#include <StepWiseRNA_Clusterer.hh>

Inheritance diagram for protocols::swa::rna::StepWiseRNA_Clusterer:

Collaboration diagram for protocols::swa::rna::StepWiseRNA_Clusterer:

Public Member Functions
	StepWiseRNA_Clusterer (utility::vector1< std::string > const &silent_files_in)

	StepWiseRNA_Clusterer (std::string const &silent_file_in)

	StepWiseRNA_Clusterer (core::io::silent::SilentFileDataOP &sfd)

virtual	~StepWiseRNA_Clusterer ()

void	set_max_decoys (core::Size const &setting)
	Filter a list of poses by score. More...

void	set_score_diff_cut (core::Real const &setting)

void	set_perform_score_diff_cut (bool const &setting)

void	set_cluster_radius (core::Real const &setting)

void	set_suite_cluster_radius (core::Real const &setting)

void	set_loop_cluster_radius (core::Real const &setting)

void	set_rename_tags (core::Real const &setting)

void	set_distinguish_pucker (core::Real const &setting)

void	set_add_lead_zero_to_tag (core::Real const &setting)

void	set_job_parameters (protocols::swa::rna::StepWiseRNA_JobParametersCOP &job_parameters)

void	set_job_parameters_exist (bool const job_parameters_exist)

void	set_quick_alignment (bool const &setting)

void	set_align_only_over_base_atoms (bool const &setting)

void	set_optimize_memory_usage (bool const &setting)

void	set_keep_pose_in_memory (bool const &setting)

void	set_two_stage_clustering (bool const &setting)

void	set_verbose (bool const &setting)

void	cluster ()

void	output_silent_file (std::string const &silent_file)

void	recalculate_rmsd_and_output_silent_file (std::string const &silent_file, protocols::swa::rna::StepWiseRNA_PoseSetupOP &stepwise_rna_pose_setup, bool const write_score_only)

void	get_best_neighboring_shift_RMSD_and_output_silent_file (std::string const &silent_file)

void	set_PBP_clustering_at_chain_closure (bool const &setting)

void	set_skip_clustering (bool const &setting)

void	set_filter_virtual_res_list (utility::vector1< core::Size > const &setting)

void	set_perform_VDW_rep_screen (bool const &setting)

void	set_perform_filters (bool const &setting)

void	set_min_num_south_ribose_filter (Size const &setting)

void	set_VDW_rep_screen_info (utility::vector1< std::string > const &setting)

void	set_user_input_VDW_bin_screener (protocols::swa::rna::StepWiseRNA_VDW_Bin_ScreenerOP const &user_input_VDW_bin_screener)

void	set_full_length_loop_rmsd_clustering (bool const &setting)

void	set_ignore_FARFAR_no_auto_bulge_tag (bool const &setting)

void	set_ignore_FARFAR_no_auto_bulge_parent_tag (bool const &setting)

void	set_ignore_unmatched_virtual_res (bool const &setting)

void	set_output_pdb (bool const setting)

Private Member Functions
void	initialize_parameters_and_input ()

void	create_silent_file_and_tag_list ()

void	do_some_clustering ()

void	two_stage_clustering ()

void	create_large_cluster_centers_member_list ()

bool	Is_old_individual_suite_cluster (core::pose::Pose const &current_pose, core::pose::Pose const &cluster_center_pose, utility::vector1< core::Size > const &rmsd_res_list, std::map< core::Size, core::Size > const &full_to_sub, std::map< core::Size, bool > const &Is_prepend_map, core::Real const &cluster_radius) const

core::pose::PoseOP	get_poseOP (Size const n)

void	setup_fail_triangle_inequailty_list (core::pose::Pose &current_pose, std::string const &tag, utility::vector1< bool > &fail_triangle_inequality_list)

bool	Is_new_cluster_center_with_job_parameters (core::pose::PoseOP const &pose_op, std::string const &tag)

bool	check_for_closeness_without_job_parameters (core::pose::PoseOP const &pose_op)

bool	check_for_closeness (core::pose::PoseOP const &pose_op, std::string const &tag)

utility::vector1< core::Size > const &	get_act_alignment_res () const

utility::vector1< core::Size > const &	get_act_rmsd_res_list () const

std::map< core::Size, core::Size > const &	get_act_full_to_sub () const

std::map< core::Size, bool > const &	get_act_Is_prepend_map () const

void	initialize_quick_alignment_pose ()

void	initialize_max_memory_pose_num ()

void	align_to_quick_alignment_pose (core::pose::Pose &pose, std::string const &tag) const

void	initialize_VDW_rep_screener ()

void	create_tags_map ()

bool	pass_FARFAR_no_auto_bulge_filter (core::io::silent::SilentStructOP const &silent_struct) const

