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protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer Class Reference

#include <StepWiseRNA_CombineLongLoopFilterer.hh>

Inheritance diagram for protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer:
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Public Member Functions

 StepWiseRNA_CombineLongLoopFilterer (working_parameters::StepWiseWorkingParametersCOP working_parameters, bool const combine_helical_silent_file)
 
 ~StepWiseRNA_CombineLongLoopFilterer () override
 
void set_silent_files_in (utility::vector1< std::string > const &setting)
 
void set_parin_favorite_output (bool const setting)
 
void filter ()
 
void set_output_filename (std::string const &setting)
 
void set_filter_for_previous_contact (core::Real const setting)
 
void set_filter_for_previous_clash (core::Real const setting)
 
void set_undercount_sugar_rotamers (bool const setting)
 
void set_max_decoys (core::Size const &setting)
 

Private Member Functions

void figure_out_appended_and_prepended_res_list ()
 
void figure_out_last_appended_and_last_prepended_res ()
 
utility::vector1
< core::pose::PoseOP
convert_silent_file_to_pose_data_list (core::import_pose::pose_stream::SilentFilePoseInputStreamOP &silent_file_stream, core::Size const pose_list_id)
 
bool previously_builded_res_VDW_filter (core::pose::PoseOP const &side_ONE_pose_data, core::pose::PoseOP const &side_TWO_pose_data, core::Real const overlap_dist_cutoff, core::Size const num_atom_contacts_cutoff)
 
bool previously_builded_res_contact_filter (core::pose::PoseOP const &side_ONE_pose_data, core::pose::PoseOP const &side_TWO_pose_data)
 
bool previously_builded_res_clash_filter (core::pose::PoseOP const &side_ONE_pose_data, core::pose::PoseOP const &side_TWO_pose_data)
 
bool moving_res_contact_filter (core::pose::PoseOP const &side_ONE_pose_data, core::pose::PoseOP const &side_TWO_pose_data)
 
void align_all_pose (utility::vector1< core::pose::PoseOP > const &side_ONE_pose_data_list, utility::vector1< core::pose::PoseOP > const &side_TWO_pose_data_list)
 
void do_some_filtering ()
 
bool pass_all_filters (core::pose::PoseOP const &side_ONE_pose_data, core::pose::PoseOP const &side_TWO_pose_data)
 
void setup_silent_file_stream ()
 
void figure_out_NUM_pose_list ()
 
void setup_tag_to_source_map ()
 
void sort_Combine_Tags_Info (utility::vector1< Combine_Tags_Info > &combine_tags_info_list)
 
std::string get_parent_tag (utility::vector1< std::string > const &tag_token) const
 
bool is_virt_sample_sugar_tag (std::string const &tag, utility::vector1< std::string > const &tag_token) const
 
bool is_sibling_sugar_rotamer_pose (std::string const &curr_tag, std::string const &prev_tag, std::map< std::string, std::string > const &tag_to_source_map) const
 

Private Attributes

Filterer_Count filterer_count_
 
core::chemical::ResidueTypeSetCAP rsd_set_
 
utility::vector1< std::string > silent_files_in_
 
core::import_pose::pose_stream::SilentFilePoseInputStreamOP silent_file_stream_ONE_
 
core::import_pose::pose_stream::SilentFilePoseInputStreamOP silent_file_stream_TWO_
 
