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protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer Class Reference

#include <StepWiseRNA_CombineLongLoopFilterer.hh>

Inheritance diagram for protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer:
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Collaboration diagram for protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer:
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Public Member Functions

 StepWiseRNA_CombineLongLoopFilterer (StepWiseRNA_JobParametersCOP const &job_parameters, bool const combine_helical_silent_file)
 
virtual ~StepWiseRNA_CombineLongLoopFilterer ()
 
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_ribose_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
< pose_data_struct2 > 		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 (pose_data_struct2 const &side_ONE_pose_data, pose_data_struct2 const &side_TWO_pose_data, core::Real const overlap_dist_cutoff, core::Size const num_atom_contacts_cutoff)
 
bool previously_builded_res_contact_filter (pose_data_struct2 const &side_ONE_pose_data, pose_data_struct2 const &side_TWO_pose_data)
 
bool previously_builded_res_clash_filter (pose_data_struct2 const &side_ONE_pose_data, pose_data_struct2 const &side_TWO_pose_data)
 
bool moving_res_contact_filter (pose_data_struct2 const &side_ONE_pose_data, pose_data_struct2 const &side_TWO_pose_data)
 
void align_all_pose (utility::vector1< pose_data_struct2 > const &side_ONE_pose_data_list, utility::vector1< pose_data_struct2 > const &side_TWO_pose_data_list)
 
void do_some_filtering ()
 
bool pass_all_filters (pose_data_struct2 const &side_ONE_pose_data, pose_data_struct2 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_ribose_tag (std::string const &tag, utility::vector1< std::string > const &tag_token) const
 
bool Is_sibling_ribose_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_
 
StepWiseRNA_JobParametersCOP const job_parameters_
 
bool verbose_
 
bool parin_favorite_output_
 
bool filter_for_previous_contact_
 
bool filter_for_previous_clash_
 
bool undercount_ribose_rotamers_
 
bool const filter_for_chain_closable_
 
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::Size > input_pose_ONE_appended_res_list_
 
utility::vector1< core::Size > input_pose_TWO_prepended_res_list_
 
std::map< core::Size, core::Size > full_to_input_res_map_ONE_
 
std::map< core::Size, core::Size > full_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_
 
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_
 

Detailed Description

Definition at line 93 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Constructor & Destructor Documentation

protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::StepWiseRNA_CombineLongLoopFilterer ( StepWiseRNA_JobParametersCOP const &  job_parameters,
bool const  combine_helical_silent_file 
)

Definition at line 89 of file StepWiseRNA_CombineLongLoopFilterer.cc.

References clash_dist_cutoff_, combine_helical_silent_file_, contact_dist_cutoff_, protocols::swa::rna::create_full_to_input_res_map(), figure_out_appended_and_prepended_res_list(), figure_out_last_appended_and_last_prepended_res(), full_to_input_res_map_ONE_, full_to_input_res_map_TWO_, job_parameters_, moving_res_contact_dist_cutoff_, num_clash_cutoff_, and num_contact_cutoff_.

protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::~StepWiseRNA_CombineLongLoopFilterer ( )
virtual

Definition at line 158 of file StepWiseRNA_CombineLongLoopFilterer.cc.

Member Function Documentation

void protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::align_all_pose ( utility::vector1< pose_data_struct2 > const &  side_ONE_pose_data_list,
utility::vector1< pose_data_struct2 > const &  side_TWO_pose_data_list 
)
private

Definition at line 382 of file StepWiseRNA_CombineLongLoopFilterer.cc.

References core::id::BOGUS_ATOM_ID, core::pose::initialize_atomid_map(), protocols::swa::rna::Output_title_text(), core::pose::Pose::residue(), protocols::swa::rna::setup_suite_atom_id_map(), core::scoring::superimpose_pose(), and core::pose::Pose::total_residue().

Referenced by do_some_filtering().

utility::vector1< pose_data_struct2 > protocols::swa::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

Definition at line 307 of file StepWiseRNA_CombineLongLoopFilterer.cc.

References protocols::swa::rna::check_for_messed_up_structure(), core::pose::getPoseExtraScores(), max_pose_data_list_size_, protocols::swa::rna::pose_data_struct2::pose_OP, rsd_set_, protocols::swa::rna::pose_data_struct2::score, and protocols::swa::rna::pose_data_struct2::tag.