Private Attributes
utility::vector1< std::string >	silent_files_

core::import_pose::pose_stream::SilentFilePoseInputStreamOP	input_

utility::vector1 < core::pose::PoseOP >	pose_output_list_

utility::vector1< std::string >	tag_output_list_

utility::vector1 < core::io::silent::SilentStructOP >	silent_struct_output_list_

Size	max_decoys_

core::Real	score_diff_cut_

bool	perform_score_diff_cut_

core::Real	whole_struct_cluster_radius_

core::Real	suite_cluster_radius_

core::Real	loop_cluster_radius_

bool	rename_tags_

protocols::swa::rna::StepWiseRNA_JobParametersCOP	job_parameters_

bool	job_parameters_exist_

bool	distinguish_pucker_

bool	add_lead_zero_to_tag_

bool	quick_alignment_

bool	align_only_over_base_atoms_

bool	optimize_memory_usage_

SlicedPoseJobParameters	sliced_pose_job_params_

bool	verbose_

bool	keep_pose_in_memory_

bool	keep_pose_in_memory_hydrid_

Size	max_memory_pose_num_

bool	two_stage_clustering_

bool	use_triangle_inequality_

core::pose::Pose	first_pose_

utility::vector1 < utility::vector1 < Cluster_Member > >	cluster_centers_neighbor_list_

utility::vector1 < core::pose::PoseOP >	large_cluster_pose_list_

utility::vector1< core::Size >	all_pose_to_output_pose_ID_map_

bool	PBP_clustering_at_chain_closure_

bool	quick_alignment_pose_is_intialized_

core::pose::Pose	quick_alignment_pose_

std::string	quick_alignment_tag_

bool	skip_clustering_

protocols::swa::rna::StepWiseRNA_VDW_Bin_ScreenerOP	user_input_VDW_bin_screener_

bool	perform_VDW_rep_screen_

bool	perform_filters_

Size	min_num_south_ribose_filter_

utility::vector1< std::string >	VDW_rep_screen_info_

bool	full_length_loop_rmsd_clustering_

utility::vector1< core::Size >	filter_virtual_res_list_

std::map< std::string, bool >	current_tags_map_

std::map< std::string, bool >	parent_tags_map_

bool	ignore_FARFAR_no_auto_bulge_parent_tag_

bool	ignore_FARFAR_no_auto_bulge_tag_

bool	ignore_unmatched_virtual_res_

bool	output_pdb_

core::chemical::ResidueTypeSetCAP	rsd_set_

Detailed Description

Definition at line 105 of file StepWiseRNA_Clusterer.hh.

Constructor & Destructor Documentation

protocols::swa::rna::StepWiseRNA_Clusterer::StepWiseRNA_Clusterer ( utility::vector1< std::string > const & silent_files_in)

Definition at line 76 of file StepWiseRNA_Clusterer.cc.

protocols::swa::rna::StepWiseRNA_Clusterer::StepWiseRNA_Clusterer ( std::string const & silent_file_in)

Definition at line 83 of file StepWiseRNA_Clusterer.cc.

protocols::swa::rna::StepWiseRNA_Clusterer::StepWiseRNA_Clusterer ( core::io::silent::SilentFileDataOP & sfd)

Definition at line 93 of file StepWiseRNA_Clusterer.cc.

protocols::swa::rna::StepWiseRNA_Clusterer::~StepWiseRNA_Clusterer ( )

virtual

Definition at line 101 of file StepWiseRNA_Clusterer.cc.

Member Function Documentation

void protocols::swa::rna::StepWiseRNA_Clusterer::align_to_quick_alignment_pose	(	core::pose::Pose &	pose,
		std::string const &	tag
	)		const

private

Definition at line 451 of file StepWiseRNA_Clusterer.cc.

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

bool protocols::swa::rna::StepWiseRNA_Clusterer::check_for_closeness	(	core::pose::PoseOP const &	pose_op,
		std::string const &	tag
	)

private

Definition at line 1201 of file StepWiseRNA_Clusterer.cc.

bool protocols::swa::rna::StepWiseRNA_Clusterer::check_for_closeness_without_job_parameters ( core::pose::PoseOP const & pose_op)

private

Definition at line 1183 of file StepWiseRNA_Clusterer.cc.

