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protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased Class Reference

#include <StepWiseLegacyClustererSilentBased.hh>

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

 StepWiseLegacyClustererSilentBased (utility::vector1< std::string > const &silent_files_in)
 
 StepWiseLegacyClustererSilentBased (std::string const &silent_file_in)
 
 StepWiseLegacyClustererSilentBased (core::io::silent::SilentFileDataOP &sfd)
 
 StepWiseLegacyClustererSilentBased (core::io::silent::SilentFileDataOP silent_file_data, utility::vector1< core::Size > const &moving_res_list, options::StepWiseModelerOptionsCOP options, bool const force_align)
 
 ~StepWiseLegacyClustererSilentBased () override
 
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_numbered_pdb_output (bool const numbered_pdb_output)
 
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::pose::PoseOP
get_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 ()
 
core::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 ()
 
core::io::silent::SilentStructOP setup_silent_struct (core::Size const n)
 

Private Attributes

utility::vector1< std::string > silent_files_
 
core::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_
 
bool numbered_pdb_output_ = false
 
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::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::StepWiseLegacyClustererSilentBased ( utility::vector1< std::string > const &  silent_files_in)
protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::StepWiseLegacyClustererSilentBased ( std::string const &  silent_file_in)
protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::StepWiseLegacyClustererSilentBased ( core::io::silent::SilentFileDataOP sfd)
protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::StepWiseLegacyClustererSilentBased ( core::io::silent::SilentFileDataOP  silent_file_data,
utility::vector1< core::Size > const &  moving_res_list,
options::StepWiseModelerOptionsCOP  options,
bool const  force_align 
)
protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::~StepWiseLegacyClustererSilentBased ( )
overridedefault

Member Function Documentation

Size protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::check_for_closeness ( core::pose::PoseOP const &  pose_op)
private
void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::cluster ( )
void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::cluster_with_auto_tune ( )
private

References core::pose::TR().

PoseList protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::clustered_pose_list ( )
void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::do_some_clustering ( )
private
utility::vector1< PoseOP > protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::get_pose_list ( )
void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::initialize_auto_tune_cluster_rmsds ( )
private
void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::initialize_cluster_list ( )
private
void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::initialize_corresponding_atom_id_map ( core::pose::Pose const &  pose)
private
void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::initialize_parameters_and_input ( )
private
void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::output_silent_file ( std::string const &  silent_file)
void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::recluster_current_pose_list ( )
private

References core::pose::TR().

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_auto_tune ( bool const  auto_tune)
inline

References auto_tune_.

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_calc_rms_res ( utility::vector1< core::Size > const &  calc_rms_res)
void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_cluster_by_all_atom_rmsd ( core::Real const &  setting)
inline
void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_cluster_radius ( core::Real const &  setting)
inline
void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_force_align ( bool const  force_align)
inline

References force_align_.

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_max_decoys ( core::Size const &  setting)
inline

Filter a list of poses by score.

References max_decoys_.

Referenced by protocols::stepwise::sampler::protein::generate_beta_database_test().

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_numbered_pdb_output ( bool const  numbered_pdb_output)
inline

References numbered_pdb_output_.

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_rename_tags ( core::Real const &  setting)
inline
void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_rsd_type_set ( std::string const &  setting)
inline

References rsd_type_set_.

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_score_diff_cut ( core::Real const &  setting)
inline
void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_silent_file_data ( core::io::silent::SilentFileDataOP sfd)
core::io::silent::SilentStructOP protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::setup_silent_struct ( core::Size const  n)
private
core::io::silent::SilentFileDataOP protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::silent_file_data ( )
utility::vector1< core::io::silent::SilentStructOP >& protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::silent_struct_output_list ( )
inline

Member Data Documentation

bool protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::auto_tune_
private

Referenced by set_auto_tune().

utility::vector1< core::Size > protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::calc_rms_res_
private
bool protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::cluster_by_all_atom_rmsd_
private
core::Real protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::cluster_radius_
private

Referenced by set_cluster_radius().

utility::vector1< core::Real > protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::cluster_rmsds_to_try_with_auto_tune_
private
std::map< core::id::AtomID, core::id::AtomID > protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::corresponding_atom_id_map_
private
bool protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::force_align_
private

Referenced by set_force_align().

bool protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::hit_score_cutoff_
private
bool protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::initialized_atom_id_map_for_rmsd_
private
core::import_pose::pose_stream::SilentFilePoseInputStreamOP protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::input_
private
core::Size protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::max_decoys_
private

Referenced by set_max_decoys().

utility::vector1< core::Size > protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::num_pose_in_cluster_
private
bool protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::numbered_pdb_output_ = false
private

Referenced by set_numbered_pdb_output().

utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::pose_output_list_
private
bool protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::rename_tags_
private

Referenced by set_rename_tags().

core::chemical::ResidueTypeSetCAP protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::rsd_set_
private
std::string protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::rsd_type_set_
private

Referenced by set_rsd_type_set().

core::Real protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::score_diff_cut_
private

Referenced by set_score_diff_cut().

core::Real protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::score_min_
private
bool protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::score_min_defined_
private
utility::vector1< std::string > protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::silent_files_
private
utility::vector1< core::io::silent::SilentStructOP > protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::silent_struct_output_list_
private
utility::vector1< std::string > protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::tag_output_list_
private

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