Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Classes | Typedefs | Functions
protocols::features::strand_assembly Namespace Reference

Classes

class  SandwichFeatures
 
class  SandwichFeaturesCreator
 creator for the SandwichFeatures class More...
 
class  SandwichFragment
 
class  StrandBundleFeatures
 
class  StrandBundleFeaturesCreator
 creator for the StrandBundleFeatures class More...
 
class  StrandFragment
 

Typedefs

typedef
utility::pointer::shared_ptr
< SandwichFeatures
SandwichFeaturesOP
 
typedef
utility::pointer::shared_ptr
< SandwichFeatures const > 
SandwichFeaturesCOP
 
typedef
utility::pointer::shared_ptr
< StrandBundleFeatures
StrandBundleFeaturesOP
 
typedef
utility::pointer::shared_ptr
< StrandBundleFeatures const > 
StrandBundleFeaturesCOP
 

Functions

static basic::Tracer TR ("protocols.features.strand_assembly.CheckForSandwichFeatures")
 
Real absolute_vec (numeric::xyzVector< Real > vector)
 
Real 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< Realcal_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)
 
pair< Real, Realcal_min_avg_dis_between_sheets_by_cen_res (StructureID struct_id, sessionOP db_session, Pose &dssp_pose, utility::vector1< core::Size > all_distinct_sheet_ids, core::Size min_num_strands_in_sheet_)
 
pair< float, float > cal_min_avg_dis_between_two_sheets_by_cen_res (StructureID struct_id, sessionOP db_session, Pose &dssp_pose, core::Size sheet_id_1, core::Size sheet_id_2)
 
float cal_min_dis_between_sheets_by_all_res (StructureID struct_id, sessionOP db_session, Pose &dssp_pose, utility::vector1< core::Size > all_distinct_sheet_ids)
 
float cal_min_dis_between_two_sheets_by_all_res (StructureID struct_id, sessionOP db_session, Pose &dssp_pose, core::Size sheet_id_1, core::Size sheet_id_2)
 
Size cal_num_of_sheets_that_surround_this_sheet (StructureID struct_id, sessionOP db_session, Pose &dssp_pose, utility::vector1< core::Size > all_distinct_sheet_ids, core::Size sheet_id, core::Size min_num_strands_in_sheet_, Real inter_sheet_distance_to_see_whether_a_sheet_is_surrounded_by_other_sheets_)
 
float cal_shortest_dis_between_facing_aro_in_sw (StructureID struct_id, sessionOP db_session, Pose const &pose, utility::vector1< core::Size > all_distinct_sheet_ids, core::Size min_num_strands_in_sheet_)
 
string check_canonicalness_of_LR (core::Size loop_size, bool intra_sheet, string const &LR)
 
string 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 check_canonicalness_of_parallel_EE (core::Size loop_size, bool intra_sheet, string const &parallel_EE)
 
string check_heading_direction (Pose &dssp_pose, core::Size residue_begin, core::Size residue_end, string const &check_N_to_C_direction_by_)
 
bool check_helix_existence (Pose const &dssp_pose)
 
string check_LR (Pose &dssp_pose, core::Size residue_begin, core::Size residue_end)
 
pair< string, string > check_PA (Pose &dssp_pose, core::Size residue_begin, core::Size residue_end)
 
bool check_strand_too_closeness (Pose const &pose, SandwichFragment strand_i, SandwichFragment strand_j, Real min_inter_sheet_dis_CA_CA_)
 
Real check_sw_by_dis (Pose const &pose, SandwichFragment strand_i, SandwichFragment strand_j, bool antiparallel, Real min_sheet_dis_, Real max_sheet_dis_)
 
bool check_whether_hairpin_connects_short_strand (StructureID struct_id, sessionOP db_session, core::Size start_res, core::Size next_start_res)
 
bool check_whether_same_direction_strands_connect_two_sheets_or_a_loop (StructureID struct_id, sessionOP db_session, Pose const &pose, core::Size start_res, core::Size next_start_res)
 
bool check_whether_sheets_are_connected_with_near_bb_atoms (StructureID struct_id, sessionOP db_session, Pose &dssp_pose, core::Size sw_can_by_sh_id, Real min_N_O_dis_between_two_sheets_, Real min_N_H_O_angle_between_two_sheets_)
 
bool check_whether_sw_by_sh_id_still_alive (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id)
 
string check_whether_sw_is_not_connected_with_continuous_atoms (StructureID struct_id, sessionOP db_session, Pose &dssp_pose, core::Size sw_can_by_sh_id)
 
bool check_whether_this_pdb_should_be_excluded (string const &tag)
 
bool check_whether_this_sheet_is_too_short (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_i)
 
bool check_whether_strand_i_is_in_sheet (StructureID struct_id, sessionOP db_session, core::Size segment_id)
 
vector< core::Sizecount_AA_w_direction (StructureID struct_id, sessionOP db_session, Pose const &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::Sizecount_AA_wo_direction (Pose const &pose, core::Size residue_begin, core::Size residue_end)
 
string determine_core_heading_surface_heading_by_distance (Pose const &pose_w_center_000, core::Size ii)
 
string 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)
 
utility::vector1
< SandwichFragment
get_current_strands_in_sheet (StructureID struct_id, sessionOP db_session)
 
utility::vector1< core::Sizeget_distinct_sheet_id_from_sheet_table (StructureID struct_id, sessionOP db_session)
 
utility::vector1
< SandwichFragment
get_full_strands (StructureID struct_id, sessionOP db_session)
 Select all strand segments reported by the ResidueSecondaryStructureFeatures and save them in a vector. More...
 
Size 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::pair< vector< core::Size >
, vector< core::Size > > 
query_begin_end (StructureID struct_id, sessionOP db_session, core::Size sheet_id)
 
vector< core::Sizeget_all_residues_in_this_sheet (StructureID struct_id, sessionOP db_session, core::Size sheet_id)
 
utility::vector1
< SandwichFragment
get_all_strands_in_sheet_i (StructureID struct_id, sessionOP db_session, core::Size sheet_id)
 
vector< core::Sizeget_aro_residues_in_this_sheet (StructureID struct_id, sessionOP db_session, Pose const &pose, core::Size sheet_id)
 
Real 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 get_avg_dis_strands (Pose const &pose, SandwichFragment strand_i, SandwichFragment strand_j)
 
vector< core::Sizeget_central_residues_in_other_sheet (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id, core::Size sheet_id)
 
vector< core::Sizeget_central_residues_in_this_sheet (StructureID struct_id, sessionOP db_session, core::Size sheet_id)
 
utility::vector1< core::Sizeget_chain_B_resNum (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id)
 
Real get_closest_distance_between_strands (Pose const &pose, SandwichFragment strand_i, SandwichFragment strand_j)
 
pair< int, int > 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_)
 
pair< core::Size, core::Sizeget_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< core::Sizeget_distinct_sw_id_from_sandwich_table (StructureID struct_id, sessionOP db_session)
 
utility::vector1
< SandwichFragment
get_full_strands_from_sheet (StructureID struct_id, sessionOP db_session, core::Size sheet_id)
 Select all strand segments reported by the ResidueSecondaryStructureFeatures and save them in a vector. More...
 
pair< core::Size, core::Sizeget_next_starting_res_for_connecting_strands (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id, core::Size former_ending_res)
 
Size get_num_of_distinct_sheet_id (StructureID struct_id, sessionOP db_session)
 
Size get_num_of_sheets_that_surround_this_sheet (StructureID struct_id, sessionOP db_session, core::Size sheet_id)
 
utility::vector1< core::Sizeget_list_of_residues_in_sheet_i (utility::vector1< SandwichFragment > all_strands_in_sheet_i)
 
Size get_max_sheet_id (StructureID struct_id, sessionOP db_session)
 
Size get_num_strands_in_this_sheet (StructureID struct_id, sessionOP db_session, core::Size sheet_id)
 
string get_sheet_antiparallel_info (StructureID struct_id, sessionOP db_session, core::Size sheet_id)
 
Size get_segment_id (StructureID struct_id, sessionOP db_session, core::Size all_strands_index)
 
Real get_shortest_among_4_vals (const Real arr_dis_inter_sheet[])
 
