignerOP pose_aligner_
 

Constructor & Destructor Documentation

protocols::stepwise::modeler::align::StepWiseClusterer::StepWiseClusterer ( )
protocols::stepwise::modeler::align::StepWiseClusterer::StepWiseClusterer ( options::StepWiseModelerOptionsCOP  options)
protocols::stepwise::modeler::align::StepWiseClusterer::~StepWiseClusterer ( )
overridedefault

Member Function Documentation

void protocols::stepwise::modeler::align::StepWiseClusterer::apply ( core::pose::Pose const &  pose)
bool protocols::stepwise::modeler::align::StepWiseClusterer::check_for_closeness ( core::pose::Pose const &  pose1,
core::pose::Pose const &  pose2 
)
private
bool protocols::stepwise::modeler::align::StepWiseClusterer::check_screen_and_kick_out_displaced_model ( core::pose::Pose const &  pose)
private
void protocols::stepwise::modeler::align::StepWiseClusterer::cluster ( )
core::Real protocols::stepwise::modeler::align::StepWiseClusterer::cluster_rmsd ( ) const
inline
void protocols::stepwise::modeler::align::StepWiseClusterer::initialize_parameters ( core::pose::Pose const &  pose)
private
void protocols::stepwise::modeler::align::StepWiseClusterer::kick_out_pose_at_idx ( core::Size const  n)
private
utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::align::StepWiseClusterer::pose_list ( )
inline
void protocols::stepwise::modeler::align::StepWiseClusterer::set_assume_atom_ids_invariant ( core::Size const &  setting)
inline
void protocols::stepwise::modeler::align::StepWiseClusterer::set_calc_rms_res ( utility::vector1< core::Size > const &  setting)
inline
void protocols::stepwise::modeler::align::StepWiseClusterer::set_do_checks ( core::Size const &  setting)
inline

References do_checks_.

void protocols::stepwise::modeler::align::StepWiseClusterer::set_max_decoys ( core::Size const &  setting)
inline
void protocols::stepwise::modeler::align::StepWiseClusterer::set_pose_list ( utility::vector1< core::pose::PoseOP > const &  setting)
inline
void protocols::stepwise::modeler::align::StepWiseClusterer::set_silent_file ( std::string const &  setting)
inline

References silent_file_.

core::Size protocols::stepwise::modeler::align::StepWiseClusterer::size ( ) const
inline
void protocols::stepwise::modeler::align::StepWiseClusterer::sort_pose_list ( )
private

References pose_list_, and core::pose::sort_pose_by_score().

Referenced by apply(), and cluster().

Member Data Documentation

bool protocols::stepwise::modeler::align::StepWiseClusterer::assume_atom_ids_invariant_
private
utility::vector1< core::Size > protocols::stepwise::modeler::align::StepWiseClusterer::calc_rms_res_
private
core::Real protocols::stepwise::modeler::align::StepWiseClusterer::cluster_rmsd_
private
core::Real protocols::stepwise::modeler::align::StepWiseClusterer::cluster_size_
private
core::Size protocols::stepwise::modeler::align::StepWiseClusterer::count_
private

Referenced by apply().

bool protocols::stepwise::modeler::align::StepWiseClusterer::do_checks_
private
bool protocols::stepwise::modeler::align::StepWiseClusterer::initialized_
private

Referenced by initialize_parameters().

core::Size protocols::stepwise::modeler::align::StepWiseClusterer::max_decoys_
private
bool protocols::stepwise::modeler::align::StepWiseClusterer::output_cluster_size_
private
StepWisePoseAlignerOP protocols::stepwise::modeler::align::StepWiseClusterer::pose_aligner_
private

Referenced by check_for_closeness().

utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::align::StepWiseClusterer::pose_list_
private
core::Real protocols::stepwise::modeler::align::StepWiseClusterer::rmsd_
private

Referenced by check_for_closeness().

core::Real protocols::stepwise::modeler::align::StepWiseClusterer::score_diff_cut_
private
std::string protocols::stepwise::modeler::align::StepWiseClusterer::silent_file_
private

Referenced by apply(), and set_silent_file().


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