References core::scoring::all_atom_rmsd().

void protocols::swa::rna::StepWiseRNA_Clusterer::cluster ( )

Definition at line 150 of file StepWiseRNA_Clusterer.cc.

References protocols::swa::rna::Output_boolean(), and protocols::swa::rna::Output_title_text().

void protocols::swa::rna::StepWiseRNA_Clusterer::create_large_cluster_centers_member_list ( )

private

Definition at line 521 of file StepWiseRNA_Clusterer.cc.

References protocols::swa::rna::align_poses(), protocols::swa::rna::check_for_messed_up_structure(), core::pose::getPoseExtraScores(), protocols::swa::rna::Cluster_Member::ID, protocols::swa::rna::Output_title_text(), protocols::swa::rna::Cluster_Member::RMSD, protocols::swa::rna::rmsd_over_residue_list(), and protocols::swa::rna::Cluster_Member::score.

void protocols::swa::rna::StepWiseRNA_Clusterer::create_silent_file_and_tag_list ( )

private

Definition at line 607 of file StepWiseRNA_Clusterer.cc.

References protocols::swa::rna::apply_full_to_sub_mapping(), protocols::swa::rna::check_for_messed_up_structure(), protocols::swa::rna::Get_residue_base_state(), protocols::swa::rna::Get_residue_pucker_state(), protocols::swa::rna::NORTH, protocols::swa::rna::Output_seq_num_list(), protocols::swa::rna::Output_title_text(), protocols::swa::rna::SOUTH, and protocols::swa::rna::SYN.

void protocols::swa::rna::StepWiseRNA_Clusterer::create_tags_map ( )

private

Definition at line 1529 of file StepWiseRNA_Clusterer.cc.

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

void protocols::swa::rna::StepWiseRNA_Clusterer::do_some_clustering ( )

private

Definition at line 773 of file StepWiseRNA_Clusterer.cc.

References protocols::swa::rna::check_for_messed_up_structure(), core::pose::getPoseExtraScores(), and core::TR().

utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_Clusterer::get_act_alignment_res ( ) const

private

Definition at line 1671 of file StepWiseRNA_Clusterer.cc.

std::map< core::Size, core::Size > const & protocols::swa::rna::StepWiseRNA_Clusterer::get_act_full_to_sub ( ) const

private

Definition at line 1683 of file StepWiseRNA_Clusterer.cc.

std::map< core::Size, bool > const & protocols::swa::rna::StepWiseRNA_Clusterer::get_act_Is_prepend_map ( ) const

private

Definition at line 1689 of file StepWiseRNA_Clusterer.cc.

utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_Clusterer::get_act_rmsd_res_list ( ) const

private

Definition at line 1677 of file StepWiseRNA_Clusterer.cc.

void protocols::swa::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file ( std::string const & silent_file)

Definition at line 1387 of file StepWiseRNA_Clusterer.cc.

References protocols::swa::rna::align_poses(), protocols::swa::rna::check_for_messed_up_structure(), protocols::swa::rna::full_length_rmsd_over_residue_list(), core::pose::getPoseExtraScores(), protocols::loops::loop_rmsd(), protocols::swa::rna::Output_boolean(), protocols::swa::rna::Output_title_text(), protocols::swa::rna::rmsd_over_residue_list(), and core::pose::Pose::total_residue().

core::pose::PoseOP protocols::swa::rna::StepWiseRNA_Clusterer::get_poseOP ( Size const n)

private

Definition at line 1012 of file StepWiseRNA_Clusterer.cc.

void protocols::swa::rna::StepWiseRNA_Clusterer::initialize_max_memory_pose_num ( )

private

Definition at line 253 of file StepWiseRNA_Clusterer.cc.

References protocols::swa::rna::check_for_messed_up_structure(), and protocols::swa::rna::Output_boolean().

void protocols::swa::rna::StepWiseRNA_Clusterer::initialize_parameters_and_input ( )

private

Definition at line 106 of file StepWiseRNA_Clusterer.cc.

References core::chemical::ChemicalManager::get_instance(), core::chemical::ChemicalManager::residue_type_set(), and core::chemical::RNA.

void protocols::swa::rna::StepWiseRNA_Clusterer::initialize_quick_alignment_pose ( )

private

Definition at line 387 of file StepWiseRNA_Clusterer.cc.