Size get_size_sandwich_PK_id (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id)
 
utility::vector1
< SandwichFragment
get_start_end_res_num_in_the_longest_strand (StructureID struct_id, sessionOP db_session, core::Size sheet_id)
 
pair< core::Size, core::Sizeget_starting_res_for_connecting_strands (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id, core::Size former_res_end)
 
string get_tag (StructureID struct_id, sessionOP db_session)
 
utility::vector1< core::Sizeget_vec_AA_kind (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id)
 
utility::vector1< core::Sizeget_vec_of_sw_can_by_sh_id (StructureID struct_id, sessionOP db_session)
 
utility::vector1< core::Sizeget_vector_of_strand_AA_distribution (StructureID struct_id, sessionOP db_session, string const &heading_direction, string const &strand_location)
 
utility::vector1< core::Sizeget_vec_distinct_sheet_id (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id)
 
Size identify_sheet_id_by_residue_end (StructureID struct_id, sessionOP db_session, core::Size residue_end)
 
string 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_)
 
string is_this_strand_at_edge_by_looking_db (StructureID struct_id, sessionOP db_session, core::Size residue_begin)
 
int 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 process_decoy (Pose &dssp_pose, core::scoring::ScoreFunction const &scorefxn)
 
string 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 > retrieve_residue_num_of_rkde (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id, string const &dssp_code, string const &heading_direction)
 
float round_to_float (float x)
 
Real round_to_Real (Real x)
 
Size round_to_Size (Real x)
 
string see_edge_or_core_or_loop_or_short_edge (StructureID struct_id, sessionOP db_session, core::Size residue_num)
 
string 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 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_)
 
bool see_whether_this_sw_has_SS_bond (StructureID struct_id, sessionOP db_session)
 
core::Real absolute_vec (numeric::xyzVector< core::Real > vector)
 
std::pair< core::Real, core::Realcal_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 > 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 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 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 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 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_)
 
bool 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 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 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 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 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 check_whether_strand_i_is_in_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size segment_id)
 
std::vector< core::Sizecount_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)
 
std::vector< core::Sizeget_all_residues_in_this_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id)
 
utility::vector1
< SandwichFragment
get_all_strands_in_sheet_i (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id)
 
std::vector< core::Sizeget_aro_residues_in_this_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::Size sheet_id)
 
std::vector< core::Sizeget_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::Sizeget_central_residues_in_this_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id)
 
utility::vector1< core::Sizeget_chain_B_resNum (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
 
utility::vector1
< SandwichFragment
get_current_strands_in_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
utility::vector1< core::Sizeget_distinct_sheet_id_from_sheet_table (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
utility::vector1< core::Sizeget_distinct_sw_id_from_sandwich_table (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
utility::vector1
< SandwichFragment
get_full_strands (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
utility::vector1
< SandwichFragment
get_full_strands_from_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id)
 
core::Size get_max_sheet_id (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
std::pair< core::Size, core::Sizeget_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 get_num_of_distinct_sheet_id (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
core::Size get_num_of_sheets_that_surround_this_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id)
 
core::Size get_num_strands_in_this_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id)
 
core::Size get_segment_id (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size all_strands_index)
 
std::string get_sheet_antiparallel_info (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id)
 
core::Size get_size_sandwich_PK_id (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
 
utility::vector1
< SandwichFragment
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::Sizeget_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 get_tag (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
utility::vector1< core::Sizeget_vec_AA_kind (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
 
utility::vector1< core::Sizeget_vec_distinct_sheet_id (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
 
utility::vector1< core::Sizeget_vec_of_sw_can_by_sh_id (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
utility::vector1< core::Sizeget_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 identify_sheet_id_by_residue_end (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size residue_end)
 
std::string is_this_strand_at_edge_by_looking_db (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size residue_begin)
 
utility::vector1< int > 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)
 
std::string see_edge_or_core_or_loop_or_short_edge (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size residue_num)
 
bool see_whether_this_sw_has_SS_bond (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
static basic::Tracer TR ("protocols.features.strand_assembly.SandwichFeatures")
 
static basic::Tracer TR ("protocols.features.strand_assembly.StrandBundleFeatures")
 
static basic::Tracer TR ("protocols.features.strand_assembly.WriteToDBFromSandwichFeatures")
 
bool change_sheet_id_if_possible (StructureID struct_id, utility::sql_database::sessionOP db_session, Pose const &pose, Real min_CA_CA_dis_, Real max_CA_CA_dis_, Real min_C_O_N_angle_)
 
Size delete_this_sw_can_by_sh_id_from_sw_by_comp (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id)
 
Size delete_this_struct_id (StructureID struct_id, sessionOP db_session)
 
utility::vector1
< SandwichFragment
prepare_WriteToDB_sandwich (StructureID struct_id, sessionOP db_session)
 
void WriteToDB_AA_to_terminal_loops (StructureID struct_id, sessionOP db_session, Pose &dssp_pose, core::Size sandwich_PK_id_counter, core::Size sw_can_by_sh_id, string const &tag, bool starting_loop, core::Size residue_begin, core::Size residue_end)
 
Size WriteToDB_ending_loop (StructureID struct_id, sessionOP db_session, Pose &dssp_pose, core::Size sandwich_PK_id_counter, core::Size sw_can_by_sh_id, string const &tag, core::Size max_starting_loop_size_)
 
Size WriteToDB_long_strand_id_in_each_sw (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id)
 
Size WriteToDB_avg_b_factor_CB_at_each_component (StructureID struct_id, utility::sql_database::sessionOP db_session, Pose const &pose, core::Size sw_can_by_sh_id)
 
Size WriteToDB_dihedral_angle_between_core_strands_across_facing_sheets (StructureID struct_id, utility::sql_database::sessionOP db_session, Pose const &pose, core::Size sw_can_by_sh_id)
 
Size WriteToDB_dssp_ratio_in_sw (StructureID struct_id, sessionOP db_session, Pose &dssp_pose, core::Size sw_can_by_sh_id)
 
Size WriteToDB_hydrophobic_ratio_net_charge (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
 
Size WriteToDB_min_avg_dis_between_sheets_by_cen_res (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id, Pose &dssp_pose, utility::vector1< core::Size > const &all_distinct_sheet_ids, core::Size min_num_strands_in_sheet_)
 
Size WriteToDB_min_dis_between_sheets_by_all_res (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id, Pose &dssp_pose, utility::vector1< core::Size > const &all_distinct_sheet_ids)
 
Size WriteToDB_number_of_edge_strands_in_each_sw (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id)
 
Size WriteToDB_number_of_AAs_in_a_pair_of_edge_strands (StructureID struct_id, sessionOP db_session, core::pose::Pose const &pose, utility::vector1< SandwichFragment > const &bs_of_sw_can_by_sh, core::Size max_num_sw_per_pdb_, Real min_CA_CA_dis_, Real max_CA_CA_dis_)
 
Size WriteToDB_number_of_core_heading_LWY_in_core_strands_in_sw (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id)
 
void WriteToDB_number_of_core_heading_FWY_in_sw (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id)
 
void WriteToDB_number_of_core_heading_W_in_sw (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id)
 
Size WriteToDB_number_of_core_heading_charged_AAs_in_a_pair_of_edge_strands (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id, core::Size current_bs_id, core::Size closest_bs_id)
 
Size WriteToDB_number_of_core_heading_aro_AAs_in_a_pair_of_edge_strands (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id, core::Size current_bs_id, core::Size closest_bs_id)
 
Size WriteToDB_number_of_sheets_that_surround_this_sheet (StructureID struct_id, sessionOP db_session, core::Size sheet_id, core::Size num_of_sheets_that_surround_this_sheet)
 
Size WriteToDB_number_strands_in_each_sw (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id)
 
Size WriteToDB_prolines_that_seem_to_prevent_aggregation (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id, Real wt_for_pro_in_starting_loop_, Real wt_for_pro_in_1st_inter_sheet_loop_, Real wt_for_pro_in_3rd_inter_sheet_loop_)
 
Size WriteToDB_ratio_of_core_heading_FWY_in_sw (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id, Pose const &pose)
 
Size WriteToDB_rkde (StructureID struct_id, sessionOP db_session, core::Size rkde_PK_id_counter, string const &tag, core::Size residue_number, string const &residue_type)
 