Referenced by do_some_filtering().

void protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::do_some_filtering ( )
private

Definition at line 640 of file StepWiseRNA_CombineLongLoopFilterer.cc.

References align_all_pose(), best_combine_score_, combine_helical_silent_file_, protocols::swa::rna::Combine_Tags_Info::combine_score, convert_silent_file_to_pose_data_list(), filterer_count_, filterered_combine_tag_info_list_, protocols::swa::rna::Output_title_text(), pass_all_filters(), pass_screen_struct_pair_, protocols::swa::rna::pose_data_struct2::score, protocols::swa::rna::Filterer_Count::score_cut_count, side_ONE_NUM_pose_list_, side_ONE_pose_list_id_, protocols::swa::rna::Combine_Tags_Info::side_one_tag, side_TWO_NUM_pose_list_, side_TWO_pose_list_id_, protocols::swa::rna::Combine_Tags_Info::side_two_tag, silent_file_stream_ONE_, silent_file_stream_TWO_, protocols::swa::rna::pose_data_struct2::tag, protocols::swa::rna::Filterer_Count::total_count, and total_input_struct_pair_.

Referenced by filter().

void protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::figure_out_appended_and_prepended_res_list ( )
private

Definition at line 164 of file StepWiseRNA_CombineLongLoopFilterer.cc.

References protocols::swa::rna::Contain_seq_num(), full_to_input_res_map_ONE_, full_to_input_res_map_TWO_, input_pose_ONE_appended_res_list_, input_pose_TWO_prepended_res_list_, job_parameters_, and protocols::swa::rna::Output_seq_num_list().

Referenced by StepWiseRNA_CombineLongLoopFilterer().

void protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::figure_out_last_appended_and_last_prepended_res ( )
private

Definition at line 222 of file StepWiseRNA_CombineLongLoopFilterer.cc.

References input_pose_ONE_appended_res_list_, input_pose_ONE_last_appended_res_, input_pose_TWO_last_prepended_res_, input_pose_TWO_prepended_res_list_, and job_parameters_.

Referenced by StepWiseRNA_CombineLongLoopFilterer().

void protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::figure_out_NUM_pose_list ( )
private

Definition at line 715 of file StepWiseRNA_CombineLongLoopFilterer.cc.

References max_pose_data_list_size_, side_ONE_NUM_pose_list_, side_TWO_NUM_pose_list_, silent_file_stream_ONE_, and silent_file_stream_TWO_.

Referenced by filter().

void protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::filter ( )

Definition at line 962 of file StepWiseRNA_CombineLongLoopFilterer.cc.

References protocols::swa::rna::Filterer_Count::chain_closable_screen, combine_helical_silent_file_, protocols::swa::rna::Combine_Tags_Info::combine_score, do_some_filtering(), figure_out_NUM_pose_list(), filter_for_chain_closable_, protocols::swa::rna::Filterer_Count::filter_for_moving_res_contact, filter_for_moving_res_contact_, protocols::swa::rna::Filterer_Count::filter_for_previous_clash, filter_for_previous_clash_, protocols::swa::rna::Filterer_Count::filter_for_previous_contact, filter_for_previous_contact_, filterer_count_, filterered_combine_tag_info_list_, Is_sibling_ribose_rotamer_pose(), core::sequence::left, max_decoys_, moving_res_to_base_contact_only_, protocols::swa::rna::Output_boolean(), output_filename_, protocols::swa::rna::Output_title_text(), parin_favorite_output_, pass_screen_struct_pair_, protocols::swa::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::swa::rna::Combine_Tags_Info::side_one_tag, side_TWO_NUM_pose_list_, side_TWO_pose_list_id_, protocols::swa::rna::Combine_Tags_Info::side_two_tag, sort_Combine_Tags_Info(), tag_to_source_map_ONE_, tag_to_source_map_TWO_, protocols::swa::rna::Filterer_Count::total_count, total_input_struct_pair_, and undercount_ribose_rotamers_.

std::string protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::get_parent_tag ( utility::vector1< std::string > const &  tag_token) const
private

Definition at line 882 of file StepWiseRNA_CombineLongLoopFilterer.cc.

Referenced by Is_sibling_ribose_rotamer_pose().

bool protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::Is_sibling_ribose_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

Definition at line 914 of file StepWiseRNA_CombineLongLoopFilterer.cc.