working_parameters::StepWiseWorkingParametersCOP
const 
working_parameters_
 
bool parin_favorite_output_
 
bool filter_for_previous_contact_
 
bool filter_for_previous_clash_
 
bool undercount_sugar_rotamers_
 
bool const filter_for_chain_closable_geometry_
 
bool const filter_for_moving_res_contact_
 
bool const moving_res_to_base_contact_only_
 
core::Size total_input_struct_pair_
 
core::Size pass_screen_struct_pair_
 
core::Size input_pose_ONE_last_appended_res_
 
core::Size input_pose_TWO_last_prepended_res_
 
utility::vector1< core::Sizeinput_pose_ONE_appended_res_list_
 
utility::vector1< core::Sizeinput_pose_TWO_prepended_res_list_
 
std::map< core::Size, core::Sizefull_to_input_res_map_ONE_
 
std::map< core::Size, core::Sizefull_to_input_res_map_TWO_
 
std::string output_filename_
 
core::Real best_combine_score_
 
core::Real worst_combine_score_
 
core::Real const contact_dist_cutoff_
 
core::Real const clash_dist_cutoff_
 
core::Size const num_contact_cutoff_
 
core::Size const num_clash_cutoff_
 
core::Size const max_pose_data_list_size_
 
core::Size side_ONE_NUM_pose_list_
 
core::Size side_TWO_NUM_pose_list_
 
core::Size side_ONE_pose_list_id_
 
core::Size side_TWO_pose_list_id_
 
core::Real moving_res_contact_dist_cutoff_
 
utility::vector1
< Combine_Tags_Info
filterered_combine_tag_info_list_
 
core::Size max_decoys_
 
bool combine_helical_silent_file_
 
std::map< std::string,
std::string > 
tag_to_source_map_ONE_
 
std::map< std::string,
std::string > 
tag_to_source_map_TWO_
 

Constructor & Destructor Documentation

protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::StepWiseRNA_CombineLongLoopFilterer ( working_parameters::StepWiseWorkingParametersCOP  working_parameters,
bool const  combine_helical_silent_file 
)
protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::~StepWiseRNA_CombineLongLoopFilterer ( )
overridedefault

Member Function Documentation

void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::align_all_pose ( utility::vector1< core::pose::PoseOP > const &  side_ONE_pose_data_list,
utility::vector1< core::pose::PoseOP > const &  side_TWO_pose_data_list 
)
private
utility::vector1< PoseOP > protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::convert_silent_file_to_pose_data_list ( core::import_pose::pose_stream::SilentFilePoseInputStreamOP silent_file_stream,
core::Size const  pose_list_id 
)
private
void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::do_some_filtering ( )
private
void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::figure_out_appended_and_prepended_res_list ( )
private
void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::figure_out_last_appended_and_last_prepended_res ( )
private
void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::figure_out_NUM_pose_list ( )
private
void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::filter ( )

References protocols::stepwise::modeler::rna::Filterer_Count::chain_closable_geometry_screen, combine_helical_silent_file_, protocols::stepwise::modeler::rna::Combine_Tags_Info::combine_score, do_some_filtering(), figure_out_NUM_pose_list(), filter_for_chain_closable_geometry_, protocols::stepwise::modeler::rna::Filterer_Count::filter_for_moving_res_contact, filter_for_moving_res_contact_, protocols::stepwise::modeler::rna::Filterer_Count::filter_for_previous_clash, filter_for_previous_clash_, protocols::stepwise::modeler::rna::Filterer_Count::filter_for_previous_contact, filter_for_previous_contact_, filterer_count_, filterered_combine_tag_info_list_, is_sibling_sugar_rotamer_pose(), core::sequence::left, max_decoys_, moving_res_to_base_contact_only_, protocols::stepwise::modeler::output_boolean(), output_filename_, protocols::stepwise::modeler::rna::output_title_text(), parin_favorite_output_, pass_screen_struct_pair_, protocols::stepwise::modeler::rna::Filterer_Count::score_cut_count, setup_silent_file_stream(), setup_tag_to_source_map(), side_ONE_NUM_pose_list_, side_ONE_pose_list_id_, protocols::stepwise::modeler::rna::Combine_Tags_Info::side_one_tag, side_TWO_NUM_pose_list_, side_TWO_pose_list_id_, protocols::stepwise::modeler::rna::Combine_Tags_Info::side_two_tag, sort_Combine_Tags_Info(), tag_to_source_map_ONE_, tag_to_source_map_TWO_, protocols::stepwise::modeler::rna::Filterer_Count::total_count, total_input_struct_pair_, protocols::TR(), and undercount_sugar_rotamers_.

std::string protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::get_parent_tag ( utility::vector1< std::string > const &  tag_token) const
private
bool protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::is_sibling_sugar_rotamer_pose ( std::string const &  curr_tag,
std::string const &  prev_tag,
std::map< std::string, std::string > const &  tag_to_source_map 
) const
private
bool protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::is_virt_sample_sugar_tag ( std::string const &  tag,
utility::vector1< std::string > const &  tag_token 
) const
private
bool protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_contact_filter ( core::pose::PoseOP const &  side_ONE_pose_data,
core::pose::PoseOP const &  side_TWO_pose_data 
)
private
bool protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::pass_all_filters ( core::pose::PoseOP const &  side_ONE_pose_data,
core::pose::PoseOP const &  side_TWO_pose_data 
)
private
bool protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::previously_builded_res_clash_filter ( core::pose::PoseOP const &  side_ONE_pose_data,
core::pose::PoseOP const &  side_TWO_pose_data 
)
private
bool protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::previously_builded_res_contact_filter ( core::pose::PoseOP const &  side_ONE_pose_data,
core::pose::PoseOP const &  side_TWO_pose_data 
)
private
bool protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::previously_builded_res_VDW_filter ( core::pose::PoseOP const &  side_ONE_pose_data,
core::pose::PoseOP const &  side_TWO_pose_data,
core::Real const  overlap_dist_cutoff,
core::Size const  num_atom_contacts_cutoff 
)
private
void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::set_filter_for_previous_clash ( core::Real const  setting)
inline
void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::set_filter_for_previous_contact ( core::Real const  setting)
inline
void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::set_max_decoys ( core::Size const &  setting)
inline