Size WriteToDB_rkde_in_strands (StructureID struct_id, sessionOP db_session, core::Size rkde_in_strands_PK_id_counter, string const &tag, core::Size sw_can_by_sh_id, core::Size residue_number, string const &residue_type, string const &heading_direction)
 
Size WriteToDB_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_PK_id_counter, core::Size sheet_id, core::Size segment_id)
 
Size WriteToDB_sheet_antiparallel (StructureID struct_id, sessionOP db_session, core::Size sheet_id, string const &antiparallel)
 
Size WriteToDB_sheet_id (StructureID struct_id, sessionOP db_session, core::Size new_sheet_id, core::Size old_sheet_id)
 
Size WriteToDB_sheet_connectivity (StructureID struct_id, sessionOP db_session, Pose const &pose, core::Size sandwich_PK_id_counter, string const &tag, core::Size sw_can_by_sh_id, string const &loop_kind, core::Size intra_sheet_con_id, core::Size inter_sheet_con_id, string const &LR, string const &canonical_LR, string const &PA_by_preceding_E, string const &PA_by_following_E, string const &cano_PA, string const &heading_direction, string const &parallel_EE, string const &cano_parallel_EE, core::Size loop_size, core::Size start_res, core::Size end_res)
 
Real WriteToDB_shortest_dis_between_facing_aro_in_sw (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id, Pose const &pose, utility::vector1< core::Size > const &all_distinct_sheet_ids, core::Size min_num_strands_in_sheet_)
 
Size WriteToDB_starting_loop (StructureID struct_id, sessionOP db_session, Pose &dssp_pose, core::Size sandwich_PK_id_counter, core::Size sw_can_by_sh_id, string const &tag, core::Size max_starting_loop_size_)
 
Size WriteToDB_sw_res_size (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id)
 
Size Run_WriteToDB_sandwich (string const &tag, Pose &dssp_pose, utility::vector1< SandwichFragment > const &bs_of_sw_can_by_sh, core::Size max_num_sw_per_pdb_, StructureID struct_id, sessionOP db_session, Real min_CA_CA_dis_, Real max_CA_CA_dis_, core::Size sandwich_PK_id_counter)
 
Size WriteToDB_sandwich (StructureID struct_id, utility::sql_database::sessionOP db_session, Pose const &pose, core::Size sandwich_PK_id_counter, string const &tag, core::Size sw_can_by_sh_id, core::Size sheet_id, string const &sheet_antiparallel, core::Size sandwich_bs_id, string const &strand_is_at_edge, core::Size component_size, core::Size residue_begin, core::Size residue_end)
 
Size WriteToDB_sandwich_by_AA_w_direction (StructureID struct_id, utility::sql_database::sessionOP db_session, Pose const &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)
 
Size WriteToDB_sw_can_by_sh (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_PK_id_counter, string const &tag, core::Size sw_can_by_sh_id_counter, core::Size sheet_id, core::Size num_strands_from_sheet)
 
Size WriteToDB_topology_candidate (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
 
void WriteToDB_turn_AA (Pose const &pose, core::Size sw_can_by_sh_id, core::Size i, StructureID struct_id, sessionOP db_session, string const &turn_type)
 
string WriteToDB_turn_type (Pose const &pose, core::Size sw_can_by_sh_id, core::Size first_res, core::Size second_res, StructureID struct_id, sessionOP db_session, Real allowed_deviation_for_turn_type_id_)
 
Size WriteToDB_whether_sw_is_not_connected_with_continuous_atoms (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id, string const &sw_is_not_connected_with_continuous_atoms)
 
core::Size delete_this_struct_id (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
core::Size delete_this_sw_can_by_sh_id_from_sw_by_comp (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
 
utility::vector1
< SandwichFragment
prepare_WriteToDB_sandwich (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
void WriteToDB_AA_to_terminal_loops (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose &dssp_pose, core::Size sandwich_PK_id_counter, core::Size sw_can_by_sh_id, std::string const &tag, bool starting_loop, core::Size residue_begin, core::Size residue_end)
 
core::Size WriteToDB_ending_loop (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose &dssp_pose, core::Size sandwich_PK_id_counter, core::Size sw_can_by_sh_id, std::string const &tag, core::Size max_starting_loop_size_)
 
core::Size WriteToDB_long_strand_id_in_each_sw (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
 
core::Size WriteToDB_dssp_ratio_in_sw (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose &dssp_pose, core::Size sw_can_by_sh_id)
 
core::Size WriteToDB_number_of_AAs_in_a_pair_of_edge_strands (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, utility::vector1< SandwichFragment > const &bs_of_sw_can_by_sh, core::Size max_num_sw_per_pdb_, core::Real min_CA_CA_dis_, core::Real max_CA_CA_dis_)
 
void WriteToDB_number_of_core_heading_W_in_sw (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
 
core::Size WriteToDB_number_of_core_heading_LWY_in_core_strands_in_sw (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
 
void WriteToDB_number_of_core_heading_FWY_in_sw (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
 
core::Size WriteToDB_number_of_edge_strands_in_each_sw (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
 
core::Size WriteToDB_number_of_sheets_that_surround_this_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id, core::Size num_of_sheets_that_surround_this_sheet)
 
core::Size WriteToDB_number_strands_in_each_sw (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
 
core::Size WriteToDB_prolines_that_seem_to_prevent_aggregation (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id, core::Real wt_for_pro_in_starting_loop_, core::Real wt_for_pro_in_1st_inter_sheet_loop_, core::Real wt_for_pro_in_3rd_inter_sheet_loop_)
 
core::Size WriteToDB_ratio_of_core_heading_FWY_in_sw (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id, core::pose::Pose const &pose)
 
core::Size WriteToDB_rkde (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size rkde_PK_id_counter, std::string const &tag, core::Size residue_number, std::string const &residue_type)
 
core::Size WriteToDB_rkde_in_strands (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size rkde_in_strands_PK_id_counter, std::string const &tag, core::Size sw_can_by_sh_id, core::Size residue_number, std::string const &residue_type, std::string const &heading_direction)
 
core::Size WriteToDB_sheet_antiparallel (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id, std::string const &antiparallel)
 
core::Size WriteToDB_sheet_connectivity (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::Size sandwich_PK_id_counter, std::string const &tag, core::Size sw_can_by_sh_id, std::string const &loop_kind, core::Size intra_sheet_con_id, core::Size inter_sheet_con_id, std::string const &LR, std::string const &cano_LR, std::string const &PA_by_preceding_E, std::string const &PA_by_following_E, std::string const &cano_PA, std::string const &heading_direction, std::string const &heading_parallel, std::string const &cano_parallel_EE, core::Size loop_size, core::Size start_res, core::Size end_res)
 
core::Size WriteToDB_sheet_id (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size new_sheet_id, core::Size old_sheet_id)
 
core::Size WriteToDB_starting_loop (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose &dssp_pose, core::Size sandwich_PK_id_counter, core::Size sw_can_by_sh_id, std::string const &tag, core::Size max_starting_loop_size_)
 
core::Size Run_WriteToDB_sandwich (std::string const &tag, core::pose::Pose &dssp_pose, utility::vector1< SandwichFragment > const &bs_of_sw_can_by_sh, core::Size max_num_sw_per_pdb_, StructureID struct_id, utility::sql_database::sessionOP db_session, core::Real min_CA_CA_dis_, core::Real max_CA_CA_dis_, core::Size sandwich_PK_id_counter)
 
core::Size WriteToDB_sw_res_size (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
 
void WriteToDB_turn_AA (core::pose::Pose const &pose, core::Size sw_can_by_sh_id, core::Size i, StructureID struct_id, utility::sql_database::sessionOP db_session, std::string const &turn_type)
 
std::string WriteToDB_turn_type (core::pose::Pose const &pose, core::Size sw_can_by_sh_id, core::Size start_res, core::Size end_res, StructureID struct_id, utility::sql_database::sessionOP db_session, core::Real allowed_deviation_for_turn_type_id_)
 
core::Size WriteToDB_whether_sw_is_not_connected_with_continuous_atoms (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id, std::string const &sw_is_not_connected_with_continuous_atoms)
 
static basic::Tracer TR ("protocols.features.strand_assembly.WriteToFileFromSandwichFeatures")
 
utility::vector1< core::Sizeget_vector_of_loop_AA_distribution (StructureID struct_id, sessionOP db_session, string loop_kind)
 
