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protocols::swa::StepWiseClusterer Class Reference

#include <StepWiseClusterer.hh>

Inheritance diagram for protocols::swa::StepWiseClusterer:
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Collaboration diagram for protocols::swa::StepWiseClusterer:
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Public Member Functions

 StepWiseClusterer (utility::vector1< std::string > const &silent_files_in)
 
 StepWiseClusterer (std::string const &silent_file_in)
 
 StepWiseClusterer (core::io::silent::SilentFileDataOP &sfd)
 
virtual ~StepWiseClusterer ()
 
void set_max_decoys (core::Size const &setting)
 Filter a list of poses by score. More...
 
void set_cluster_radius (core::Real const &setting)
 
void set_cluster_by_all_atom_rmsd (core::Real const &setting)
 
void set_rename_tags (core::Real const &setting)
 
void set_score_diff_cut (core::Real const &setting)
 
void set_auto_tune (bool const auto_tune)
 
void set_force_align (bool const force_align)
 
void set_calc_rms_res (utility::vector1< core::Size > const &calc_rms_res)
 
void set_silent_file_data (core::io::silent::SilentFileDataOP &sfd)
 
void set_rsd_type_set (std::string const &setting)
 
void cluster ()
 
core::io::silent::SilentFileDataOP silent_file_data ()
 
void output_silent_file (std::string const &silent_file)
 
PoseList clustered_pose_list ()
 
utility::vector1
< core::io::silent::SilentStructOP > & 
silent_struct_output_list ()
 

Private Member Functions

void initialize_parameters_and_input ()
 
void initialize_cluster_list ()
 
void initialize_corresponding_atom_id_map (core::pose::Pose const &pose)
 
void do_some_clustering ()
 
Size check_for_closeness (core::pose::PoseOP const &pose_op)
 
void cluster_with_auto_tune ()
 
void recluster_current_pose_list ()
 
void initialize_auto_tune_cluster_rmsds ()
 

Private Attributes

utility::vector1< std::string > silent_files_
 
Size max_decoys_
 
core::Real cluster_radius_
 
bool cluster_by_all_atom_rmsd_
 
core::Real score_diff_cut_
 
bool auto_tune_
 
bool rename_tags_
 
bool force_align_
 
std::string rsd_type_set_
 
core::Real score_min_
 
bool score_min_defined_
 
utility::vector1
< core::pose::PoseOP
pose_output_list_
 
utility::vector1< std::string > tag_output_list_
 
utility::vector1
< core::io::silent::SilentStructOP
silent_struct_output_list_
 
utility::vector1< core::Sizenum_pose_in_cluster_
 
core::import_pose::pose_stream::SilentFilePoseInputStreamOP input_
 
utility::vector1< core::Realcluster_rmsds_to_try_with_auto_tune_
 
bool hit_score_cutoff_
 
bool initialized_atom_id_map_for_rmsd_
 
utility::vector1< core::Sizecalc_rms_res_
 
std::map< core::id::AtomID,
core::id::AtomID
corresponding_atom_id_map_
 
core::chemical::ResidueTypeSetCAP rsd_set_
 

Constructor & Destructor Documentation

protocols::swa::StepWiseClusterer::StepWiseClusterer ( utility::vector1< std::string > const &  silent_files_in)
protocols::swa::StepWiseClusterer::StepWiseClusterer ( std::string const &  silent_file_in)
protocols::swa::StepWiseClusterer::StepWiseClusterer ( core::io::silent::SilentFileDataOP sfd)
protocols::swa::StepWiseClusterer::~StepWiseClusterer ( )
virtual

Member Function Documentation

Size protocols::swa::StepWiseClusterer::check_for_closeness ( core::pose::PoseOP const &  pose_op)
private
void protocols::swa::StepWiseClusterer::cluster ( )
void protocols::swa::StepWiseClusterer::cluster_with_auto_tune ( )
private
PoseList protocols::swa::StepWiseClusterer::clustered_pose_list ( )
void protocols::swa::StepWiseClusterer::do_some_clustering ( )
private
void protocols::swa::StepWiseClusterer::initialize_auto_tune_cluster_rmsds ( )
private
void protocols::swa::StepWiseClusterer::initialize_cluster_list ( )
private
void protocols::swa::StepWiseClusterer::initialize_corresponding_atom_id_map ( core::pose::Pose const &  pose)
private
void protocols::swa::StepWiseClusterer::initialize_parameters_and_input ( )
private
void protocols::swa::StepWiseClusterer::output_silent_file ( std::string const &  silent_file)
void protocols::swa::StepWiseClusterer::recluster_current_pose_list ( )
private