References get_parent_tag(), Is_virt_sample_ribose_tag(), and protocols::swa::rna::Tokenize().

Referenced by filter().

bool protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::Is_virt_sample_ribose_tag ( std::string const &  tag,
utility::vector1< std::string > const &  tag_token 
) const
private

Definition at line 891 of file StepWiseRNA_CombineLongLoopFilterer.cc.

Referenced by Is_sibling_ribose_rotamer_pose().

bool protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_contact_filter ( pose_data_struct2 const &  side_ONE_pose_data,
pose_data_struct2 const &  side_TWO_pose_data 
)
private

Definition at line 527 of file StepWiseRNA_CombineLongLoopFilterer.cc.

References core::io::serialization::at(), core::chemical::ResidueType::atom_name(), core::conformation::Residue::first_sidechain_atom(), input_pose_ONE_last_appended_res_, input_pose_TWO_last_prepended_res_, job_parameters_, moving_res_contact_dist_cutoff_, moving_res_to_base_contact_only_, core::conformation::Residue::natoms(), core::conformation::Residue::nheavyatoms(), protocols::swa::rna::pose_data_struct2::pose_OP, core::pose::Pose::residue(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by pass_all_filters().

bool protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::pass_all_filters ( pose_data_struct2 const &  side_ONE_pose_data,
pose_data_struct2 const &  side_TWO_pose_data 
)
private

Definition at line 566 of file StepWiseRNA_CombineLongLoopFilterer.cc.

References best_combine_score_, protocols::swa::rna::Filterer_Count::chain_closable_screen, protocols::swa::rna::Check_chain_closable(), filter_for_chain_closable_, protocols::swa::rna::Filterer_Count::filter_for_moving_res_contact, filter_for_moving_res_contact_, protocols::swa::rna::Filterer_Count::filter_for_previous_clash, filter_for_previous_clash_, protocols::swa::rna::Filterer_Count::filter_for_previous_contact, filter_for_previous_contact_, filterer_count_, input_pose_ONE_last_appended_res_, input_pose_TWO_last_prepended_res_, job_parameters_, moving_res_contact_filter(), protocols::swa::rna::pose_data_struct2::pose_OP, previously_builded_res_clash_filter(), previously_builded_res_contact_filter(), protocols::swa::rna::pose_data_struct2::score, protocols::swa::rna::Filterer_Count::score_cut_count, protocols::swa::rna::Filterer_Count::total_count, and worst_combine_score_.

Referenced by do_some_filtering().

bool protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::previously_builded_res_clash_filter ( pose_data_struct2 const &  side_ONE_pose_data,
pose_data_struct2 const &  side_TWO_pose_data 
)
private

Definition at line 520 of file StepWiseRNA_CombineLongLoopFilterer.cc.

References clash_dist_cutoff_, num_clash_cutoff_, and previously_builded_res_VDW_filter().

Referenced by pass_all_filters().

bool protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::previously_builded_res_contact_filter ( pose_data_struct2 const &  side_ONE_pose_data,
pose_data_struct2 const &  side_TWO_pose_data 
)
private

Definition at line 512 of file StepWiseRNA_CombineLongLoopFilterer.cc.

References contact_dist_cutoff_, num_contact_cutoff_, and previously_builded_res_VDW_filter().

Referenced by pass_all_filters().

bool protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::previously_builded_res_VDW_filter ( pose_data_struct2 const &  side_ONE_pose_data,
pose_data_struct2 const &  side_TWO_pose_data,
core::Real const  overlap_dist_cutoff,
core::Size const  num_atom_contacts_cutoff 
)
private

Definition at line 441 of file StepWiseRNA_CombineLongLoopFilterer.cc.

References input_pose_ONE_appended_res_list_, input_pose_TWO_prepended_res_list_, protocols::swa::rna::Is_residues_in_contact(), and protocols::swa::rna::pose_data_struct2::pose_OP.

Referenced by previously_builded_res_clash_filter(), and previously_builded_res_contact_filter().

void protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::set_filter_for_previous_clash ( core::Real const  setting)
inline

Definition at line 124 of file StepWiseRNA_CombineLongLoopFilterer.hh.