core::Size prepare_and_write_number_of_electrostatic_interactions_of_residues_to_files (string tag, StructureID struct_id, sessionOP db_session, Pose const &pose, utility::vector1< SandwichFragment > bs_of_sw_can_by_sh, Real distance_cutoff_for_electrostatic_interactions_, Real CB_b_factor_cutoff_for_electrostatic_interactions_, core::Size min_primary_seq_distance_diff_for_electrostatic_interactions_, bool write_electrostatic_interactions_of_surface_residues_in_a_strand_, bool write_electrostatic_interactions_of_all_residues_in_a_strand_, bool write_electrostatic_interactions_of_all_residues_, core::Size rkde_PK_id_counter, core::Size rkde_in_strands_PK_id_counter)
 
core::Size write_AA_kind_to_a_file (string tag, StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id, core::Size sw_res_size)
 
core::Size write_AA_distribution_with_direction_to_a_file (string tag, StructureID struct_id, utility::sql_database::sessionOP db_session)
 
core::Size write_AA_distribution_without_direction_to_a_file (string tag, StructureID struct_id, utility::sql_database::sessionOP db_session)
 
core::Size write_beta_sheet_capping_info_to_a_file (string tag, core::pose::Pose const &pose, utility::vector1< SandwichFragment > bs_of_sw_can_by_sh, int primary_seq_distance_cutoff_for_beta_sheet_capping_before_N_term_capping_, int primary_seq_distance_cutoff_for_beta_sheet_capping_after_N_term_capping_, int primary_seq_distance_cutoff_for_beta_sheet_capping_before_C_term_capping_, int primary_seq_distance_cutoff_for_beta_sheet_capping_after_C_term_capping_)
 
core::Size write_chain_B_resNum_to_a_file (string tag, StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id)
 
core::Size write_heading_direction_of_all_AA_in_a_strand_to_a_file (string tag, StructureID struct_id, sessionOP db_session, core::pose::Pose const &pose, utility::vector1< SandwichFragment > bs_of_sw_can_by_sh)
 
core::Size write_number_of_electrostatic_interactions_of_residues_to_files (string tag, StructureID struct_id, sessionOP db_session, Pose const &pose, string dssp_code, string heading_direction, Real distance_cutoff_for_electrostatic_interactions_, Real CB_b_factor_cutoff_for_electrostatic_interactions_, core::Size min_primary_seq_distance_diff_for_electrostatic_interactions_)
 
core::Size write_p_aa_pp_of_AAs_to_a_file (string tag, Pose &dssp_pose)
 
core::Size write_phi_psi_of_each_residue_to_a_file (string tag, Pose &dssp_pose, utility::vector1< SandwichFragment > bs_of_sw_can_by_sh, bool write_phi_psi_of_E_, bool write_phi_psi_of_all_, core::Size max_num_sw_per_pdb_, StructureID struct_id, sessionOP db_session, Real min_CA_CA_dis_, Real max_CA_CA_dis_)
 
core::Size write_rama_of_AAs_to_a_file (string tag, Pose &dssp_pose)
 
core::Size write_resfile_to_a_file_when_seq_rec_is_bad (string tag, StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, utility::vector1< SandwichFragment > bs_of_sw_can_by_sh, bool write_resfile_to_minimize_too_much_hydrophobic_surface_, bool write_resfile_to_minimize_too_many_core_heading_FWY_on_core_strands_, bool write_resfile_to_minimize_too_many_core_heading_FWY_on_edge_strands_)
 
core::Size write_resfile_to_a_file (string tag, StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, utility::vector1< SandwichFragment > bs_of_sw_can_by_sh, bool write_resfile_NOT_FWY_on_surface_)
 
utility::vector1< core::Sizeget_vector_of_loop_AA_distribution (StructureID struct_id, utility::sql_database::sessionOP db_session, std::string loop_kind)
 
core::Size prepare_and_write_number_of_electrostatic_interactions_of_residues_to_files (std::string tag, StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, utility::vector1< SandwichFragment > bs_of_sw_can_by_sh, core::Real distance_cutoff_for_electrostatic_interactions_, core::Real CB_b_factor_cutoff_for_electrostatic_interactions_, core::Size min_primary_seq_distance_diff_for_electrostatic_interactions_, bool write_electrostatic_interactions_of_surface_residues_in_a_strand_, bool write_electrostatic_interactions_of_all_residues_in_a_strand_, bool write_electrostatic_interactions_of_all_residues_, core::Size rkde_PK_id_counter, core::Size rkde_in_strands_PK_id_counter)
 
core::Size write_chain_B_resNum_to_a_file (std::string tag, StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
 
core::Size write_heading_direction_of_all_AA_in_a_strand_to_a_file (std::string tag, StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, utility::vector1< SandwichFragment > bs_of_sw_can_by_sh)
 
core::Size write_number_of_electrostatic_interactions_of_residues_to_files (std::string tag, StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, std::string dssp_code, std::string heading_direction, core::Real distance_cutoff_for_electrostatic_interactions_, core::Real CB_b_factor_cutoff_for_electrostatic_interactions_, core::Size min_primary_seq_distance_diff_for_electrostatic_interactions_)
 
core::Size write_phi_psi_of_each_residue_to_a_file (std::string tag, core::pose::Pose &dssp_pose, utility::vector1< SandwichFragment > bs_of_sw_can_by_sh, bool write_phi_psi_of_E_, bool write_phi_psi_of_all_, core::Size max_num_sw_per_pdb_, StructureID struct_id, utility::sql_database::sessionOP db_session, core::Real min_CA_CA_dis_, core::Real max_CA_CA_dis_)
 

Typedef Documentation

typedef utility::pointer::shared_ptr< SandwichFeatures const > protocols::features::strand_assembly::SandwichFeaturesCOP

Function Documentation

core::Real protocols::features::strand_assembly::absolute_vec ( numeric::xyzVector< core::Real vector)
Real protocols::features::strand_assembly::absolute_vec ( numeric::xyzVector< Real vector)
std::vector< core::Real > protocols::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::Real> protocols::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_ 
)
pair<Real, Real> protocols::features::strand_assembly::cal_min_avg_dis_between_sheets_by_cen_res ( StructureID  struct_id,
sessionOP  db_session,
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 
)
pair<float, float> protocols::features::strand_assembly::cal_min_avg_dis_between_two_sheets_by_cen_res ( StructureID  struct_id,
sessionOP  db_session,
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_sheets_by_all_res ( StructureID  struct_id,
sessionOP  db_session,
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 
)
float protocols::features::strand_assembly::cal_min_dis_between_two_sheets_by_all_res ( StructureID  struct_id,
sessionOP  db_session,
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_ 
)
Size protocols::features::strand_assembly::cal_num_of_sheets_that_surround_this_sheet ( StructureID  struct_id,
sessionOP  db_session,
Pose dssp_pose,
utility::vector1< core::Size all_distinct_sheet_ids,
core::Size  sheet_id,
core::Size  min_num_strands_in_sheet_,
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_ 
)
float protocols::features::strand_assembly::cal_shortest_dis_between_facing_aro_in_sw ( StructureID  struct_id,
sessionOP  db_session,
Pose const &  pose,
utility::vector1< core::Size all_distinct_sheet_ids,
core::Size  min_num_strands_in_sheet_ 
)
core::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 
)
bool protocols::features::strand_assembly::change_sheet_id_if_possible ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
Pose const &  pose,
Real  min_CA_CA_dis_,
Real  max_CA_CA_dis_,
Real  min_C_O_N_angle_ 
)
std::string protocols::features::strand_assembly::check_canonicalness_of_LR ( core::Size  loop_size,
bool  intra_sheet,
string const &  LR 
)
std::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_ 
)
std::string protocols::features::strand_assembly::check_canonicalness_of_parallel_EE ( core::Size  loop_size,
bool  intra_sheet,
string const &  parallel_EE 
)
std::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)
std::string protocols::features::strand_assembly::check_LR ( Pose dssp_pose,
core::Size  residue_begin,
core::Size  residue_end 
)
std::pair< std::string, std::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_ 
)
core::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_hairpin_connects_short_strand ( StructureID  struct_id,
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_same_direction_strands_connect_two_sheets_or_a_loop ( StructureID  struct_id,
sessionOP  db_session,
Pose const &  pose,
core::Size  start_res,
core::Size  next_start_res 
)
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_sheets_are_connected_with_near_bb_atoms ( StructureID  struct_id,
sessionOP  db_session,
Pose dssp_pose,
core::Size  sw_can_by_sh_id,
Real  min_N_O_dis_between_two_sheets_,
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 
)
bool protocols::features::strand_assembly::check_whether_strand_i_is_in_sheet ( StructureID  struct_id,
sessionOP  db_session,
core::Size  segment_id 
)
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 
)
bool protocols::features::strand_assembly::check_whether_sw_by_sh_id_still_alive ( StructureID  struct_id,
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 
)
string protocols::features::strand_assembly::check_whether_sw_is_not_connected_with_continuous_atoms ( StructureID  struct_id,
sessionOP  db_session,
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 
)

References get_full_strands_from_sheet().