References protocols::swa::rna::check_for_messed_up_structure(), core::scoring::rna::chemical_shift::Contain_seq_num(), and protocols::swa::rna::Output_seq_num_list().

void protocols::swa::rna::StepWiseRNA_Clusterer::initialize_VDW_rep_screener ( )

private

Definition at line 346 of file StepWiseRNA_Clusterer.cc.

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

bool protocols::swa::rna::StepWiseRNA_Clusterer::Is_new_cluster_center_with_job_parameters	(	core::pose::PoseOP const &	pose_op,
		std::string const &	tag
	)

private

Definition at line 1117 of file StepWiseRNA_Clusterer.cc.

References protocols::swa::rna::align_poses(), protocols::swa::rna::full_length_rmsd_over_residue_list(), protocols::loops::loop_rmsd(), protocols::swa::rna::Output_boolean(), and protocols::swa::rna::rmsd_over_residue_list().

bool protocols::swa::rna::StepWiseRNA_Clusterer::Is_old_individual_suite_cluster	(	core::pose::Pose const &	current_pose,
		core::pose::Pose const &	cluster_center_pose,
		utility::vector1< core::Size > const &	rmsd_res_list,
		std::map< core::Size, core::Size > const &	full_to_sub,
		std::map< core::Size, bool > const &	Is_prepend_map,
		core::Real const &	cluster_radius
	)		const

private

Definition at line 892 of file StepWiseRNA_Clusterer.cc.

References protocols::swa::rna::Get_residue_pucker_state(), core::conformation::Residue::has_variant_type(), protocols::swa::rna::Is_same_ribose_pucker(), protocols::swa::rna::Output_boolean(), protocols::swa::rna::phosphate_base_phosphate_rmsd(), protocols::swa::rna::print_ribose_pucker_state(), core::pose::Pose::residue(), and protocols::swa::rna::suite_rmsd().

void protocols::swa::rna::StepWiseRNA_Clusterer::output_silent_file ( std::string const & silent_file)

Definition at line 1219 of file StepWiseRNA_Clusterer.cc.

bool protocols::swa::rna::StepWiseRNA_Clusterer::pass_FARFAR_no_auto_bulge_filter ( core::io::silent::SilentStructOP const & silent_struct) const

private

Definition at line 1582 of file StepWiseRNA_Clusterer.cc.

void protocols::swa::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file	(	std::string const &	silent_file,
		protocols::swa::rna::StepWiseRNA_PoseSetupOP &	stepwise_rna_pose_setup,
		bool const	write_score_only
	)

Definition at line 1250 of file StepWiseRNA_Clusterer.cc.

References protocols::swa::rna::align_poses(), protocols::swa::rna::check_for_messed_up_structure(), protocols::swa::rna::full_length_rmsd_over_residue_list(), core::pose::getPoseExtraScores(), protocols::swa::rna::Output_boolean(), protocols::swa::rna::Output_title_text(), protocols::swa::rna::remove_all_variant_types(), core::scoring::rms_at_corresponding_heavy_atoms(), protocols::swa::rna::rmsd_over_residue_list(), and core::pose::Pose::total_residue().

void protocols::swa::rna::StepWiseRNA_Clusterer::set_add_lead_zero_to_tag ( core::Real const & setting)

inline

Definition at line 137 of file StepWiseRNA_Clusterer.hh.

References add_lead_zero_to_tag_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_align_only_over_base_atoms ( bool const & setting)

inline

Definition at line 145 of file StepWiseRNA_Clusterer.hh.

References align_only_over_base_atoms_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_cluster_radius ( core::Real const & setting)

inline

Definition at line 127 of file StepWiseRNA_Clusterer.hh.

References whole_struct_cluster_radius_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_distinguish_pucker ( core::Real const & setting)

inline

Definition at line 135 of file StepWiseRNA_Clusterer.hh.

References distinguish_pucker_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_filter_virtual_res_list ( utility::vector1< core::Size > const & setting)

inline

Definition at line 176 of file StepWiseRNA_Clusterer.hh.

References filter_virtual_res_list_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_full_length_loop_rmsd_clustering ( bool const & setting)

inline

Definition at line 194 of file StepWiseRNA_Clusterer.hh.