References core::TR().

void protocols::swa::StepWiseClusterer::set_auto_tune ( bool const  auto_tune)
inline

References auto_tune_.

void protocols::swa::StepWiseClusterer::set_calc_rms_res ( utility::vector1< core::Size > const &  calc_rms_res)
void protocols::swa::StepWiseClusterer::set_cluster_by_all_atom_rmsd ( core::Real const &  setting)
inline
void protocols::swa::StepWiseClusterer::set_cluster_radius ( core::Real const &  setting)
inline
void protocols::swa::StepWiseClusterer::set_force_align ( bool const  force_align)
inline

References force_align_.

void protocols::swa::StepWiseClusterer::set_max_decoys ( core::Size const &  setting)
inline

Filter a list of poses by score.

References max_decoys_.

Referenced by protocols::swa::protein::generate_beta_database_test().

void protocols::swa::StepWiseClusterer::set_rename_tags ( core::Real const &  setting)
inline
void protocols::swa::StepWiseClusterer::set_rsd_type_set ( std::string const &  setting)
inline

References rsd_type_set_.

void protocols::swa::StepWiseClusterer::set_score_diff_cut ( core::Real const &  setting)
inline
void protocols::swa::StepWiseClusterer::set_silent_file_data ( core::io::silent::SilentFileDataOP sfd)
core::io::silent::SilentFileDataOP protocols::swa::StepWiseClusterer::silent_file_data ( )
utility::vector1< core::io::silent::SilentStructOP >& protocols::swa::StepWiseClusterer::silent_struct_output_list ( )
inline

Member Data Documentation

bool protocols::swa::StepWiseClusterer::auto_tune_
private

Referenced by set_auto_tune().

utility::vector1< core::Size > protocols::swa::StepWiseClusterer::calc_rms_res_
private
bool protocols::swa::StepWiseClusterer::cluster_by_all_atom_rmsd_
private
core::Real protocols::swa::StepWiseClusterer::cluster_radius_
private

Referenced by set_cluster_radius().

utility::vector1< core::Real > protocols::swa::StepWiseClusterer::cluster_rmsds_to_try_with_auto_tune_
private
std::map< core::id::AtomID, core::id::AtomID > protocols::swa::StepWiseClusterer::corresponding_atom_id_map_
private
bool protocols::swa::StepWiseClusterer::force_align_
private

Referenced by set_force_align().

bool protocols::swa::StepWiseClusterer::hit_score_cutoff_
private
bool protocols::swa::StepWiseClusterer::initialized_atom_id_map_for_rmsd_
private
core::import_pose::pose_stream::SilentFilePoseInputStreamOP protocols::swa::StepWiseClusterer::input_
private
Size protocols::swa::StepWiseClusterer::max_decoys_
private

Referenced by set_max_decoys().

utility::vector1< core::Size > protocols::swa::StepWiseClusterer::num_pose_in_cluster_
private
utility::vector1< core::pose::PoseOP > protocols::swa::StepWiseClusterer::pose_output_list_
private
bool protocols::swa::StepWiseClusterer::rename_tags_
private

Referenced by set_rename_tags().

core::chemical::ResidueTypeSetCAP protocols::swa::StepWiseClusterer::rsd_set_
private
std::string protocols::swa::StepWiseClusterer::rsd_type_set_
private

Referenced by set_rsd_type_set().

core::Real protocols::swa::StepWiseClusterer::score_diff_cut_
private

Referenced by set_score_diff_cut().

core::Real protocols::swa::StepWiseClusterer::score_min_
private
bool protocols::swa::StepWiseClusterer::score_min_defined_
private
utility::vector1< std::string > protocols::swa::StepWiseClusterer::silent_files_
private
utility::vector1< core::io::silent::SilentStructOP > protocols::swa::StepWiseClusterer::silent_struct_output_list_
private
utility::vector1< std::string > protocols::swa::StepWiseClusterer::tag_output_list_
private

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