Referenced by judge_facing().

std::vector<core::Size> protocols::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::Size> protocols::features::strand_assembly::count_AA_w_direction ( StructureID  struct_id,
sessionOP  db_session,
Pose const &  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 
)
std::vector< core::Size > protocols::features::strand_assembly::count_AA_wo_direction ( Pose const &  pose,
core::Size  residue_begin,
core::Size  residue_end 
)
core::Size protocols::features::strand_assembly::delete_this_struct_id ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
Size protocols::features::strand_assembly::delete_this_struct_id ( StructureID  struct_id,
sessionOP  db_session 
)
core::Size protocols::features::strand_assembly::delete_this_sw_can_by_sh_id_from_sw_by_comp ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sw_can_by_sh_id 
)
Size protocols::features::strand_assembly::delete_this_sw_can_by_sh_id_from_sw_by_comp ( StructureID  struct_id,
sessionOP  db_session,
core::Size  sw_can_by_sh_id 
)
std::string protocols::features::strand_assembly::determine_core_heading_surface_heading_by_distance ( Pose const &  pose_w_center_000,
core::Size  ii 
)
std::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 
)
core::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::Size> protocols::features::strand_assembly::get_all_residues_in_this_sheet ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sheet_id 
)
vector<core::Size> protocols::features::strand_assembly::get_all_residues_in_this_sheet ( StructureID  struct_id,
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 
)
utility::vector1<SandwichFragment> protocols::features::strand_assembly::get_all_strands_in_sheet_i ( StructureID  struct_id,
sessionOP  db_session,
core::Size  sheet_id 
)
std::vector<core::Size> protocols::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 
)
vector<core::Size> protocols::features::strand_assembly::get_aro_residues_in_this_sheet ( StructureID  struct_id,
sessionOP  db_session,
Pose const &  pose,
core::Size  sheet_id 
)
core::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_ 
)
core::Real protocols::features::strand_assembly::get_avg_dis_strands ( Pose const &  pose,
SandwichFragment  strand_i,
SandwichFragment  strand_j 
)
std::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_ 
)
std::vector<core::Size> protocols::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 
)
vector<core::Size> protocols::features::strand_assembly::get_central_residues_in_other_sheet ( StructureID  struct_id,
sessionOP  db_session,
core::Size  sw_can_by_sh_id,
core::Size  sheet_id 
)
std::vector<core::Size> protocols::features::strand_assembly::get_central_residues_in_this_sheet ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sheet_id 
)
vector<core::Size> protocols::features::strand_assembly::get_central_residues_in_this_sheet ( StructureID  struct_id,
sessionOP  db_session,
core::Size  sheet_id 
)
utility::vector1<core::Size> protocols::features::strand_assembly::get_chain_B_resNum ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sw_can_by_sh_id 
)
utility::vector1<core::Size> protocols::features::strand_assembly::get_chain_B_resNum ( StructureID  struct_id,
sessionOP  db_session,
core::Size  sw_can_by_sh_id 
)
core::Real protocols::features::strand_assembly::get_closest_distance_between_strands ( Pose const &  pose,
SandwichFragment  strand_i,
SandwichFragment  strand_j 
)
std::pair< core::Size, core::Size > protocols::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<SandwichFragment> protocols::features::strand_assembly::get_current_strands_in_sheet ( StructureID  struct_id,
sessionOP  db_session 
)
utility::vector1<core::Size> protocols::features::strand_assembly::get_distinct_sheet_id_from_sheet_table ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
utility::vector1<core::Size> protocols::features::strand_assembly::get_distinct_sheet_id_from_sheet_table ( StructureID  struct_id,
sessionOP  db_session 
)
utility::vector1<core::Size> protocols::features::strand_assembly::get_distinct_sw_id_from_sandwich_table ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
utility::vector1<core::Size> protocols::features::strand_assembly::get_distinct_sw_id_from_sandwich_table ( StructureID  struct_id,
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 ( StructureID  struct_id,
sessionOP  db_session 
)

Select all strand segments reported by the ResidueSecondaryStructureFeatures and save them in a vector.

Referenced by protocols::features::strand_assembly::SandwichFeatures::report_features().

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<SandwichFragment> protocols::features::strand_assembly::get_full_strands_from_sheet ( StructureID  struct_id,
sessionOP  db_session,
core::Size  sheet_id 
)
utility::vector1< core::Size > protocols::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 
)
Size protocols::features::strand_assembly::get_max_sheet_id ( StructureID  struct_id,
sessionOP  db_session 
)
std::pair<core::Size, core::Size> protocols::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 
)
pair<core::Size, core::Size> protocols::features::strand_assembly::get_next_starting_res_for_connecting_strands ( StructureID  struct_id,
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 
)
Size protocols::features::strand_assembly::get_num_of_distinct_sheet_id ( StructureID  struct_id,
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 
)
Size protocols::features::strand_assembly::get_num_of_sheets_that_surround_this_sheet ( StructureID  struct_id,
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 
)
Size protocols::features::strand_assembly::get_num_strands_in_this_sheet ( StructureID  struct_id,
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 
)
Size protocols::features::strand_assembly::get_segment_id ( StructureID  struct_id,
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 
)
string protocols::features::strand_assembly::get_sheet_antiparallel_info ( StructureID  struct_id,
sessionOP  db_session,
core::Size  sheet_id 
)
core::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 
)
Size protocols::features::strand_assembly::get_size_sandwich_PK_id ( StructureID  struct_id,
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 
)
utility::vector1<SandwichFragment> protocols::features::strand_assembly::get_start_end_res_num_in_the_longest_strand ( StructureID  struct_id,
sessionOP  db_session,
core::Size  sheet_id 
)

References get_all_strands_in_sheet_i().

Referenced by judge_facing().

std::pair<core::Size, core::Size> protocols::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 
)
pair<core::Size, core::Size> protocols::features::strand_assembly::get_starting_res_for_connecting_strands ( StructureID  struct_id,
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 
)
string protocols::features::strand_assembly::get_tag ( StructureID  struct_id,
sessionOP  db_session 
)
utility::vector1<core::Size> protocols::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::Size> protocols::features::strand_assembly::get_vec_AA_kind ( StructureID  struct_id,
sessionOP  db_session,
core::Size  sw_can_by_sh_id 
)

Referenced by write_AA_kind_to_a_file().