References full_length_loop_rmsd_clustering_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_ignore_FARFAR_no_auto_bulge_parent_tag ( bool const & setting)

inline

Definition at line 200 of file StepWiseRNA_Clusterer.hh.

References ignore_FARFAR_no_auto_bulge_parent_tag_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_ignore_FARFAR_no_auto_bulge_tag ( bool const & setting)

inline

Definition at line 197 of file StepWiseRNA_Clusterer.hh.

References ignore_FARFAR_no_auto_bulge_tag_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_ignore_unmatched_virtual_res ( bool const & setting)

inline

Definition at line 203 of file StepWiseRNA_Clusterer.hh.

References ignore_unmatched_virtual_res_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_job_parameters ( protocols::swa::rna::StepWiseRNA_JobParametersCOP & job_parameters)

Definition at line 1656 of file StepWiseRNA_Clusterer.cc.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_job_parameters_exist ( bool const job_parameters_exist)

Definition at line 1663 of file StepWiseRNA_Clusterer.cc.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_keep_pose_in_memory ( bool const & setting)

inline

Definition at line 149 of file StepWiseRNA_Clusterer.hh.

References keep_pose_in_memory_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_loop_cluster_radius ( core::Real const & setting)

inline

Definition at line 131 of file StepWiseRNA_Clusterer.hh.

References loop_cluster_radius_.

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

inline

Filter a list of poses by score.

Definition at line 121 of file StepWiseRNA_Clusterer.hh.

References max_decoys_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_min_num_south_ribose_filter ( Size const & setting)

inline

Definition at line 185 of file StepWiseRNA_Clusterer.hh.

References min_num_south_ribose_filter_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_optimize_memory_usage ( bool const & setting)

inline

Definition at line 147 of file StepWiseRNA_Clusterer.hh.

References optimize_memory_usage_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_output_pdb ( bool const setting)

inline

Definition at line 206 of file StepWiseRNA_Clusterer.hh.

References output_pdb_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_PBP_clustering_at_chain_closure ( bool const & setting)

inline

Definition at line 170 of file StepWiseRNA_Clusterer.hh.

References PBP_clustering_at_chain_closure_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_perform_filters ( bool const & setting)

inline

Definition at line 182 of file StepWiseRNA_Clusterer.hh.

References perform_filters_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_perform_score_diff_cut ( bool const & setting)

inline

Definition at line 125 of file StepWiseRNA_Clusterer.hh.

References perform_score_diff_cut_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_perform_VDW_rep_screen ( bool const & setting)

inline

Definition at line 179 of file StepWiseRNA_Clusterer.hh.

References perform_VDW_rep_screen_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_quick_alignment ( bool const & setting)

inline

Definition at line 143 of file StepWiseRNA_Clusterer.hh.

References quick_alignment_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_rename_tags ( core::Real const & setting)

inline

Definition at line 133 of file StepWiseRNA_Clusterer.hh.

References rename_tags_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_score_diff_cut ( core::Real const & setting)

inline

Definition at line 123 of file StepWiseRNA_Clusterer.hh.

References score_diff_cut_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_skip_clustering ( bool const & setting)

inline

Definition at line 173 of file StepWiseRNA_Clusterer.hh.

References skip_clustering_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_suite_cluster_radius ( core::Real const & setting)

inline

Definition at line 129 of file StepWiseRNA_Clusterer.hh.

References suite_cluster_radius_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_two_stage_clustering ( bool const & setting)

inline

Definition at line 151 of file StepWiseRNA_Clusterer.hh.

References two_stage_clustering_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_user_input_VDW_bin_screener ( protocols::swa::rna::StepWiseRNA_VDW_Bin_ScreenerOP const & user_input_VDW_bin_screener)

inline

Definition at line 191 of file StepWiseRNA_Clusterer.hh.

References user_input_VDW_bin_screener_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_VDW_rep_screen_info ( utility::vector1< std::string > const & setting)

inline

Definition at line 188 of file StepWiseRNA_Clusterer.hh.

References VDW_rep_screen_info_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_verbose ( bool const & setting)

inline

Definition at line 153 of file StepWiseRNA_Clusterer.hh.

References verbose_.

void protocols::swa::rna::StepWiseRNA_Clusterer::setup_fail_triangle_inequailty_list	(	core::pose::Pose &	current_pose,
		std::string const &	tag,
		utility::vector1< bool > &	fail_triangle_inequality_list
	)