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protocols::swa::rna::StepWiseRNA_Clusterer Class Reference

#include <StepWiseRNA_Clusterer.hh>

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

Constructor & Destructor Documentation

protocols::swa::rna::StepWiseRNA_Clusterer::StepWiseRNA_Clusterer ( utility::vector1< std::string > const &  silent_files_in)
protocols::swa::rna::StepWiseRNA_Clusterer::StepWiseRNA_Clusterer ( std::string const &  silent_file_in)
protocols::swa::rna::StepWiseRNA_Clusterer::StepWiseRNA_Clusterer ( core::io::silent::SilentFileDataOP &  sfd)
protocols::swa::rna::StepWiseRNA_Clusterer::~StepWiseRNA_Clusterer ( )
virtual

Member Function Documentation

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

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

References core::scoring::all_atom_rmsd().

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

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

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

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

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

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

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
std::map< core::Size, core::Size > const & protocols::swa::rna::StepWiseRNA_Clusterer::get_act_full_to_sub ( ) const
private
std::map< core::Size, bool > const & protocols::swa::rna::StepWiseRNA_Clusterer::get_act_Is_prepend_map ( ) const
private
utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_Clusterer::get_act_rmsd_res_list ( ) const
private
void protocols::swa::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file ( std::string const &  silent_file)

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

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

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

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

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

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

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

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

References add_lead_zero_to_tag_.

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

References align_only_over_base_atoms_.

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

References whole_struct_cluster_radius_.

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

References distinguish_pucker_.

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

References filter_virtual_res_list_.

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

References full_length_loop_rmsd_clustering_.

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

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

References ignore_FARFAR_no_auto_bulge_tag_.

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

References ignore_unmatched_virtual_res_.

void protocols::swa::rna::StepWiseRNA_Clusterer::set_job_parameters ( protocols::swa::rna::StepWiseRNA_JobParametersCOP &  job_parameters)
void protocols::swa::rna::StepWiseRNA_Clusterer::set_job_parameters_exist ( bool const  job_parameters_exist)
void protocols::swa::rna::StepWiseRNA_Clusterer::set_keep_pose_in_memory ( bool const &  setting)
inline

References keep_pose_in_memory_.

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

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.

References max_decoys_.

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

References min_num_south_ribose_filter_.

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

References optimize_memory_usage_.

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

References output_pdb_.

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

References PBP_clustering_at_chain_closure_.

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

References perform_filters_.

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

References perform_score_diff_cut_.

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

References perform_VDW_rep_screen_.

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

References quick_alignment_.

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

References rename_tags_.

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

References score_diff_cut_.

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

References skip_clustering_.

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

References suite_cluster_radius_.

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

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

References user_input_VDW_bin_screener_.

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

References VDW_rep_screen_info_.

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

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 
)
private

References protocols::swa::rna::align_poses(), core::pose::getPoseExtraScores(), protocols::swa::rna::Cluster_Member::ID, 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::two_stage_clustering ( )
private

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

Member Data Documentation

bool protocols::swa::rna::StepWiseRNA_Clusterer::add_lead_zero_to_tag_
private

Referenced by set_add_lead_zero_to_tag().

bool protocols::swa::rna::StepWiseRNA_Clusterer::align_only_over_base_atoms_
private

Referenced by set_align_only_over_base_atoms().

utility::vector1< core::Size> protocols::swa::rna::StepWiseRNA_Clusterer::all_pose_to_output_pose_ID_map_
private
utility::vector1< utility::vector1< Cluster_Member > > protocols::swa::rna::StepWiseRNA_Clusterer::cluster_centers_neighbor_list_
private
std::map< std::string, bool > protocols::swa::rna::StepWiseRNA_Clusterer::current_tags_map_
private
bool protocols::swa::rna::StepWiseRNA_Clusterer::distinguish_pucker_
private

Referenced by set_distinguish_pucker().

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_Clusterer::filter_virtual_res_list_
private

Referenced by set_filter_virtual_res_list().

core::pose::Pose protocols::swa::rna::StepWiseRNA_Clusterer::first_pose_
private
bool protocols::swa::rna::StepWiseRNA_Clusterer::full_length_loop_rmsd_clustering_
private

Referenced by set_full_length_loop_rmsd_clustering().

bool protocols::swa::rna::StepWiseRNA_Clusterer::ignore_FARFAR_no_auto_bulge_parent_tag_
private

Referenced by set_ignore_FARFAR_no_auto_bulge_parent_tag().

bool protocols::swa::rna::StepWiseRNA_Clusterer::ignore_FARFAR_no_auto_bulge_tag_
private

Referenced by set_ignore_FARFAR_no_auto_bulge_tag().

bool protocols::swa::rna::StepWiseRNA_Clusterer::ignore_unmatched_virtual_res_
private

Referenced by set_ignore_unmatched_virtual_res().

