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

#include <StepWiseRNA_CombineLongLoopFilterer.hh>

Public Member Functions
	StepWiseRNA_CombineLongLoopFilterer (working_parameters::StepWiseWorkingParametersCOP const &working_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_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< 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 (PoseOP const &side_ONE_pose_data, 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 (PoseOP const &side_ONE_pose_data, PoseOP const &side_TWO_pose_data)
bool	previously_builded_res_clash_filter (PoseOP const &side_ONE_pose_data, PoseOP const &side_TWO_pose_data)
bool	moving_res_contact_filter (PoseOP const &side_ONE_pose_data, PoseOP const &side_TWO_pose_data)
void	align_all_pose (utility::vector1< PoseOP > const &side_ONE_pose_data_list, utility::vector1< PoseOP > const &side_TWO_pose_data_list)
void	do_some_filtering ()
bool	pass_all_filters (PoseOP const &side_ONE_pose_data, 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	verbose_
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::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_

Constructor & Destructor Documentation

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

References chemical, clash_dist_cutoff_, combine_helical_silent_file_, contact_dist_cutoff_, protocols::stepwise::modeler::rna::create_full_to_input_res_map(), FA_RNA, 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_, moving_res_contact_dist_cutoff_, num_clash_cutoff_, num_contact_cutoff_, residue_type_set, protocols::TR, utility_exit_with_message, and working_parameters_.

protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::~StepWiseRNA_CombineLongLoopFilterer ( )

virtual

Member Function Documentation

void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::align_all_pose ( utility::vector1< PoseOP > const &  side_ONE_pose_data_list, utility::vector1< PoseOP > const &  side_TWO_pose_data_list  )

private

References chemical, protocols::stepwise::modeler::rna::output_title_text(), core::pose::Pose::residue(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), core::scoring::superimpose_pose(), core::pose::Pose::total_residue(), protocols::TR, and utility_exit_with_message.

Referenced by do_some_filtering().

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

References protocols::stepwise::modeler::rna::check_for_messed_up_structure(), getPoseExtraScore(), max_pose_data_list_size_, rsd_set_, score, tag, tag_into_pose(), and utility_exit_with_message.

Referenced by do_some_filtering().

void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::do_some_filtering ( )

private

References align_all_pose(), best_combine_score_, combine_helical_silent_file_, protocols::stepwise::modeler::rna::Combine_Tags_Info::combine_score, convert_silent_file_to_pose_data_list(), filterer_count_, filterered_combine_tag_info_list_, protocols::stepwise::modeler::rna::output_title_text(), pass_all_filters(), pass_screen_struct_pair_, protocols::stepwise::modeler::rna::Filterer_Count::score_cut_count, 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, silent_file_stream_ONE_, silent_file_stream_TWO_, tag_from_pose(), protocols::stepwise::modeler::rna::Filterer_Count::total_count, total_energy_from_pose(), total_input_struct_pair_, and protocols::TR.

Referenced by filter().

void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::figure_out_appended_and_prepended_res_list ( )

private

References full_to_input_res_map_ONE_, full_to_input_res_map_TWO_, has_value(), utility::vector1< T, class >::has_value(), input_pose_ONE_appended_res_list_, input_pose_TWO_prepended_res_list_, protocols::stepwise::modeler::rna::output_seq_num_list(), protocols::TR, and working_parameters_.

Referenced by StepWiseRNA_CombineLongLoopFilterer().

void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::figure_out_last_appended_and_last_prepended_res ( )

private

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_, protocols::TR, utility_exit_with_message, and working_parameters_.

Referenced by StepWiseRNA_CombineLongLoopFilterer().

void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::figure_out_NUM_pose_list ( )

private

References max_pose_data_list_size_, side_ONE_NUM_pose_list_, side_TWO_NUM_pose_list_, silent_file_stream_ONE_, silent_file_stream_TWO_, and protocols::TR.

Referenced by filter().

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(), 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, undercount_sugar_rotamers_, and utility_exit_with_message.

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

private

References utility_exit_with_message.

Referenced by is_sibling_sugar_rotamer_pose().

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

References get_parent_tag(), is_virt_sample_sugar_tag(), protocols::stepwise::modeler::rna::tokenize(), and utility_exit_with_message.

Referenced by filter().

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

References utility_exit_with_message.

Referenced by is_sibling_sugar_rotamer_pose().

bool protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_contact_filter ( PoseOP const &  side_ONE_pose_data, PoseOP const &  side_TWO_pose_data  )

private

References at(), core::chemical::ResidueType::atom_name(), core::conformation::Residue::first_sidechain_atom(), input_pose_ONE_last_appended_res_, input_pose_TWO_last_prepended_res_, moving_res_contact_dist_cutoff_, moving_res_to_base_contact_only_, core::conformation::Residue::natoms(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::conformation::Residue::type(), utility_exit_with_message, working_parameters_, and core::conformation::Residue::xyz().

