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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::Size > num_pose_in_cluster_
 
core::import_pose::pose_stream::SilentFilePoseInputStreamOP input_
 
utility::vector1< core::Real > cluster_rmsds_to_try_with_auto_tune_
 
bool hit_score_cutoff_
 
bool initialized_atom_id_map_for_rmsd_
 
utility::vector1< core::Size > calc_rms_res_
 
std::map< core::id::AtomID,
core::id::AtomID > 		corresponding_atom_id_map_
 
core::chemical::ResidueTypeSetCAP rsd_set_
 

Detailed Description

Definition at line 40 of file StepWiseClusterer.hh.

Constructor & Destructor Documentation

protocols::swa::StepWiseClusterer::StepWiseClusterer ( utility::vector1< std::string > const &  silent_files_in)

Definition at line 62 of file StepWiseClusterer.cc.

protocols::swa::StepWiseClusterer::StepWiseClusterer ( std::string const &  silent_file_in)

Definition at line 69 of file StepWiseClusterer.cc.

protocols::swa::StepWiseClusterer::StepWiseClusterer ( core::io::silent::SilentFileDataOP &  sfd)

Definition at line 79 of file StepWiseClusterer.cc.

protocols::swa::StepWiseClusterer::~StepWiseClusterer ( )
virtual

Definition at line 88 of file StepWiseClusterer.cc.

Member Function Documentation

Size protocols::swa::StepWiseClusterer::check_for_closeness ( core::pose::PoseOP const &  pose_op)
private

Definition at line 297 of file StepWiseClusterer.cc.

References core::scoring::rms_at_corresponding_atoms(), and core::scoring::rms_at_corresponding_atoms_no_super().

void protocols::swa::StepWiseClusterer::cluster ( )

Definition at line 118 of file StepWiseClusterer.cc.

References core::chemical::ChemicalManager::get_instance(), and core::chemical::ChemicalManager::residue_type_set().

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

void protocols::swa::StepWiseClusterer::cluster_with_auto_tune ( )
private

Definition at line 234 of file StepWiseClusterer.cc.

PoseList protocols::swa::StepWiseClusterer::clustered_pose_list ( )

Definition at line 366 of file StepWiseClusterer.cc.

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

void protocols::swa::StepWiseClusterer::do_some_clustering ( )
private

Definition at line 160 of file StepWiseClusterer.cc.

References core::pose::getPoseExtraScores(), protocols::swa::pdbslice(), and core::TR().

void protocols::swa::StepWiseClusterer::initialize_auto_tune_cluster_rmsds ( )
private

Definition at line 392 of file StepWiseClusterer.cc.

void protocols::swa::StepWiseClusterer::initialize_cluster_list ( )
private

Definition at line 219 of file StepWiseClusterer.cc.

void protocols::swa::StepWiseClusterer::initialize_corresponding_atom_id_map ( core::pose::Pose const &  pose)
private

Definition at line 146 of file StepWiseClusterer.cc.

References core::scoring::setup_matching_heavy_atoms(), and core::scoring::setup_matching_protein_backbone_heavy_atoms().

void protocols::swa::StepWiseClusterer::initialize_parameters_and_input ( )
private

Definition at line 93 of file StepWiseClusterer.cc.

void protocols::swa::StepWiseClusterer::output_silent_file ( std::string const &  silent_file)

Definition at line 328 of file StepWiseClusterer.cc.

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

void protocols::swa::StepWiseClusterer::recluster_current_pose_list ( )
private

Definition at line 262 of file StepWiseClusterer.cc.

References core::TR().

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

Definition at line 65 of file StepWiseClusterer.hh.

References auto_tune_.

void protocols::swa::StepWiseClusterer::set_calc_rms_res ( utility::vector1< core::Size > const &  calc_rms_res)

Definition at line 380 of file StepWiseClusterer.cc.

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

void protocols::swa::StepWiseClusterer::set_cluster_by_all_atom_rmsd ( core::Real const &  setting)
inline

Definition at line 59 of file StepWiseClusterer.hh.

References cluster_by_all_atom_rmsd_.

void protocols::swa::StepWiseClusterer::set_cluster_radius ( core::Real const &  setting)
inline

Definition at line 57 of file StepWiseClusterer.hh.

References cluster_radius_.

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

void protocols::swa::StepWiseClusterer::set_force_align ( bool const  force_align)
inline

Definition at line 67 of file StepWiseClusterer.hh.

References force_align_.

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

Filter a list of poses by score.

Definition at line 55 of file StepWiseClusterer.hh.

References max_decoys_.

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

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

Definition at line 61 of file StepWiseClusterer.hh.

