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CheckForSandwichFeatures.hh File Reference

Check various properties for SandwichFeatures. More...

#include <protocols/features/strand_assembly/SandwichFragment.hh>
#include <protocols/features/strand_assembly/StrandAssemblyCommon.hh>

Namespaces

 protocols
 The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
 
 protocols::features
 
 protocols::features::strand_assembly
 

Functions

core::Real protocols::features::strand_assembly::absolute_vec (numeric::xyzVector< core::Real > vector)
 
Real protocols::features::strand_assembly::calculate_dihedral_w_4_resnums (Pose const &pose, core::Size res1_sheet_i, core::Size res2_sheet_i, core::Size res1_sheet_j, core::Size res2_sheet_j)
 
vector< Realprotocols::features::strand_assembly::cal_dis_angle_to_find_sheet (Pose const &pose, core::Size res_i_0, core::Size res_i_1, core::Size res_i_2, core::Size res_j_0, core::Size res_j_1, core::Size res_j_2)
 
std::pair< core::Real, core::Realprotocols::features::strand_assembly::cal_min_avg_dis_between_sheets_by_cen_res (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose &dssp_pose, utility::vector1< core::Size > all_distinct_sheet_ids, core::Size min_num_strands_in_sheet_)
 
std::pair< float, float > protocols::features::strand_assembly::cal_min_avg_dis_between_two_sheets_by_cen_res (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose &dssp_pose, core::Size sheet_id_1, core::Size sheet_id_2)
 
float protocols::features::strand_assembly::cal_min_dis_between_sheets_by_all_res (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose &dssp_pose, utility::vector1< core::Size > all_distinct_sheet_ids)
 
float protocols::features::strand_assembly::cal_min_dis_between_two_sheets_by_all_res (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose &dssp_pose, core::Size sheet_id_1, core::Size sheet_id_2)
 
core::Size protocols::features::strand_assembly::cal_num_of_sheets_that_surround_this_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose &dssp_pose, utility::vector1< core::Size > all_distinct_sheet_ids, core::Size sheet_id, core::Size min_num_strands_in_sheet_, core::Real inter_sheet_distance_to_see_whether_a_sheet_is_surrounded_by_other_sheets_)
 
float protocols::features::strand_assembly::cal_shortest_dis_between_facing_aro_in_sw (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, utility::vector1< core::Size > all_distinct_sheet_ids, core::Size min_num_strands_in_sheet_)
 
string protocols::features::strand_assembly::check_canonicalness_of_LR (core::Size loop_size, bool intra_sheet, string const &LR)
 
string protocols::features::strand_assembly::check_canonicalness_of_PA (core::Size loop_size, bool intra_sheet, string const &PA_by_preceding_E, string const &PA_by_following_E, Real canocheck_canonicalness_cutoff_)
 
string protocols::features::strand_assembly::check_canonicalness_of_parallel_EE (core::Size loop_size, bool intra_sheet, string const &parallel_EE)
 
string protocols::features::strand_assembly::check_heading_direction (Pose &dssp_pose, core::Size residue_begin, core::Size residue_end, string const &check_N_to_C_direction_by_)
 
bool protocols::features::strand_assembly::check_helix_existence (Pose const &dssp_pose)
 
string protocols::features::strand_assembly::check_LR (Pose &dssp_pose, core::Size residue_begin, core::Size residue_end)
 
pair< string, string > protocols::features::strand_assembly::check_PA (Pose &dssp_pose, core::Size residue_begin, core::Size residue_end)
 
bool protocols::features::strand_assembly::check_strand_too_closeness (Pose const &pose, SandwichFragment strand_i, SandwichFragment strand_j, Real min_inter_sheet_dis_CA_CA_)
 
Real protocols::features::strand_assembly::check_sw_by_dis (Pose const &pose, SandwichFragment strand_i, SandwichFragment strand_j, bool antiparallel, Real min_sheet_dis_, Real max_sheet_dis_)
 
bool protocols::features::strand_assembly::check_whether_hairpin_connects_short_strand (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size start_res, core::Size next_start_res)
 
bool protocols::features::strand_assembly::check_whether_same_direction_strands_connect_two_sheets_or_a_loop (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::Size start_res, core::Size next_start_res)
 
bool protocols::features::strand_assembly::check_whether_sw_by_sh_id_still_alive (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
 
std::string protocols::features::strand_assembly::check_whether_sw_is_not_connected_with_continuous_atoms (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose &dssp_pose, core::Size sw_can_by_sh_id)
 
bool protocols::features::strand_assembly::check_whether_this_pdb_should_be_excluded (string const &tag)
 