Referenced by pass_all_filters().

bool protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::pass_all_filters ( PoseOP const &  side_ONE_pose_data, PoseOP const &  side_TWO_pose_data  )

private

References best_combine_score_, protocols::stepwise::modeler::rna::Filterer_Count::chain_closable_geometry_screen, protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_screen(), 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_, input_pose_ONE_last_appended_res_, input_pose_TWO_last_prepended_res_, moving_res_contact_filter(), previously_builded_res_clash_filter(), previously_builded_res_contact_filter(), protocols::stepwise::modeler::rna::Filterer_Count::score_cut_count, protocols::stepwise::modeler::rna::Filterer_Count::total_count, total_energy_from_pose(), utility_exit_with_message, working_parameters_, and worst_combine_score_.

Referenced by do_some_filtering().

bool protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::previously_builded_res_clash_filter ( PoseOP const &  side_ONE_pose_data, PoseOP const &  side_TWO_pose_data  )

private

References clash_dist_cutoff_, num_clash_cutoff_, and previously_builded_res_VDW_filter().

Referenced by pass_all_filters().

bool protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::previously_builded_res_contact_filter ( PoseOP const &  side_ONE_pose_data, PoseOP const &  side_TWO_pose_data  )

private

References contact_dist_cutoff_, num_contact_cutoff_, and previously_builded_res_VDW_filter().

Referenced by pass_all_filters().

bool protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::previously_builded_res_VDW_filter ( PoseOP const &  side_ONE_pose_data, PoseOP const &  side_TWO_pose_data, core::Real const  overlap_dist_cutoff, core::Size const  num_atom_contacts_cutoff  )

private

References input_pose_ONE_appended_res_list_, input_pose_TWO_prepended_res_list_, and protocols::stepwise::modeler::rna::is_residues_in_contact().

Referenced by previously_builded_res_clash_filter(), and previously_builded_res_contact_filter().

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

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

inline

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

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

References silent_file_stream_ONE_, silent_file_stream_TWO_, silent_files_in_, and utility_exit_with_message.

Referenced by filter().

void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::setup_tag_to_source_map ( )

private

References silent_file_stream_ONE_, silent_file_stream_TWO_, tag, tag_to_source_map_ONE_, tag_to_source_map_TWO_, protocols::TR, and utility_exit_with_message.

Referenced by filter().

void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::sort_Combine_Tags_Info ( utility::vector1< Combine_Tags_Info > &  combine_tags_info_list )

private

References protocols::stepwise::modeler::rna::score_sort_criterion().

Referenced by filter().

Member Data Documentation

core::Real protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::best_combine_score_

private

Referenced by do_some_filtering(), and pass_all_filters().

core::Real const protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::clash_dist_cutoff_

private

Referenced by previously_builded_res_clash_filter(), and StepWiseRNA_CombineLongLoopFilterer().

bool protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::combine_helical_silent_file_

private

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

core::Real const protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::contact_dist_cutoff_

private

Referenced by previously_builded_res_contact_filter(), and StepWiseRNA_CombineLongLoopFilterer().

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

Referenced by filter(), and pass_all_filters().

bool protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::filter_for_previous_contact_

private

Referenced by filter(), and pass_all_filters().

Filterer_Count protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::filterer_count_

private

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

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

Referenced by figure_out_appended_and_prepended_res_list(), and StepWiseRNA_CombineLongLoopFilterer().

std::map< core::Size, core::Size > protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::full_to_input_res_map_TWO_

private

Referenced by figure_out_appended_and_prepended_res_list(), and StepWiseRNA_CombineLongLoopFilterer().

utility::vector1< core::Size > protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::input_pose_ONE_appended_res_list_

private

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::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::input_pose_ONE_last_appended_res_

private

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

core::Size protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::input_pose_TWO_last_prepended_res_

private

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

utility::vector1< core::Size > protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::input_pose_TWO_prepended_res_list_

private

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

Size protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::max_decoys_

private

Referenced by filter().

core::Size const protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::max_pose_data_list_size_

private

Referenced by convert_silent_file_to_pose_data_list(), and figure_out_NUM_pose_list().

core::Real protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_contact_dist_cutoff_

private

Referenced by moving_res_contact_filter(), and StepWiseRNA_CombineLongLoopFilterer().

bool const protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_to_base_contact_only_

private

Referenced by filter(), and moving_res_contact_filter().

core::Size const protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::num_clash_cutoff_

private

Referenced by previously_builded_res_clash_filter(), and StepWiseRNA_CombineLongLoopFilterer().

core::Size const protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::num_contact_cutoff_

private

Referenced by previously_builded_res_contact_filter(), and StepWiseRNA_CombineLongLoopFilterer().

std::string protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::output_filename_

private

Referenced by filter().

bool protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::parin_favorite_output_

private

Referenced by filter().

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

Referenced by convert_silent_file_to_pose_data_list().

core::Size protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::side_ONE_NUM_pose_list_

private

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

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

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

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

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::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::silent_file_stream_TWO_

private

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::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::silent_files_in_

private

Referenced by setup_silent_file_stream().

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

Referenced by filter().

bool protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::verbose_

private

working_parameters::StepWiseWorkingParametersCOP const protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::working_parameters_

private

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().

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:

• src/protocols/stepwise/modeler/rna/StepWiseRNA_CombineLongLoopFilterer.hh
• src/protocols/stepwise/modeler/rna/StepWiseRNA_CombineLongLoopFilterer.cc