References max_decoys_.

void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::set_output_filename ( std::string const &  setting)
inline

References output_filename_.

void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::set_parin_favorite_output ( bool const  setting)
inline
void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::set_silent_files_in ( utility::vector1< std::string > const &  setting)
inline

References silent_files_in_.

void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::set_undercount_sugar_rotamers ( bool const  setting)
inline
void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::setup_silent_file_stream ( )
private
void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::setup_tag_to_source_map ( )
private
void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::sort_Combine_Tags_Info ( utility::vector1< Combine_Tags_Info > &  combine_tags_info_list)
private

Member Data Documentation

core::Real protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::best_combine_score_
private
core::Real const protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::clash_dist_cutoff_
private
bool protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::combine_helical_silent_file_
private
core::Real const protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::contact_dist_cutoff_
private
bool const protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::filter_for_chain_closable_geometry_
private

Referenced by filter(), and pass_all_filters().

bool const protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::filter_for_moving_res_contact_
private

Referenced by filter(), and pass_all_filters().

bool protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::filter_for_previous_clash_
private
bool protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::filter_for_previous_contact_
private
Filterer_Count protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::filterer_count_
private
utility::vector1< Combine_Tags_Info > protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::filterered_combine_tag_info_list_
private

Referenced by do_some_filtering(), and filter().

std::map< core::Size, core::Size > protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::full_to_input_res_map_ONE_
private
std::map< core::Size, core::Size > protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::full_to_input_res_map_TWO_
private
utility::vector1< core::Size > protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::input_pose_ONE_appended_res_list_
private
core::Size protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::input_pose_ONE_last_appended_res_
private
core::Size protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::input_pose_TWO_last_prepended_res_
private
utility::vector1< core::Size > protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::input_pose_TWO_prepended_res_list_
private
core::Size protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::max_decoys_
private

Referenced by filter(), and set_max_decoys().

core::Size const protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::max_pose_data_list_size_
private
core::Real protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_contact_dist_cutoff_
private
bool const protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_to_base_contact_only_
private
core::Size const protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::num_clash_cutoff_
private
core::Size const protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::num_contact_cutoff_
private
std::string protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::output_filename_
private

Referenced by filter(), and set_output_filename().

bool protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::parin_favorite_output_
private
core::Size protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::pass_screen_struct_pair_
private

Referenced by do_some_filtering(), and filter().

core::chemical::ResidueTypeSetCAP protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::rsd_set_
private
core::Size protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::side_ONE_NUM_pose_list_
private
core::Size protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::side_ONE_pose_list_id_
private

Referenced by do_some_filtering(), and filter().

core::Size protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::side_TWO_NUM_pose_list_
private
core::Size protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::side_TWO_pose_list_id_
private

Referenced by do_some_filtering(), and filter().

core::import_pose::pose_stream::SilentFilePoseInputStreamOP protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::silent_file_stream_ONE_
private
core::import_pose::pose_stream::SilentFilePoseInputStreamOP protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::silent_file_stream_TWO_
private
utility::vector1< std::string > protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::silent_files_in_
private
std::map< std::string, std::string > protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::tag_to_source_map_ONE_
private

Referenced by filter(), and setup_tag_to_source_map().

std::map< std::string, std::string > protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::tag_to_source_map_TWO_
private

Referenced by filter(), and setup_tag_to_source_map().

core::Size protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::total_input_struct_pair_
private

Referenced by do_some_filtering(), and filter().

bool protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::undercount_sugar_rotamers_
private
working_parameters::StepWiseWorkingParametersCOP const protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::working_parameters_
private
core::Real protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::worst_combine_score_
private

Referenced by pass_all_filters().


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