bool protocols::features::strand_assembly::check_whether_this_sheet_is_too_short (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_i)
 
bool protocols::features::strand_assembly::check_whether_sheets_are_connected_with_near_bb_atoms (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose &dssp_pose, core::Size sw_can_by_sh_id, core::Real min_N_O_dis_between_two_sheets_, core::Real min_N_H_O_angle_between_two_sheets_)
 
bool protocols::features::strand_assembly::check_whether_strand_i_is_in_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size segment_id)
 
std::vector< core::Sizeprotocols::features::strand_assembly::count_AA_w_direction (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::pose::Pose const &pose_w_center_000, core::Size sw_can_by_sh_id, core::Size sheet_id, core::Size residue_begin, core::Size residue_end)
 
vector< core::Sizeprotocols::features::strand_assembly::count_AA_wo_direction (Pose const &pose, core::Size residue_begin, core::Size residue_end)
 
string protocols::features::strand_assembly::determine_core_heading_surface_heading_by_distance (Pose const &pose_w_center_000, core::Size ii)
 
string protocols::features::strand_assembly::determine_heading_direction_by_vector (StructureID struct_id, utility::sql_database::sessionOP db_session, Pose const &pose, core::Size sw_can_by_sh_id, core::Size sheet_id, core::Size residue_begin, core::Size residue_end, core::Size ii)
 
Size protocols::features::strand_assembly::find_sheet (Pose const &pose, SandwichFragment strand_i, SandwichFragment strand_j, bool antiparallel, Real min_CA_CA_dis_, Real max_CA_CA_dis_, Real min_C_O_N_angle_, bool care_smaller_sheet)
 
std::vector< core::Sizeprotocols::features::strand_assembly::get_all_residues_in_this_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id)
 
utility::vector1
< SandwichFragment > 
protocols::features::strand_assembly::get_all_strands_in_sheet_i (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id)
 
std::vector< core::Sizeprotocols::features::strand_assembly::get_aro_residues_in_this_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::Size sheet_id)
 
Real protocols::features::strand_assembly::get_avg_dis_CA_CA (Pose const &pose, core::Size i_resnum, core::Size i_resnum_1, core::Size i_resnum_2, core::Size i_resnum_3, core::Size j_resnum, core::Size j_resnum_1, core::Size j_resnum_2, core::Size j_resnum_3, Real min_sheet_dis_, Real max_sheet_dis_)
 
Real protocols::features::strand_assembly::get_avg_dis_strands (Pose const &pose, SandwichFragment strand_i, SandwichFragment strand_j)
 
std::vector< core::Sizeprotocols::features::strand_assembly::get_central_residues_in_other_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id, core::Size sheet_id)
 
std::vector< core::Sizeprotocols::features::strand_assembly::get_central_residues_in_this_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id)
 
pair< int, int > protocols::features::strand_assembly::get_central_residues_in_each_of_two_edge_strands (StructureID struct_id, utility::sql_database::sessionOP db_session, Pose const &pose, core::Size sheet_i, Real min_CA_CA_dis_, Real max_CA_CA_dis_)
 
utility::vector1< core::Sizeprotocols::features::strand_assembly::get_chain_B_resNum (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
 
Real protocols::features::strand_assembly::get_closest_distance_between_strands (Pose const &pose, SandwichFragment strand_i, SandwichFragment strand_j)
 
pair< core::Size, core::Sizeprotocols::features::strand_assembly::get_current_bs_id_and_closest_edge_bs_id_in_different_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, Pose const &pose, core::Size sw_can_by_sh_id, core::Size sheet_id, core::Size residue_begin, core::Size residue_end)
 
utility::vector1
< SandwichFragment > 
protocols::features::strand_assembly::get_current_strands_in_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
utility::vector1< core::Sizeprotocols::features::strand_assembly::get_distinct_sheet_id_from_sheet_table (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
utility::vector1< core::Sizeprotocols::features::strand_assembly::get_distinct_sw_id_from_sandwich_table (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
utility::vector1
< SandwichFragment > 
protocols::features::strand_assembly::get_full_strands (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
utility::vector1
< SandwichFragment > 
protocols::features::strand_assembly::get_full_strands_from_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id)
 
utility::vector1< core::Sizeprotocols::features::strand_assembly::get_list_of_residues_in_sheet_i (utility::vector1< SandwichFragment > all_strands_in_sheet_i)
 
core::Size protocols::features::strand_assembly::get_max_sheet_id (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
std::pair< core::Size, core::Sizeprotocols::features::strand_assembly::get_next_starting_res_for_connecting_strands (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id, core::Size former_ending_res)
 
core::Size protocols::features::strand_assembly::get_num_of_distinct_sheet_id (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
core::Size protocols::features::strand_assembly::get_num_of_sheets_that_surround_this_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id)
 
core::Size protocols::features::strand_assembly::get_num_strands_in_this_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id)
 
core::Size protocols::features::strand_assembly::get_segment_id (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size all_strands_index)
 
std::string protocols::features::strand_assembly::get_sheet_antiparallel_info (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id)
 