core::import_pose::pose_stream::SilentFilePoseInputStreamOP protocols::swa::rna::StepWiseRNA_Clusterer::input_
private
protocols::swa::rna::StepWiseRNA_JobParametersCOP protocols::swa::rna::StepWiseRNA_Clusterer::job_parameters_
private
bool protocols::swa::rna::StepWiseRNA_Clusterer::job_parameters_exist_
private
bool protocols::swa::rna::StepWiseRNA_Clusterer::keep_pose_in_memory_
private

Referenced by set_keep_pose_in_memory().

bool protocols::swa::rna::StepWiseRNA_Clusterer::keep_pose_in_memory_hydrid_
private
utility::vector1< core::pose::PoseOP > protocols::swa::rna::StepWiseRNA_Clusterer::large_cluster_pose_list_
private
core::Real protocols::swa::rna::StepWiseRNA_Clusterer::loop_cluster_radius_
private

Referenced by set_loop_cluster_radius().

Size protocols::swa::rna::StepWiseRNA_Clusterer::max_decoys_
private

Referenced by set_max_decoys().

Size protocols::swa::rna::StepWiseRNA_Clusterer::max_memory_pose_num_
private
Size protocols::swa::rna::StepWiseRNA_Clusterer::min_num_south_ribose_filter_
private

Referenced by set_min_num_south_ribose_filter().

bool protocols::swa::rna::StepWiseRNA_Clusterer::optimize_memory_usage_
private

Referenced by set_optimize_memory_usage().

bool protocols::swa::rna::StepWiseRNA_Clusterer::output_pdb_
private

Referenced by set_output_pdb().

std::map< std::string, bool > protocols::swa::rna::StepWiseRNA_Clusterer::parent_tags_map_
private
bool protocols::swa::rna::StepWiseRNA_Clusterer::PBP_clustering_at_chain_closure_
private

Referenced by set_PBP_clustering_at_chain_closure().

bool protocols::swa::rna::StepWiseRNA_Clusterer::perform_filters_
private

Referenced by set_perform_filters().

bool protocols::swa::rna::StepWiseRNA_Clusterer::perform_score_diff_cut_
private

Referenced by set_perform_score_diff_cut().

bool protocols::swa::rna::StepWiseRNA_Clusterer::perform_VDW_rep_screen_
private

Referenced by set_perform_VDW_rep_screen().

utility::vector1< core::pose::PoseOP > protocols::swa::rna::StepWiseRNA_Clusterer::pose_output_list_
private
bool protocols::swa::rna::StepWiseRNA_Clusterer::quick_alignment_
private

Referenced by set_quick_alignment().

core::pose::Pose protocols::swa::rna::StepWiseRNA_Clusterer::quick_alignment_pose_
private
bool protocols::swa::rna::StepWiseRNA_Clusterer::quick_alignment_pose_is_intialized_
private
std::string protocols::swa::rna::StepWiseRNA_Clusterer::quick_alignment_tag_
private
bool protocols::swa::rna::StepWiseRNA_Clusterer::rename_tags_
private

Referenced by set_rename_tags().

core::chemical::ResidueTypeSetCAP protocols::swa::rna::StepWiseRNA_Clusterer::rsd_set_
private
core::Real protocols::swa::rna::StepWiseRNA_Clusterer::score_diff_cut_
private

Referenced by set_score_diff_cut().

utility::vector1< std::string > protocols::swa::rna::StepWiseRNA_Clusterer::silent_files_
private
utility::vector1< core::io::silent::SilentStructOP > protocols::swa::rna::StepWiseRNA_Clusterer::silent_struct_output_list_
private
bool protocols::swa::rna::StepWiseRNA_Clusterer::skip_clustering_
private

Referenced by set_skip_clustering().

SlicedPoseJobParameters protocols::swa::rna::StepWiseRNA_Clusterer::sliced_pose_job_params_
private
core::Real protocols::swa::rna::StepWiseRNA_Clusterer::suite_cluster_radius_
private

Referenced by set_suite_cluster_radius().

utility::vector1< std::string > protocols::swa::rna::StepWiseRNA_Clusterer::tag_output_list_
private
bool protocols::swa::rna::StepWiseRNA_Clusterer::two_stage_clustering_
private

Referenced by set_two_stage_clustering().

bool protocols::swa::rna::StepWiseRNA_Clusterer::use_triangle_inequality_
private
protocols::swa::rna::StepWiseRNA_VDW_Bin_ScreenerOP protocols::swa::rna::StepWiseRNA_Clusterer::user_input_VDW_bin_screener_
private

Referenced by set_user_input_VDW_bin_screener().

utility::vector1< std::string > protocols::swa::rna::StepWiseRNA_Clusterer::VDW_rep_screen_info_
private

Referenced by set_VDW_rep_screen_info().

bool protocols::swa::rna::StepWiseRNA_Clusterer::verbose_
private

Referenced by set_verbose().

core::Real protocols::swa::rna::StepWiseRNA_Clusterer::whole_struct_cluster_radius_
private

Referenced by set_cluster_radius().

The documentation for this class was generated from the following files:
Generated on Sat Jun 1 2013 12:55:56 for Rosetta 3.5 by   doxygen 1.8.4