utility::vector1<core::Size> protocols::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::Size> protocols::features::strand_assembly::get_vec_distinct_sheet_id ( StructureID  struct_id,
sessionOP  db_session,
core::Size  sw_can_by_sh_id 
)
utility::vector1<core::Size> protocols::features::strand_assembly::get_vec_of_sw_can_by_sh_id ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
utility::vector1<core::Size> protocols::features::strand_assembly::get_vec_of_sw_can_by_sh_id ( StructureID  struct_id,
sessionOP  db_session 
)
utility::vector1<core::Size> protocols::features::strand_assembly::get_vector_of_loop_AA_distribution ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
std::string  loop_kind 
)
utility::vector1<core::Size> protocols::features::strand_assembly::get_vector_of_loop_AA_distribution ( StructureID  struct_id,
sessionOP  db_session,
string  loop_kind 
)
utility::vector1<core::Size> protocols::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 
)
utility::vector1<core::Size> protocols::features::strand_assembly::get_vector_of_strand_AA_distribution ( StructureID  struct_id,
sessionOP  db_session,
string const &  heading_direction,
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 
)
Size protocols::features::strand_assembly::identify_sheet_id_by_residue_end ( StructureID  struct_id,
sessionOP  db_session,
core::Size  residue_end 
)
std::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 
)
string protocols::features::strand_assembly::is_this_strand_at_edge_by_looking_db ( StructureID  struct_id,
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_ 
)
core::Size protocols::features::strand_assembly::prepare_and_write_number_of_electrostatic_interactions_of_residues_to_files ( std::string  tag,
StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::pose::Pose const &  pose,
utility::vector1< SandwichFragment >  bs_of_sw_can_by_sh,
core::Real  distance_cutoff_for_electrostatic_interactions_,
core::Real  CB_b_factor_cutoff_for_electrostatic_interactions_,
core::Size  min_primary_seq_distance_diff_for_electrostatic_interactions_,
bool  write_electrostatic_interactions_of_surface_residues_in_a_strand_,
bool  write_electrostatic_interactions_of_all_residues_in_a_strand_,
bool  write_electrostatic_interactions_of_all_residues_,
core::Size  rkde_PK_id_counter,
core::Size  rkde_in_strands_PK_id_counter 
)
core::Size protocols::features::strand_assembly::prepare_and_write_number_of_electrostatic_interactions_of_residues_to_files ( string  tag,
StructureID  struct_id,
sessionOP  db_session,
Pose const &  pose,
utility::vector1< SandwichFragment >  bs_of_sw_can_by_sh,
Real  distance_cutoff_for_electrostatic_interactions_,
Real  CB_b_factor_cutoff_for_electrostatic_interactions_,
core::Size  min_primary_seq_distance_diff_for_electrostatic_interactions_,
bool  write_electrostatic_interactions_of_surface_residues_in_a_strand_,
bool  write_electrostatic_interactions_of_all_residues_in_a_strand_,
bool  write_electrostatic_interactions_of_all_residues_,
core::Size  rkde_PK_id_counter,
core::Size  rkde_in_strands_PK_id_counter 
)
utility::vector1<SandwichFragment> protocols::features::strand_assembly::prepare_WriteToDB_sandwich ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
utility::vector1<SandwichFragment> protocols::features::strand_assembly::prepare_WriteToDB_sandwich ( StructureID  struct_id,
sessionOP  db_session 
)
void protocols::features::strand_assembly::process_decoy ( Pose dssp_pose,
core::scoring::ScoreFunction const &  scorefxn 
)
std::pair< vector<core::Size >, vector<core::Size > > protocols::features::strand_assembly::query_begin_end ( StructureID  struct_id,
sessionOP  db_session,
core::Size  sheet_id 
)
std::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 
)
utility::vector1<int> protocols::features::strand_assembly::retrieve_residue_num_of_rkde ( StructureID  struct_id,
sessionOP  db_session,
core::Size  sw_can_by_sh_id,
string const &  dssp_code,
string const &  heading_direction 
)
float protocols::features::strand_assembly::round_to_float ( float  x)
core::Real protocols::features::strand_assembly::round_to_Real ( Real  x)
core::Size protocols::features::strand_assembly::round_to_Size ( Real  x)
core::Size protocols::features::strand_assembly::Run_WriteToDB_sandwich ( std::string const &  tag,
core::pose::Pose dssp_pose,
utility::vector1< SandwichFragment > const &  bs_of_sw_can_by_sh,
core::Size  max_num_sw_per_pdb_,
StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Real  min_CA_CA_dis_,
core::Real  max_CA_CA_dis_,
core::Size  sandwich_PK_id_counter 
)
Size protocols::features::strand_assembly::Run_WriteToDB_sandwich ( string const &  tag,
Pose dssp_pose,
utility::vector1< SandwichFragment > const &  bs_of_sw_can_by_sh,
core::Size  max_num_sw_per_pdb_,
StructureID  struct_id,
sessionOP  db_session,
Real  min_CA_CA_dis_,
Real  max_CA_CA_dis_,
core::Size  sandwich_PK_id_counter 
)
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 
)
string protocols::features::strand_assembly::see_edge_or_core_or_loop_or_short_edge ( StructureID  struct_id,
sessionOP  db_session,
core::Size  residue_num 
)
std::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_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_ 
)
bool protocols::features::strand_assembly::see_whether_this_sw_has_SS_bond ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
bool protocols::features::strand_assembly::see_whether_this_sw_has_SS_bond ( StructureID  struct_id,
sessionOP  db_session 
)
static basic::Tracer protocols::features::strand_assembly::TR ( "protocols.features.strand_assembly.WriteToDBFromSandwichFeatures"  )
static
static basic::Tracer protocols::features::strand_assembly::TR ( "protocols.features.strand_assembly.CheckForSandwichFeatures"  )
static
static basic::Tracer protocols::features::strand_assembly::TR ( "protocols.features.strand_assembly.WriteToFileFromSandwichFeatures"  )
static
static basic::Tracer protocols::features::strand_assembly::TR ( "protocols.features.strand_assembly.SandwichFeatures"  )
static
static basic::Tracer protocols::features::strand_assembly::TR ( "protocols.features.strand_assembly.StrandBundleFeatures"  )
static
core::Size protocols::features::strand_assembly::write_AA_distribution_with_direction_to_a_file ( string  tag,
StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
core::Size protocols::features::strand_assembly::write_AA_distribution_without_direction_to_a_file ( string  tag,
StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
core::Size protocols::features::strand_assembly::write_AA_kind_to_a_file ( string  tag,
StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sw_can_by_sh_id,
core::Size  sw_res_size 
)
core::Size protocols::features::strand_assembly::write_beta_sheet_capping_info_to_a_file ( string  tag,
core::pose::Pose const &  pose,
utility::vector1< SandwichFragment >  bs_of_sw_can_by_sh,
int  primary_seq_distance_cutoff_for_beta_sheet_capping_before_N_term_capping_,
int  primary_seq_distance_cutoff_for_beta_sheet_capping_after_N_term_capping_,
int  primary_seq_distance_cutoff_for_beta_sheet_capping_before_C_term_capping_,
int  primary_seq_distance_cutoff_for_beta_sheet_capping_after_C_term_capping_ 
)
core::Size protocols::features::strand_assembly::write_chain_B_resNum_to_a_file ( std::string  tag,
StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sw_can_by_sh_id 
)
core::Size protocols::features::strand_assembly::write_chain_B_resNum_to_a_file ( string  tag,
StructureID  struct_id,
sessionOP  db_session,
core::Size  sw_can_by_sh_id 
)
core::Size protocols::features::strand_assembly::write_heading_direction_of_all_AA_in_a_strand_to_a_file ( std::string  tag,
StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::pose::Pose const &  pose,
utility::vector1< SandwichFragment >  bs_of_sw_can_by_sh 
)
core::Size protocols::features::strand_assembly::write_heading_direction_of_all_AA_in_a_strand_to_a_file ( string  tag,
StructureID  struct_id,
sessionOP  db_session,
core::pose::Pose const &  pose,
utility::vector1< SandwichFragment >  bs_of_sw_can_by_sh 
)
core::Size protocols::features::strand_assembly::write_number_of_electrostatic_interactions_of_residues_to_files ( std::string  tag,
StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::pose::Pose const &  pose,
std::string  dssp_code,
std::string  heading_direction,
core::Real  distance_cutoff_for_electrostatic_interactions_,
core::Real  CB_b_factor_cutoff_for_electrostatic_interactions_,
core::Size  min_primary_seq_distance_diff_for_electrostatic_interactions_ 
)
core::Size protocols::features::strand_assembly::write_number_of_electrostatic_interactions_of_residues_to_files ( string  tag,
StructureID  struct_id,
sessionOP  db_session,
Pose const &  pose,
string  dssp_code,
string  heading_direction,
Real  distance_cutoff_for_electrostatic_interactions_,
Real  CB_b_factor_cutoff_for_electrostatic_interactions_,
core::Size  min_primary_seq_distance_diff_for_electrostatic_interactions_ 
)
core::Size protocols::features::strand_assembly::write_p_aa_pp_of_AAs_to_a_file ( string  tag,
Pose dssp_pose 
)
core::Size protocols::features::strand_assembly::write_phi_psi_of_each_residue_to_a_file ( std::string  tag,
core::pose::Pose dssp_pose,
utility::vector1< SandwichFragment >  bs_of_sw_can_by_sh,
bool  write_phi_psi_of_E_,
bool  write_phi_psi_of_all_,
core::Size  max_num_sw_per_pdb_,
StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Real  min_CA_CA_dis_,
core::Real  max_CA_CA_dis_ 
)
core::Size protocols::features::strand_assembly::write_phi_psi_of_each_residue_to_a_file ( string  tag,
Pose dssp_pose,
utility::vector1< SandwichFragment >  bs_of_sw_can_by_sh,
bool  write_phi_psi_of_E_,
bool  write_phi_psi_of_all_,
core::Size  max_num_sw_per_pdb_,
StructureID  struct_id,
sessionOP  db_session,
Real  min_CA_CA_dis_,
Real  max_CA_CA_dis_ 
)
core::Size protocols::features::strand_assembly::write_rama_of_AAs_to_a_file ( string  tag,
Pose dssp_pose 
)
core::Size protocols::features::strand_assembly::write_resfile_to_a_file ( string  tag,
StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::pose::Pose const &  pose,
utility::vector1< SandwichFragment >  bs_of_sw_can_by_sh,
bool  write_resfile_NOT_FWY_on_surface_ 
)
core::Size protocols::features::strand_assembly::write_resfile_to_a_file_when_seq_rec_is_bad ( string  tag,
StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::pose::Pose const &  pose,
utility::vector1< SandwichFragment >  bs_of_sw_can_by_sh,
bool  write_resfile_to_minimize_too_much_hydrophobic_surface_,
bool  write_resfile_to_minimize_too_many_core_heading_FWY_on_core_strands_,
bool  write_resfile_to_minimize_too_many_core_heading_FWY_on_edge_strands_ 
)
void protocols::features::strand_assembly::WriteToDB_AA_to_terminal_loops ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::pose::Pose dssp_pose,
core::Size  sandwich_PK_id_counter,
core::Size  sw_can_by_sh_id,
std::string const &  tag,
bool  starting_loop,
core::Size  residue_begin,
core::Size  residue_end 
)
void protocols::features::strand_assembly::WriteToDB_AA_to_terminal_loops ( StructureID  struct_id,
sessionOP  db_session,
Pose dssp_pose,
core::Size  sandwich_PK_id_counter,
core::Size  sw_can_by_sh_id,
string const &  tag,
bool  starting_loop,
core::Size  residue_begin,
core::Size  residue_end 
)
core::Size protocols::features::strand_assembly::WriteToDB_avg_b_factor_CB_at_each_component ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
Pose const &  pose,
core::Size  sw_can_by_sh_id 
)
core::Size protocols::features::strand_assembly::WriteToDB_dihedral_angle_between_core_strands_across_facing_sheets ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
Pose const &  pose,
core::Size  sw_can_by_sh_id 
)
core::Size protocols::features::strand_assembly::WriteToDB_dssp_ratio_in_sw ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::pose::Pose dssp_pose,
core::Size  sw_can_by_sh_id 
)
Size protocols::features::strand_assembly::WriteToDB_dssp_ratio_in_sw ( StructureID  struct_id,
sessionOP  db_session,
Pose dssp_pose,
core::Size  sw_can_by_sh_id 
)
core::Size protocols::features::strand_assembly::WriteToDB_ending_loop ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::pose::Pose dssp_pose,
core::Size  sandwich_PK_id_counter,
core::Size  sw_can_by_sh_id,
std::string const &  tag,
core::Size  max_starting_loop_size_ 
)
Size protocols::features::strand_assembly::WriteToDB_ending_loop ( StructureID  struct_id,
sessionOP  db_session,
Pose dssp_pose,
core::Size  sandwich_PK_id_counter,
core::Size  sw_can_by_sh_id,
string const &  tag,
core::Size  max_starting_loop_size_ 
)
core::Size protocols::features::strand_assembly::WriteToDB_hydrophobic_ratio_net_charge ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sw_can_by_sh_id 
)
core::Size protocols::features::strand_assembly::WriteToDB_long_strand_id_in_each_sw ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sw_can_by_sh_id 
)
Size protocols::features::strand_assembly::WriteToDB_long_strand_id_in_each_sw ( StructureID  struct_id,
sessionOP  db_session,
core::Size  sw_can_by_sh_id 
)
core::Size protocols::features::strand_assembly::WriteToDB_min_avg_dis_between_sheets_by_cen_res ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sw_can_by_sh_id,
Pose dssp_pose,
utility::vector1< core::Size > const &  all_distinct_sheet_ids,
core::Size  min_num_strands_in_sheet_ 
)
core::Size protocols::features::strand_assembly::WriteToDB_min_dis_between_sheets_by_all_res ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sw_can_by_sh_id,
Pose dssp_pose,
utility::vector1< core::Size > const &  all_distinct_sheet_ids 
)
core::Size protocols::features::strand_assembly::WriteToDB_number_of_AAs_in_a_pair_of_edge_strands ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::pose::Pose const &  pose,
utility::vector1< SandwichFragment > const &  bs_of_sw_can_by_sh,
core::Size  max_num_sw_per_pdb_,
core::Real  min_CA_CA_dis_,
core::Real  max_CA_CA_dis_ 
)
Size protocols::features::strand_assembly::WriteToDB_number_of_AAs_in_a_pair_of_edge_strands ( StructureID  struct_id,
sessionOP  db_session,
core::pose::Pose const &  pose,
utility::vector1< SandwichFragment > const &  bs_of_sw_can_by_sh,
core::Size  max_num_sw_per_pdb_,
Real  min_CA_CA_dis_,
Real  max_CA_CA_dis_ 
)
core::Size protocols::features::strand_assembly::WriteToDB_number_of_core_heading_aro_AAs_in_a_pair_of_edge_strands ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sw_can_by_sh_id,
core::Size  current_bs_id,
core::Size  closest_bs_id 
)
core::Size protocols::features::strand_assembly::WriteToDB_number_of_core_heading_charged_AAs_in_a_pair_of_edge_strands ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sw_can_by_sh_id,
core::Size  current_bs_id,
core::Size  closest_bs_id 
)
void protocols::features::strand_assembly::WriteToDB_number_of_core_heading_FWY_in_sw ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sw_can_by_sh_id 
)
void protocols::features::strand_assembly::WriteToDB_number_of_core_heading_FWY_in_sw ( StructureID  struct_id,
sessionOP  db_session,
core::Size  sw_can_by_sh_id 
)
core::Size protocols::features::strand_assembly::WriteToDB_number_of_core_heading_LWY_in_core_strands_in_sw ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sw_can_by_sh_id 
)
Size protocols::features::strand_assembly::WriteToDB_number_of_core_heading_LWY_in_core_strands_in_sw ( StructureID  struct_id,
sessionOP  db_session,
core::Size  sw_can_by_sh_id 
)
void protocols::features::strand_assembly::WriteToDB_number_of_core_heading_W_in_sw ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sw_can_by_sh_id 
)
void protocols::features::strand_assembly::WriteToDB_number_of_core_heading_W_in_sw ( StructureID  struct_id,
sessionOP  db_session,
core::Size  sw_can_by_sh_id 
)
core::Size protocols::features::strand_assembly::WriteToDB_number_of_edge_strands_in_each_sw ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sw_can_by_sh_id 
)
Size protocols::features::strand_assembly::WriteToDB_number_of_edge_strands_in_each_sw ( StructureID  struct_id,
sessionOP  db_session,
core::Size  sw_can_by_sh_id 
)
core::Size protocols::features::strand_assembly::WriteToDB_number_of_sheets_that_surround_this_sheet ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sheet_id,
core::Size  num_of_sheets_that_surround_this_sheet 
)
Size protocols::features::strand_assembly::WriteToDB_number_of_sheets_that_surround_this_sheet ( StructureID  struct_id,
sessionOP  db_session,
core::Size  sheet_id,