References filter_for_previous_clash_.

void protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::set_filter_for_previous_contact ( core::Real const  setting)
inline

Definition at line 121 of file StepWiseRNA_CombineLongLoopFilterer.hh.

References filter_for_previous_contact_.

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

Definition at line 129 of file StepWiseRNA_CombineLongLoopFilterer.hh.

References max_decoys_.

void protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::set_output_filename ( std::string const  setting)
inline

Definition at line 115 of file StepWiseRNA_CombineLongLoopFilterer.hh.

References output_filename_.

void protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::set_parin_favorite_output ( bool const  setting)
inline

Definition at line 109 of file StepWiseRNA_CombineLongLoopFilterer.hh.

References parin_favorite_output_.

void protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::set_silent_files_in ( utility::vector1< std::string > const &  setting)
inline

Definition at line 106 of file StepWiseRNA_CombineLongLoopFilterer.hh.

References silent_files_in_.

void protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::set_undercount_ribose_rotamers ( bool const  setting)
inline

Definition at line 127 of file StepWiseRNA_CombineLongLoopFilterer.hh.

References undercount_ribose_rotamers_.

void protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::setup_silent_file_stream ( )
private

Definition at line 840 of file StepWiseRNA_CombineLongLoopFilterer.cc.

References silent_file_stream_ONE_, silent_file_stream_TWO_, and silent_files_in_.

Referenced by filter().

void protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::setup_tag_to_source_map ( )
private

Definition at line 771 of file StepWiseRNA_CombineLongLoopFilterer.cc.

References silent_file_stream_ONE_, silent_file_stream_TWO_, tag_to_source_map_ONE_, and tag_to_source_map_TWO_.

Referenced by filter().

void protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::sort_Combine_Tags_Info ( utility::vector1< Combine_Tags_Info > &  combine_tags_info_list)
private

Definition at line 875 of file StepWiseRNA_CombineLongLoopFilterer.cc.

References protocols::swa::rna::score_sort_citeria().

Referenced by filter().

Member Data Documentation

core::Real protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::best_combine_score_
private

Definition at line 226 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by do_some_filtering(), and pass_all_filters().

core::Real const protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::clash_dist_cutoff_
private

Definition at line 230 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by previously_builded_res_clash_filter(), and StepWiseRNA_CombineLongLoopFilterer().

bool protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::combine_helical_silent_file_
private

Definition at line 243 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by do_some_filtering(), filter(), and StepWiseRNA_CombineLongLoopFilterer().

core::Real const protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::contact_dist_cutoff_
private

Definition at line 229 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by previously_builded_res_contact_filter(), and StepWiseRNA_CombineLongLoopFilterer().

bool const protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::filter_for_chain_closable_
private

Definition at line 212 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by filter(), and pass_all_filters().

bool const protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::filter_for_moving_res_contact_
private

Definition at line 213 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by filter(), and pass_all_filters().

bool protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::filter_for_previous_clash_
private

Definition at line 210 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by filter(), pass_all_filters(), and set_filter_for_previous_clash().

bool protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::filter_for_previous_contact_
private

Definition at line 209 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by filter(), pass_all_filters(), and set_filter_for_previous_contact().

Filterer_Count protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::filterer_count_
private

Definition at line 200 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by do_some_filtering(), filter(), and pass_all_filters().

utility::vector1< Combine_Tags_Info > protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::filterered_combine_tag_info_list_
private

Definition at line 240 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by do_some_filtering(), and filter().

std::map< core::Size, core::Size > protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::full_to_input_res_map_ONE_
private

Definition at line 223 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by figure_out_appended_and_prepended_res_list(), and StepWiseRNA_CombineLongLoopFilterer().

std::map< core::Size, core::Size > protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::full_to_input_res_map_TWO_
private

Definition at line 224 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by figure_out_appended_and_prepended_res_list(), and StepWiseRNA_CombineLongLoopFilterer().

utility::vector1<core::Size> protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::input_pose_ONE_appended_res_list_
private

Definition at line 220 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by figure_out_appended_and_prepended_res_list(), figure_out_last_appended_and_last_prepended_res(), and previously_builded_res_VDW_filter().

core::Size protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::input_pose_ONE_last_appended_res_
private

Definition at line 218 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by figure_out_last_appended_and_last_prepended_res(), moving_res_contact_filter(), and pass_all_filters().

core::Size protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::input_pose_TWO_last_prepended_res_
private

Definition at line 219 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by figure_out_last_appended_and_last_prepended_res(), moving_res_contact_filter(), and pass_all_filters().

utility::vector1<core::Size> protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::input_pose_TWO_prepended_res_list_
private

Definition at line 221 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by figure_out_appended_and_prepended_res_list(), figure_out_last_appended_and_last_prepended_res(), and previously_builded_res_VDW_filter().

