17 #ifndef INCLUDED_protocols_stepwise_rna_StepWiseRNA_Clusterer_HH
18 #define INCLUDED_protocols_stepwise_rna_StepWiseRNA_Clusterer_HH
27 #include <utility/pointer/ReferenceCount.hh>
28 #include <utility/vector1.hh>
161 bool const write_score_only );
226 utility::vector1 < core::Size >
const & calc_rms_res,
227 std::map< core::Size, core::Size >
const &
full_to_sub,
228 std::map< core::Size, bool >
const & is_prepend_map,
249 utility::vector1< core::Size >
const &
252 utility::vector1 < core::Size >
const &
255 std::map< core::Size, core::Size >
const &
258 std::map< core::Size, bool >
const &
void align_to_quick_alignment_pose(core::pose::Pose &pose, std::string const &tag) const
utility::vector1< core::Size > const & get_act_alignment_res() const
void set_loop_cluster_radius(core::Real const &setting)
utility::vector1< core::Size > filter_virtual_res_list_
core::pose::Pose create_sliced_pose(core::pose::Pose const &working_pose)
void two_stage_clustering()
SlicedPoseWorkingParameters sliced_pose_job_params_
bool ignore_FARFAR_no_auto_bulge_parent_tag_
utility::vector1< std::string > VDW_rep_screen_info_
virtual ~SlicedPoseWorkingParameters()
bool add_lead_zero_to_tag_
utility::vector1< core::Size > sliced_to_working_res_map_
void set_suite_cluster_radius(core::Real const &setting)
void set_score_diff_cut(core::Real const &setting)
void setup_fail_triangle_inequailty_list(core::pose::Pose ¤t_pose, std::string const &tag, utility::vector1< bool > &fail_triangle_inequality_list)
Pose forward declarations header.
void set_working_parameters_exist(bool const working_parameters_exist)
bool keep_pose_in_memory_hydrid_
bool optimize_memory_usage_
A molecular system including residues, kinematics, and energies.
utility::vector1< core::Size > all_pose_to_output_pose_ID_map_
void set_full_length_loop_rmsd_clustering(bool const &setting)
utility::vector1< core::pose::PoseOP > large_cluster_pose_list_
std::map< core::Size, bool > sliced_pose_is_prepend_map
utility::vector1< core::Size > sliced_pose_best_alignment
utility::vector1< core::Size > const & get_act_calc_rms_res() const
void set_distinguish_pucker(core::Real const &setting)
void set_rename_tags(core::Real const &setting)
void set_perform_filters(bool const &setting)
core::import_pose::pose_stream::SilentFilePoseInputStreamOP input_
protocols::stepwise::modeler::rna::checker::RNA_VDW_BinCheckerOP user_input_VDW_bin_checker_
void set_PBP_clustering_at_chain_closure(bool const &setting)
bool quick_alignment_pose_is_intialized_
utility::vector1< std::pair< core::Size, core::Size > > delete_res_range_list_
utility::pointer::shared_ptr< StepWiseRNA_PoseSetup > StepWiseRNA_PoseSetupOP
void create_silent_file_and_tag_list()
void set_ignore_unmatched_virtual_res(bool const &setting)
core::pose::Pose first_pose_
void set_ignore_FARFAR_no_auto_bulge_tag(bool const &setting)
void setup(protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP &working_parameters)
void set_verbose(bool const &setting)
utility::vector1< core::pose::PoseOP > pose_output_list_
core::pose::PoseOP get_poseOP(Size const n)
StepWiseRNA_Clusterer(utility::vector1< std::string > const &silent_files_in)
utility::pointer::weak_ptr< ResidueTypeSet const > ResidueTypeSetCAP
bool ignore_unmatched_virtual_res_
void set_keep_pose_in_memory(bool const &setting)
std::map< std::string, bool > current_tags_map_
utility::pointer::shared_ptr< RNA_VDW_BinChecker > RNA_VDW_BinCheckerOP
void set_working_parameters(protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP &working_parameters)
bool ignore_FARFAR_no_auto_bulge_tag_
core::Real suite_cluster_radius_
void set_perform_VDW_rep_screen(bool const &setting)
std::map< core::Size, bool > const & get_act_is_prepend_map() const
bool perform_VDW_rep_screen_
void initialize_max_memory_pose_num()