core::Size  num_of_sheets_that_surround_this_sheet 
)
core::Size protocols::features::strand_assembly::WriteToDB_number_strands_in_each_sw ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sw_can_by_sh_id 
)
Size protocols::features::strand_assembly::WriteToDB_number_strands_in_each_sw ( StructureID  struct_id,
sessionOP  db_session,
core::Size  sw_can_by_sh_id 
)
core::Size protocols::features::strand_assembly::WriteToDB_prolines_that_seem_to_prevent_aggregation ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sw_can_by_sh_id,
core::Real  wt_for_pro_in_starting_loop_,
core::Real  wt_for_pro_in_1st_inter_sheet_loop_,
core::Real  wt_for_pro_in_3rd_inter_sheet_loop_ 
)
Size protocols::features::strand_assembly::WriteToDB_prolines_that_seem_to_prevent_aggregation ( StructureID  struct_id,
sessionOP  db_session,
core::Size  sw_can_by_sh_id,
Real  wt_for_pro_in_starting_loop_,
Real  wt_for_pro_in_1st_inter_sheet_loop_,
Real  wt_for_pro_in_3rd_inter_sheet_loop_ 
)
core::Size protocols::features::strand_assembly::WriteToDB_ratio_of_core_heading_FWY_in_sw ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sw_can_by_sh_id,
core::pose::Pose const &  pose 
)
Size protocols::features::strand_assembly::WriteToDB_ratio_of_core_heading_FWY_in_sw ( StructureID  struct_id,
sessionOP  db_session,
core::Size  sw_can_by_sh_id,
Pose const &  pose 
)
core::Size protocols::features::strand_assembly::WriteToDB_rkde ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  rkde_PK_id_counter,
std::string const &  tag,
core::Size  residue_number,
std::string const &  residue_type 
)
Size protocols::features::strand_assembly::WriteToDB_rkde ( StructureID  struct_id,
sessionOP  db_session,
core::Size  rkde_PK_id_counter,
string const &  tag,
core::Size  residue_number,
string const &  residue_type 
)
core::Size protocols::features::strand_assembly::WriteToDB_rkde_in_strands ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  rkde_in_strands_PK_id_counter,
std::string const &  tag,
core::Size  sw_can_by_sh_id,
core::Size  residue_number,
std::string const &  residue_type,
std::string const &  heading_direction 
)
Size protocols::features::strand_assembly::WriteToDB_rkde_in_strands ( StructureID  struct_id,
sessionOP  db_session,
core::Size  rkde_in_strands_PK_id_counter,
string const &  tag,
core::Size  sw_can_by_sh_id,
core::Size  residue_number,
string const &  residue_type,
string const &  heading_direction 
)
core::Size protocols::features::strand_assembly::WriteToDB_sandwich ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
Pose const &  pose,
core::Size  sandwich_PK_id_counter,
string const &  tag,
core::Size  sw_can_by_sh_id,
core::Size  sheet_id,
string const &  sheet_antiparallel,
core::Size  sandwich_bs_id,
string const &  strand_is_at_edge,
core::Size  component_size,
core::Size  residue_begin,
core::Size  residue_end 
)
core::Size protocols::features::strand_assembly::WriteToDB_sandwich_by_AA_w_direction ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
Pose const &  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 
)
core::Size protocols::features::strand_assembly::WriteToDB_sheet ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sheet_PK_id_counter,
core::Size  sheet_id,
core::Size  segment_id 
)
core::Size protocols::features::strand_assembly::WriteToDB_sheet_antiparallel ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sheet_id,
std::string const &  antiparallel 
)
Size protocols::features::strand_assembly::WriteToDB_sheet_antiparallel ( StructureID  struct_id,
sessionOP  db_session,
core::Size  sheet_id,
string const &  antiparallel 
)
core::Size protocols::features::strand_assembly::WriteToDB_sheet_connectivity ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::pose::Pose const &  pose,
core::Size  sandwich_PK_id_counter,
std::string const &  tag,
core::Size  sw_can_by_sh_id,
std::string const &  loop_kind,
core::Size  intra_sheet_con_id,
core::Size  inter_sheet_con_id,
std::string const &  LR,
std::string const &  cano_LR,
std::string const &  PA_by_preceding_E,
std::string const &  PA_by_following_E,
std::string const &  cano_PA,
std::string const &  heading_direction,
std::string const &  heading_parallel,
std::string const &  cano_parallel_EE,
core::Size  loop_size,
core::Size  start_res,
core::Size  end_res 
)
Size protocols::features::strand_assembly::WriteToDB_sheet_connectivity ( StructureID  struct_id,
sessionOP  db_session,
Pose const &  pose,
core::Size  sandwich_PK_id_counter,
string const &  tag,
core::Size  sw_can_by_sh_id,
string const &  loop_kind,
core::Size  intra_sheet_con_id,
core::Size  inter_sheet_con_id,
string const &  LR,
string const &  canonical_LR,
string const &  PA_by_preceding_E,
string const &  PA_by_following_E,
string const &  cano_PA,
string const &  heading_direction,
string const &  parallel_EE,
string const &  cano_parallel_EE,
core::Size  loop_size,
core::Size  start_res,
core::Size  end_res 
)
core::Size protocols::features::strand_assembly::WriteToDB_sheet_id ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  new_sheet_id,
core::Size  old_sheet_id 
)
Size protocols::features::strand_assembly::WriteToDB_sheet_id ( StructureID  struct_id,
sessionOP  db_session,
core::Size  new_sheet_id,
core::Size  old_sheet_id 
)
core::Real protocols::features::strand_assembly::WriteToDB_shortest_dis_between_facing_aro_in_sw ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sw_can_by_sh_id,
Pose const &  pose,
utility::vector1< core::Size > const &  all_distinct_sheet_ids,
core::Size  min_num_strands_in_sheet_ 
)
core::Size protocols::features::strand_assembly::WriteToDB_starting_loop ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::pose::Pose dssp_pose,
core::Size  sandwich_PK_id_counter,
core::Size  sw_can_by_sh_id,
std::string const &  tag,
core::Size  max_starting_loop_size_ 
)
Size protocols::features::strand_assembly::WriteToDB_starting_loop ( StructureID  struct_id,
sessionOP  db_session,
Pose dssp_pose,
core::Size  sandwich_PK_id_counter,
core::Size  sw_can_by_sh_id,
string const &  tag,
core::Size  max_starting_loop_size_ 
)
core::Size protocols::features::strand_assembly::WriteToDB_sw_can_by_sh ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sw_can_by_sh_PK_id_counter,
string const &  tag,
core::Size  sw_can_by_sh_id_counter,
core::Size  sheet_id,
core::Size  num_strands_from_sheet 
)
core::Size protocols::features::strand_assembly::WriteToDB_sw_res_size ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sw_can_by_sh_id 
)
Size protocols::features::strand_assembly::WriteToDB_sw_res_size ( StructureID  struct_id,
sessionOP  db_session,
core::Size  sw_can_by_sh_id 
)
core::Size protocols::features::strand_assembly::WriteToDB_topology_candidate ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sw_can_by_sh_id 
)
void protocols::features::strand_assembly::WriteToDB_turn_AA ( core::pose::Pose const &  pose,
core::Size  sw_can_by_sh_id,
core::Size  i,
StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
std::string const &  turn_type 
)
void protocols::features::strand_assembly::WriteToDB_turn_AA ( Pose const &  pose,
core::Size  sw_can_by_sh_id,
core::Size  i,
StructureID  struct_id,
sessionOP  db_session,
string const &  turn_type 
)
std::string protocols::features::strand_assembly::WriteToDB_turn_type ( core::pose::Pose const &  pose,
core::Size  sw_can_by_sh_id,
core::Size  start_res,
core::Size  end_res,
StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Real  allowed_deviation_for_turn_type_id_ 
)
string protocols::features::strand_assembly::WriteToDB_turn_type ( Pose const &  pose,
core::Size  sw_can_by_sh_id,
core::Size  first_res,
core::Size  second_res,
StructureID  struct_id,
sessionOP  db_session,
Real  allowed_deviation_for_turn_type_id_ 
)
core::Size protocols::features::strand_assembly::WriteToDB_whether_sw_is_not_connected_with_continuous_atoms ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
core::Size  sw_can_by_sh_id,
std::string const &  sw_is_not_connected_with_continuous_atoms 
)
Size protocols::features::strand_assembly::WriteToDB_whether_sw_is_not_connected_with_continuous_atoms ( StructureID  struct_id,
sessionOP  db_session,
core::Size  sw_can_by_sh_id,
string const &  sw_is_not_connected_with_continuous_atoms 
)