#include <StepWiseRNA_CombineLongLoopFilterer.hh>

Inheritance diagram for protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer:

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::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_

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

◆ StepWiseRNA_CombineLongLoopFilterer()

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

References clash_dist_cutoff_, combine_helical_silent_file_, contact_dist_cutoff_, protocols::stepwise::modeler::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_, moving_res_contact_dist_cutoff_, num_clash_cutoff_, num_contact_cutoff_, protocols::TR(), and working_parameters_.

◆ ~StepWiseRNA_CombineLongLoopFilterer()

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

overridedefault

Member Function Documentation

◆ align_all_pose()

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

References core::pose::initialize_atomid_map(), 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(), and protocols::TR().

Referenced by do_some_filtering().

◆ convert_silent_file_to_pose_data_list()

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(), core::pose::getPoseExtraScore(), max_pose_data_list_size_, rsd_set_, protocols::hybridization::score, and core::pose::tag_into_pose().

Referenced by do_some_filtering().

◆ 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_, core::pose::tag_from_pose(), protocols::stepwise::modeler::rna::Filterer_Count::total_count, core::pose::total_energy_from_pose(), total_input_struct_pair_, and protocols::TR().

Referenced by filter().

◆ figure_out_appended_and_prepended_res_list()

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_, 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().

◆ figure_out_last_appended_and_last_prepended_res()

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(), and working_parameters_.

Referenced by StepWiseRNA_CombineLongLoopFilterer().

◆ figure_out_NUM_pose_list()

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().

◆ filter()

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

◆ get_parent_tag()

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

private

Referenced by is_sibling_sugar_rotamer_pose().

◆ 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(), and protocols::stepwise::modeler::rna::tokenize().

Referenced by filter().

◆ is_virt_sample_sugar_tag()

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

Referenced by is_sibling_sugar_rotamer_pose().

◆ moving_res_contact_filter()

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

References 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(), working_parameters_, and core::conformation::Residue::xyz().

Referenced by pass_all_filters().

◆ pass_all_filters()

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

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, core::pose::total_energy_from_pose(), working_parameters_, and worst_combine_score_.

Referenced by do_some_filtering().

◆ previously_builded_res_clash_filter()

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

References clash_dist_cutoff_, num_clash_cutoff_, and previously_builded_res_VDW_filter().

Referenced by pass_all_filters().

◆ previously_builded_res_contact_filter()

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

References contact_dist_cutoff_, num_contact_cutoff_, and previously_builded_res_VDW_filter().

Referenced by pass_all_filters().

◆ previously_builded_res_VDW_filter()

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

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().

◆ set_filter_for_previous_clash()

void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::set_filter_for_previous_clash ( core::Real const setting )

inline

References filter_for_previous_clash_.

◆ set_filter_for_previous_contact()

void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::set_filter_for_previous_contact ( core::Real const setting )

inline

References filter_for_previous_contact_.

◆ set_max_decoys()

void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::set_max_decoys ( core::Size const & setting )

inline

References max_decoys_.

◆ set_output_filename()

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

inline

References output_filename_.

◆ set_parin_favorite_output()

void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::set_parin_favorite_output ( bool const setting )

inline

References parin_favorite_output_.

◆ set_silent_files_in()

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

inline

References silent_files_in_.

◆ set_undercount_sugar_rotamers()

void protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::set_undercount_sugar_rotamers ( bool const setting )

inline

References undercount_sugar_rotamers_.

◆ setup_silent_file_stream()

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

private

References silent_file_stream_ONE_, silent_file_stream_TWO_, and silent_files_in_.

Referenced by filter().

◆ setup_tag_to_source_map()

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

private

References silent_file_stream_ONE_, silent_file_stream_TWO_, tag_to_source_map_ONE_, tag_to_source_map_TWO_, and protocols::TR().

Referenced by filter().

◆ sort_Combine_Tags_Info()

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

◆ best_combine_score_

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

private

Referenced by do_some_filtering(), and pass_all_filters().

◆ clash_dist_cutoff_

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

private

Referenced by previously_builded_res_clash_filter(), and StepWiseRNA_CombineLongLoopFilterer().

◆ combine_helical_silent_file_

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

private

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

◆ contact_dist_cutoff_

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

private

Referenced by previously_builded_res_contact_filter(), and StepWiseRNA_CombineLongLoopFilterer().

◆ filter_for_chain_closable_geometry_

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

private

Referenced by filter(), and pass_all_filters().

◆ filter_for_moving_res_contact_

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

private

Referenced by filter(), and pass_all_filters().

◆ filter_for_previous_clash_

bool protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::filter_for_previous_clash_

private

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

◆ filter_for_previous_contact_

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

private

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

◆ filterer_count_

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

private

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

◆ filterered_combine_tag_info_list_

utility::vector1< Combine_Tags_Info > protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::filterered_combine_tag_info_list_

private

Referenced by do_some_filtering(), and filter().

◆ full_to_input_res_map_ONE_

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().

◆ full_to_input_res_map_TWO_

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().

◆ input_pose_ONE_appended_res_list_

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().