rosetta project type declarations
Size max_memory_pose_num_
utility::vector1< core::Size > sliced_pose_calc_rms_res
bool is_old_individual_suite_cluster(core::pose::Pose const ¤t_pose, core::pose::Pose const &cluster_center_pose, utility::vector1< core::Size > const &calc_rms_res, 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
bool perform_score_diff_cut_
void set_user_input_VDW_bin_checker(protocols::stepwise::modeler::rna::checker::RNA_VDW_BinCheckerOP const &user_input_VDW_bin_checker)
std::string quick_alignment_tag_
void recalculate_rmsd_and_output_silent_file(std::string const &silent_file, protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetupOP &stepwise_rna_pose_setup, bool const write_score_only)
void initialize_quick_alignment_pose()
core::Real whole_struct_cluster_radius_
void initialize_VDW_rep_checker()
bool use_triangle_inequality_
void set_align_only_over_base_atoms(bool const &setting)
void create_large_cluster_centers_member_list()
void set_filter_virtual_res_list(utility::vector1< core::Size > const &setting)
bool keep_pose_in_memory_
core::scoring::ScoreFunction forward declarations
utility::pointer::shared_ptr< Pose > PoseOP
virtual ~StepWiseRNA_Clusterer()
bool pass_FARFAR_no_auto_bulge_filter(core::io::silent::SilentStructOP const &silent_struct) const
core::chemical::ResidueTypeSetCAP rsd_set_
utility::pointer::shared_ptr< SilentFileData > SilentFileDataOP
void set_add_lead_zero_to_tag(core::Real const &setting)
utility::vector1< bool > is_sliced_res_
bool PBP_clustering_at_chain_closure_
void set_two_stage_clustering(bool const &setting)
std::map< core::Size, core::Size > const & get_act_full_to_sub() const
utility::vector1< utility::vector1< Cluster_Member > > cluster_centers_neighbor_list_
core::Real score_diff_cut_
void set_min_num_south_sugar_filter(Size const &setting)
utility::pointer::shared_ptr< StepWiseWorkingParameters const > StepWiseWorkingParametersCOP
void get_best_neighboring_shift_RMSD_and_output_silent_file(std::string const &silent_file)
void set_output_pdb(bool const setting)
void set_optimize_memory_usage(bool const &setting)
protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP working_parameters_
core::pose::Pose quick_alignment_pose_
void initialize_parameters_and_input()
void do_some_clustering()
bool two_stage_clustering_
void output_silent_file(std::string const &silent_file)
void set_cluster_radius(core::Real const &setting)
void set_quick_alignment(bool const &setting)
utility::pointer::shared_ptr< SilentFilePoseInputStream > SilentFilePoseInputStreamOP
void set_VDW_rep_screen_info(utility::vector1< std::string > const &setting)
bool align_only_over_base_atoms_
SlicedPoseWorkingParameters()
bool is_new_cluster_center_with_working_parameters(core::pose::PoseOP const &pose_op, std::string const &tag)
utility::pointer::shared_ptr< SilentStruct > SilentStructOP
void set_max_decoys(core::Size const &setting)
Filter a list of poses by score.
bool working_parameters_exist_
utility::vector1< core::Size > working_to_sliced_res_map_
std::map< std::string, bool > parent_tags_map_
bool check_for_closeness(core::pose::PoseOP const &pose_op, std::string const &tag)
core::Size full_to_sub(core::Size const i, core::pose::Pose const &pose)
utility::vector1< std::string > tag_output_list_
core::Real loop_cluster_radius_
bool check_for_closeness_without_working_parameters(core::pose::PoseOP const &pose_op)
bool full_length_loop_rmsd_clustering_
Size min_num_south_sugar_filter_
utility::vector1< std::string > silent_files_
void set_skip_clustering(bool const &setting)
void set_perform_score_diff_cut(bool const &setting)
utility::vector1< core::io::silent::SilentStructOP > silent_struct_output_list_
std::map< core::Size, core::Size > sliced_pose_full_to_sub
void set_ignore_FARFAR_no_auto_bulge_parent_tag(bool const &setting)