References rename_tags_.

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

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

Definition at line 73 of file StepWiseClusterer.hh.

References rsd_type_set_.

void protocols::swa::StepWiseClusterer::set_score_diff_cut ( core::Real const &  setting)
inline

Definition at line 63 of file StepWiseClusterer.hh.

References score_diff_cut_.

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

void protocols::swa::StepWiseClusterer::set_silent_file_data ( core::io::silent::SilentFileDataOP &  sfd)

Definition at line 386 of file StepWiseClusterer.cc.

core::io::silent::SilentFileDataOP protocols::swa::StepWiseClusterer::silent_file_data ( )

Definition at line 353 of file StepWiseClusterer.cc.

References core::io::silent::SilentFileData::add_structure().

utility::vector1< core::io::silent::SilentStructOP >& protocols::swa::StepWiseClusterer::silent_struct_output_list ( )
inline

Definition at line 86 of file StepWiseClusterer.hh.

References silent_struct_output_list_.

Member Data Documentation

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

Definition at line 119 of file StepWiseClusterer.hh.

Referenced by set_auto_tune().

utility::vector1< core::Size > protocols::swa::StepWiseClusterer::calc_rms_res_
private

Definition at line 139 of file StepWiseClusterer.hh.

bool protocols::swa::StepWiseClusterer::cluster_by_all_atom_rmsd_
private

Definition at line 117 of file StepWiseClusterer.hh.

Referenced by set_cluster_by_all_atom_rmsd().

core::Real protocols::swa::StepWiseClusterer::cluster_radius_
private

Definition at line 116 of file StepWiseClusterer.hh.

Referenced by set_cluster_radius().

utility::vector1< core::Real > protocols::swa::StepWiseClusterer::cluster_rmsds_to_try_with_auto_tune_
private

Definition at line 135 of file StepWiseClusterer.hh.

std::map< core::id::AtomID, core::id::AtomID > protocols::swa::StepWiseClusterer::corresponding_atom_id_map_
private

Definition at line 141 of file StepWiseClusterer.hh.

bool protocols::swa::StepWiseClusterer::force_align_
private

Definition at line 121 of file StepWiseClusterer.hh.

Referenced by set_force_align().

bool protocols::swa::StepWiseClusterer::hit_score_cutoff_
private

Definition at line 137 of file StepWiseClusterer.hh.

bool protocols::swa::StepWiseClusterer::initialized_atom_id_map_for_rmsd_
private

Definition at line 138 of file StepWiseClusterer.hh.

core::import_pose::pose_stream::SilentFilePoseInputStreamOP protocols::swa::StepWiseClusterer::input_
private

Definition at line 133 of file StepWiseClusterer.hh.

Size protocols::swa::StepWiseClusterer::max_decoys_
private

Definition at line 115 of file StepWiseClusterer.hh.

Referenced by set_max_decoys().

utility::vector1< core::Size > protocols::swa::StepWiseClusterer::num_pose_in_cluster_
private

Definition at line 131 of file StepWiseClusterer.hh.

utility::vector1< core::pose::PoseOP > protocols::swa::StepWiseClusterer::pose_output_list_
private

Definition at line 128 of file StepWiseClusterer.hh.

bool protocols::swa::StepWiseClusterer::rename_tags_
private

Definition at line 120 of file StepWiseClusterer.hh.

Referenced by set_rename_tags().

core::chemical::ResidueTypeSetCAP protocols::swa::StepWiseClusterer::rsd_set_
private

Definition at line 143 of file StepWiseClusterer.hh.

std::string protocols::swa::StepWiseClusterer::rsd_type_set_
private

Definition at line 122 of file StepWiseClusterer.hh.

Referenced by set_rsd_type_set().

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

Definition at line 118 of file StepWiseClusterer.hh.

Referenced by set_score_diff_cut().

core::Real protocols::swa::StepWiseClusterer::score_min_
private

Definition at line 124 of file StepWiseClusterer.hh.

bool protocols::swa::StepWiseClusterer::score_min_defined_
private

Definition at line 125 of file StepWiseClusterer.hh.

utility::vector1< std::string > protocols::swa::StepWiseClusterer::silent_files_
private

Definition at line 114 of file StepWiseClusterer.hh.

utility::vector1< core::io::silent::SilentStructOP > protocols::swa::StepWiseClusterer::silent_struct_output_list_
private

Definition at line 130 of file StepWiseClusterer.hh.

Referenced by silent_struct_output_list().

utility::vector1< std::string > protocols::swa::StepWiseClusterer::tag_output_list_
private

Definition at line 129 of file StepWiseClusterer.hh.

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