◆ input_pose_ONE_last_appended_res_

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().

◆ input_pose_TWO_last_prepended_res_

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().

◆ input_pose_TWO_prepended_res_list_

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().

◆ max_decoys_

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

private

Referenced by filter(), and set_max_decoys().

◆ max_pose_data_list_size_

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().

◆ moving_res_contact_dist_cutoff_

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

private

Referenced by moving_res_contact_filter(), and StepWiseRNA_CombineLongLoopFilterer().

◆ moving_res_to_base_contact_only_

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

private

Referenced by filter(), and moving_res_contact_filter().

◆ num_clash_cutoff_

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

private

Referenced by previously_builded_res_clash_filter(), and StepWiseRNA_CombineLongLoopFilterer().

◆ num_contact_cutoff_

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

private

Referenced by previously_builded_res_contact_filter(), and StepWiseRNA_CombineLongLoopFilterer().

◆ output_filename_

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

private

Referenced by filter(), and set_output_filename().

◆ parin_favorite_output_

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

private

Referenced by filter(), and set_parin_favorite_output().

◆ pass_screen_struct_pair_

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

private

Referenced by do_some_filtering(), and filter().

◆ rsd_set_

core::chemical::ResidueTypeSetCAP protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::rsd_set_

private

Referenced by convert_silent_file_to_pose_data_list().

◆ side_ONE_NUM_pose_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().

◆ side_ONE_pose_list_id_

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

private

Referenced by do_some_filtering(), and filter().

◆ side_TWO_NUM_pose_list_

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().

◆ side_TWO_pose_list_id_

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

private

Referenced by do_some_filtering(), and filter().

◆ silent_file_stream_ONE_

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().

◆ silent_file_stream_TWO_

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().

◆ silent_files_in_

utility::vector1< std::string > protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::silent_files_in_

private

Referenced by set_silent_files_in(), and setup_silent_file_stream().

◆ tag_to_source_map_ONE_

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().

◆ tag_to_source_map_TWO_

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().

◆ total_input_struct_pair_

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

private

Referenced by do_some_filtering(), and filter().

◆ undercount_sugar_rotamers_

bool protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::undercount_sugar_rotamers_

private

Referenced by filter(), and set_undercount_sugar_rotamers().

◆ working_parameters_

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().

◆ worst_combine_score_

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

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ StepWiseRNA_CombineLongLoopFilterer()

◆ ~StepWiseRNA_CombineLongLoopFilterer()

Member Function Documentation

◆ align_all_pose()

◆ convert_silent_file_to_pose_data_list()

◆ do_some_filtering()

◆ figure_out_appended_and_prepended_res_list()

◆ figure_out_last_appended_and_last_prepended_res()

◆ figure_out_NUM_pose_list()

◆ filter()

◆ get_parent_tag()

◆ is_sibling_sugar_rotamer_pose()

◆ is_virt_sample_sugar_tag()

◆ moving_res_contact_filter()

◆ pass_all_filters()

◆ previously_builded_res_clash_filter()

◆ previously_builded_res_contact_filter()

◆ previously_builded_res_VDW_filter()

◆ set_filter_for_previous_clash()

◆ set_filter_for_previous_contact()

◆ set_max_decoys()

◆ set_output_filename()

◆ set_parin_favorite_output()

◆ set_silent_files_in()

◆ set_undercount_sugar_rotamers()

◆ setup_silent_file_stream()

◆ setup_tag_to_source_map()

◆ sort_Combine_Tags_Info()

Member Data Documentation

◆ best_combine_score_

◆ clash_dist_cutoff_

◆ combine_helical_silent_file_

◆ contact_dist_cutoff_

◆ filter_for_chain_closable_geometry_

◆ filter_for_moving_res_contact_

◆ filter_for_previous_clash_

◆ filter_for_previous_contact_

◆ filterer_count_

◆ filterered_combine_tag_info_list_

◆ full_to_input_res_map_ONE_

◆ full_to_input_res_map_TWO_

◆ input_pose_ONE_appended_res_list_

◆ input_pose_ONE_last_appended_res_

◆ input_pose_TWO_last_prepended_res_

◆ input_pose_TWO_prepended_res_list_

◆ max_decoys_

◆ max_pose_data_list_size_

◆ moving_res_contact_dist_cutoff_

◆ moving_res_to_base_contact_only_

◆ num_clash_cutoff_

◆ num_contact_cutoff_

◆ output_filename_

◆ parin_favorite_output_

◆ pass_screen_struct_pair_

◆ rsd_set_

◆ side_ONE_NUM_pose_list_

◆ side_ONE_pose_list_id_

◆ side_TWO_NUM_pose_list_

◆ side_TWO_pose_list_id_

◆ silent_file_stream_ONE_

◆ silent_file_stream_TWO_

◆ silent_files_in_

◆ tag_to_source_map_ONE_

◆ tag_to_source_map_TWO_

◆ total_input_struct_pair_

◆ undercount_sugar_rotamers_

◆ working_parameters_

◆ worst_combine_score_