Real protocols::features::strand_assembly::get_shortest_among_4_vals (const Real arr_dis_inter_sheet[])
 
core::Size protocols::features::strand_assembly::get_size_sandwich_PK_id (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
 
utility::vector1
< SandwichFragment > 
protocols::features::strand_assembly::get_start_end_res_num_in_the_longest_strand (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id)
 
std::pair< core::Size, core::Sizeprotocols::features::strand_assembly::get_starting_res_for_connecting_strands (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id, core::Size former_res_end)
 
std::string protocols::features::strand_assembly::get_tag (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
utility::vector1< core::Sizeprotocols::features::strand_assembly::get_vec_AA_kind (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
 
utility::vector1< core::Sizeprotocols::features::strand_assembly::get_vec_distinct_sheet_id (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
 
utility::vector1< core::Sizeprotocols::features::strand_assembly::get_vec_of_sw_can_by_sh_id (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
utility::vector1< core::Sizeprotocols::features::strand_assembly::get_vector_of_strand_AA_distribution (StructureID struct_id, utility::sql_database::sessionOP db_session, std::string const &heading_direction, std::string const &strand_location)
 
core::Size protocols::features::strand_assembly::identify_sheet_id_by_residue_end (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size residue_end)
 
string protocols::features::strand_assembly::is_this_strand_at_edge (Pose const &pose, StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id, core::Size residue_begin, core::Size residue_end, Real min_CA_CA_dis_, Real max_CA_CA_dis_)
 
std::string protocols::features::strand_assembly::is_this_strand_at_edge_by_looking_db (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size residue_begin)
 
int protocols::features::strand_assembly::judge_facing (StructureID struct_id, utility::sql_database::sessionOP db_session, Pose const &pose, core::Size sheet_i, core::Size sheet_j, Real min_CA_CA_dis_, Real max_CA_CA_dis_, Real min_sheet_angle_by_four_term_cen_res_, Real max_sheet_angle_by_four_term_cen_res_, Real min_sheet_torsion_cen_res_, Real max_sheet_torsion_cen_res_, Real max_sheet_angle_with_cen_res_in_smaller_sheet_and_two_terminal_res_in_larger_sheet_)
 
void protocols::features::strand_assembly::process_decoy (Pose &dssp_pose, core::scoring::ScoreFunction const &scorefxn)
 
string protocols::features::strand_assembly::report_heading_directions_of_all_AA_in_a_strand (StructureID struct_id, utility::sql_database::sessionOP db_session, Pose const &pose, core::Size sw_can_by_sh_id, core::Size sheet_id, core::Size residue_begin, core::Size residue_end)
 
utility::vector1< int > protocols::features::strand_assembly::retrieve_residue_num_of_rkde (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id, std::string const &dssp_code, std::string const &heading_direction)
 
float protocols::features::strand_assembly::round_to_float (float x)
 
Real protocols::features::strand_assembly::round_to_Real (Real x)
 
Size protocols::features::strand_assembly::round_to_Size (Real x)
 
std::string protocols::features::strand_assembly::see_edge_or_core_or_loop_or_short_edge (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size residue_num)
 
bool protocols::features::strand_assembly::see_whether_sheets_can_be_combined (StructureID struct_id, utility::sql_database::sessionOP db_session, Pose const &pose, core::Size i_sheet, core::Size j_sheet, Real min_CA_CA_dis_, Real max_CA_CA_dis_, Real min_C_O_N_angle_)
 
string protocols::features::strand_assembly::see_whether_sheet_is_antiparallel (StructureID struct_id, utility::sql_database::sessionOP db_session, Pose const &pose, core::Size i_sheet, Real min_CA_CA_dis_, Real max_CA_CA_dis_, Real min_C_O_N_angle_)
 
bool protocols::features::strand_assembly::see_whether_this_sw_has_SS_bond (StructureID struct_id, utility::sql_database::sessionOP db_session)
 

Detailed Description

Check various properties for SandwichFeatures.

Author
Doo Nam Kim (doona.nosp@m.m.ki.nosp@m.m@gma.nosp@m.il.c.nosp@m.om)