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Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::stepwise::modeler::align::StepWiseLegacyClusterer Class Reference

#include <StepWiseLegacyClusterer.hh>

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

 StepWiseLegacyClusterer (utility::vector1< core::pose::PoseOP > const &pose_list)
 
 StepWiseLegacyClusterer (utility::vector1< core::pose::PoseOP > const &pose_list, utility::vector1< core::Size > const &moving_res_list, options::StepWiseModelerOptionsCOP options, bool const force_align)
 
 ~StepWiseLegacyClusterer () 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_calc_rms_res (utility::vector1< core::Size > const &calc_rms_res)
 
void cluster ()
 
utility::vector1
< core::pose::PoseOP
rms_pose_list ()
 
utility::vector1
< core::pose::PoseOP
get_pose_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 rms_pose)
 
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

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_
 
core::Real score_min_
 
utility::vector1
< core::pose::PoseOP
input_pose_list_
 
utility::vector1
< core::pose::PoseOP
rms_pose_list_
 
utility::vector1
< core::pose::PoseOP
output_pose_list_
 
utility::vector1< core::Sizenum_pose_in_cluster_
 
utility::vector1< core::Realcluster_rmsds_to_try_with_auto_tune_
 
core::Size input_pose_counter_
 
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_
 

Constructor & Destructor Documentation

protocols::stepwise::modeler::align::StepWiseLegacyClusterer::StepWiseLegacyClusterer ( utility::vector1< core::pose::PoseOP > const &  pose_list)
protocols::stepwise::modeler::align::StepWiseLegacyClusterer::StepWiseLegacyClusterer ( utility::vector1< core::pose::PoseOP > const &  pose_list,
utility::vector1< core::Size > const &  moving_res_list,
options::StepWiseModelerOptionsCOP  options,
bool const  force_align 
)
protocols::stepwise::modeler::align::StepWiseLegacyClusterer::~StepWiseLegacyClusterer ( )
overridedefault

Member Function Documentation

Size protocols::stepwise::modeler::align::StepWiseLegacyClusterer::check_for_closeness ( core::pose::PoseOP  rms_pose)
private
void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::cluster ( )
void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::cluster_with_auto_tune ( )
private
void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::do_some_clustering ( )
private
utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::align::StepWiseLegacyClusterer::get_pose_list ( )
inline
void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::initialize_auto_tune_cluster_rmsds ( )
private
void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::initialize_cluster_list ( )
private
void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::initialize_corresponding_atom_id_map ( core::pose::Pose const &  pose)
private
void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::initialize_parameters_and_input ( )
private
void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::recluster_current_pose_list ( )
private
utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::align::StepWiseLegacyClusterer::rms_pose_list ( )
inline

References rms_pose_list_.

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

References auto_tune_.

void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::set_calc_rms_res ( utility::vector1< core::Size > const &  calc_rms_res)

References calc_rms_res_.

Referenced by StepWiseLegacyClusterer().

void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::set_cluster_by_all_atom_rmsd ( core::Real const &  setting)
inline
void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::set_cluster_radius ( core::Real const &  setting)
inline

References cluster_radius_.

Referenced by StepWiseLegacyClusterer().

void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::set_force_align ( bool const  force_align)
inline

References force_align_.

Referenced by StepWiseLegacyClusterer().

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

Filter a list of poses by score.

References max_decoys_.

Referenced by StepWiseLegacyClusterer().

void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::set_rename_tags ( core::Real const &  setting)
inline

References rename_tags_.

Referenced by StepWiseLegacyClusterer().

void protocols::stepwise::modeler::align::StepWiseLegacyClusterer::set_score_diff_cut ( core::Real const &  setting)
inline

References score_diff_cut_.

core::io::silent::SilentStructOP protocols::stepwise::modeler::align::StepWiseLegacyClusterer::setup_silent_struct ( core::Size const  n)
private

Member Data Documentation

bool protocols::stepwise::modeler::align::StepWiseLegacyClusterer::auto_tune_
private
utility::vector1< core::Size > protocols::stepwise::modeler::align::StepWiseLegacyClusterer::calc_rms_res_
private
bool protocols::stepwise::modeler::align::StepWiseLegacyClusterer::cluster_by_all_atom_rmsd_
private
core::Real protocols::stepwise::modeler::align::StepWiseLegacyClusterer::cluster_radius_
private
utility::vector1< core::Real > protocols::stepwise::modeler::align::StepWiseLegacyClusterer::cluster_rmsds_to_try_with_auto_tune_
private
std::map< core::id::AtomID, core::id::AtomID > protocols::stepwise::modeler::align::StepWiseLegacyClusterer::corresponding_atom_id_map_
private
bool protocols::stepwise::modeler::align::StepWiseLegacyClusterer::force_align_
private
bool protocols::stepwise::modeler::align::StepWiseLegacyClusterer::hit_score_cutoff_
private
bool protocols::stepwise::modeler::align::StepWiseLegacyClusterer::initialized_atom_id_map_for_rmsd_
private
core::Size protocols::stepwise::modeler::align::StepWiseLegacyClusterer::input_pose_counter_
private
utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::align::StepWiseLegacyClusterer::input_pose_list_
private
core::Size protocols::stepwise::modeler::align::StepWiseLegacyClusterer::max_decoys_
private
utility::vector1< core::Size > protocols::stepwise::modeler::align::StepWiseLegacyClusterer::num_pose_in_cluster_
private
utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::align::StepWiseLegacyClusterer::output_pose_list_
private
bool protocols::stepwise::modeler::align::StepWiseLegacyClusterer::rename_tags_
private
utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::align::StepWiseLegacyClusterer::rms_pose_list_
private
core::Real protocols::stepwise::modeler::align::StepWiseLegacyClusterer::score_diff_cut_
private
core::Real protocols::stepwise::modeler::align::StepWiseLegacyClusterer::score_min_
private

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