StepWiseRNA_JobParametersCOP const protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::job_parameters_
private

Definition at line 206 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by figure_out_appended_and_prepended_res_list(), figure_out_last_appended_and_last_prepended_res(), moving_res_contact_filter(), pass_all_filters(), and StepWiseRNA_CombineLongLoopFilterer().

Size protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::max_decoys_
private

Definition at line 242 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by filter(), and set_max_decoys().

core::Size const protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::max_pose_data_list_size_
private

Definition at line 234 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by convert_silent_file_to_pose_data_list(), and figure_out_NUM_pose_list().

core::Real protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_contact_dist_cutoff_
private

Definition at line 239 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by moving_res_contact_filter(), and StepWiseRNA_CombineLongLoopFilterer().

bool const protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_to_base_contact_only_
private

Definition at line 214 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by filter(), and moving_res_contact_filter().

core::Size const protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::num_clash_cutoff_
private

Definition at line 232 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by previously_builded_res_clash_filter(), and StepWiseRNA_CombineLongLoopFilterer().

core::Size const protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::num_contact_cutoff_
private

Definition at line 231 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by previously_builded_res_contact_filter(), and StepWiseRNA_CombineLongLoopFilterer().

std::string protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::output_filename_
private

Definition at line 225 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by filter(), and set_output_filename().

bool protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::parin_favorite_output_
private

Definition at line 208 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by filter(), and set_parin_favorite_output().

core::Size protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::pass_screen_struct_pair_
private

Definition at line 217 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by do_some_filtering(), and filter().

core::chemical::ResidueTypeSetCAP protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::rsd_set_
private

Definition at line 202 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by convert_silent_file_to_pose_data_list().

core::Size protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::side_ONE_NUM_pose_list_
private

Definition at line 235 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by do_some_filtering(), figure_out_NUM_pose_list(), and filter().

core::Size protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::side_ONE_pose_list_id_
private

Definition at line 237 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by do_some_filtering(), and filter().

core::Size protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::side_TWO_NUM_pose_list_
private

Definition at line 236 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by do_some_filtering(), figure_out_NUM_pose_list(), and filter().

core::Size protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::side_TWO_pose_list_id_
private

Definition at line 238 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by do_some_filtering(), and filter().

core::import_pose::pose_stream::SilentFilePoseInputStreamOP protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::silent_file_stream_ONE_
private

Definition at line 204 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by do_some_filtering(), figure_out_NUM_pose_list(), setup_silent_file_stream(), and setup_tag_to_source_map().

core::import_pose::pose_stream::SilentFilePoseInputStreamOP protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::silent_file_stream_TWO_
private

Definition at line 205 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by do_some_filtering(), figure_out_NUM_pose_list(), setup_silent_file_stream(), and setup_tag_to_source_map().

utility::vector1< std::string > protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::silent_files_in_
private

Definition at line 203 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by set_silent_files_in(), and setup_silent_file_stream().

std::map< std::string , std::string > protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::tag_to_source_map_ONE_
private

Definition at line 245 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by filter(), and setup_tag_to_source_map().

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

Definition at line 246 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by filter(), and setup_tag_to_source_map().

core::Size protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::total_input_struct_pair_
private

Definition at line 216 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by do_some_filtering(), and filter().

bool protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::undercount_ribose_rotamers_
private

Definition at line 211 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by filter(), and set_undercount_ribose_rotamers().

bool protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::verbose_
private

Definition at line 207 of file StepWiseRNA_CombineLongLoopFilterer.hh.

core::Real protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::worst_combine_score_
private

Definition at line 227 of file StepWiseRNA_CombineLongLoopFilterer.hh.

Referenced by pass_all_filters().

The documentation for this class was generated from the following files:
Generated on Sat Jun 1 2013 12:57:08 for Rosetta 3.5 by   doxygen 1.8.4