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< Real >	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)
pair< Real, Real >	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_)
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 const &strand_i, SandwichFragment const &strand_j, Real min_inter_sheet_dis_CA_CA_)
Real	check_sw_by_dis (Pose const &pose, SandwichFragment const &strand_i, SandwichFragment const &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::Size >	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)
vector< core::Size >	count_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::Size >	get_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 const &strand_i, SandwichFragment const &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::Size >	get_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::Size >	get_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 const &strand_i, SandwichFragment const &strand_j)
vector< core::Size >	get_central_residues_in_other_sheet (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id, core::Size sheet_id)
vector< core::Size >	get_central_residues_in_this_sheet (StructureID struct_id, sessionOP db_session, core::Size sheet_id)
utility::vector1< core::Size >	get_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 const &strand_i, SandwichFragment const &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::Size >	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< core::Size >	get_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::Size >	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)
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::Size >	get_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::Size >	get_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::Size >	get_vec_AA_kind (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id)
utility::vector1< core::Size >	get_vec_of_sw_can_by_sh_id (StructureID struct_id, sessionOP db_session)
utility::vector1< core::Size >	get_vector_of_strand_AA_distribution (StructureID struct_id, sessionOP db_session, string const &heading_direction, string const &strand_location)
utility::vector1< core::Size >	get_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::Real >	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 >	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::Size >	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)
std::vector< core::Size >	get_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::Size >	get_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::Size >	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::Size >	get_central_residues_in_this_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id)
utility::vector1< core::Size >	get_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::Size >	get_distinct_sheet_id_from_sheet_table (StructureID struct_id, utility::sql_database::sessionOP db_session)
utility::vector1< core::Size >	get_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::Size >	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	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::Size >	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	get_tag (StructureID struct_id, utility::sql_database::sessionOP db_session)
utility::vector1< core::Size >	get_vec_AA_kind (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
utility::vector1< core::Size >	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 >	get_vec_of_sw_can_by_sh_id (StructureID struct_id, utility::sql_database::sessionOP db_session)
utility::vector1< core::Size >	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	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::Size >	get_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 const &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 const &tag, StructureID struct_id, sessionOP db_session, Pose const &pose, string const &dssp_code, string const &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::Size >	get_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 const &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 const &tag, StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, std::string const &dssp_code, std::string const &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

SandwichFeaturesCOP

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

SandwichFeaturesOP

typedef utility::pointer::shared_ptr< SandwichFeatures > protocols::features::strand_assembly::SandwichFeaturesOP

StrandBundleFeaturesCOP

typedef utility::pointer::shared_ptr< StrandBundleFeatures const > protocols::features::strand_assembly::StrandBundleFeaturesCOP

StrandBundleFeaturesOP

typedef utility::pointer::shared_ptr< StrandBundleFeatures > protocols::features::strand_assembly::StrandBundleFeaturesOP

Function Documentation

absolute_vec() [1/2]

core::Real protocols::features::strand_assembly::absolute_vec

(

numeric::xyzVector< core::Real >

vector

)

Referenced by check_heading_direction(), check_LR(), check_PA(), check_whether_same_direction_strands_connect_two_sheets_or_a_loop(), and determine_heading_direction_by_vector().

absolute_vec() [2/2]

Real protocols::features::strand_assembly::absolute_vec

(

numeric::xyzVector< Real >

vector

)

Referenced by check_heading_direction(), check_LR(), check_PA(), check_whether_same_direction_strands_connect_two_sheets_or_a_loop(), and determine_heading_direction_by_vector().

cal_dis_angle_to_find_sheet()

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
	)

References core::conformation::Residue::atom(), core::pose::Pose::residue(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

Referenced by find_sheet().

cal_min_avg_dis_between_sheets_by_cen_res() [1/2]

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_
	)

References cal_min_avg_dis_between_two_sheets_by_cen_res(), and get_num_strands_in_this_sheet().

Referenced by WriteToDB_min_avg_dis_between_sheets_by_cen_res().

cal_min_avg_dis_between_sheets_by_cen_res() [2/2]

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_
	)

cal_min_avg_dis_between_two_sheets_by_cen_res() [1/2]

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
	)

References core::conformation::Residue::atom(), core::kinematics::distance(), get_central_residues_in_this_sheet(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by cal_min_avg_dis_between_sheets_by_cen_res(), and cal_num_of_sheets_that_surround_this_sheet().

cal_min_avg_dis_between_two_sheets_by_cen_res() [2/2]

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
	)

cal_min_dis_between_sheets_by_all_res() [1/2]

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
	)

References cal_min_dis_between_two_sheets_by_all_res(), and get_num_strands_in_this_sheet().

Referenced by WriteToDB_min_dis_between_sheets_by_all_res().

cal_min_dis_between_sheets_by_all_res() [2/2]

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
	)

cal_min_dis_between_two_sheets_by_all_res() [1/2]

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
	)

References core::conformation::Residue::atom(), get_all_residues_in_this_sheet(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by cal_min_dis_between_sheets_by_all_res().

cal_min_dis_between_two_sheets_by_all_res() [2/2]

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
	)

cal_num_of_sheets_that_surround_this_sheet() [1/2]

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_
	)

References cal_min_avg_dis_between_two_sheets_by_cen_res(), get_num_strands_in_this_sheet(), and TR().

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

cal_num_of_sheets_that_surround_this_sheet() [2/2]

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_
	)

cal_shortest_dis_between_facing_aro_in_sw() [1/2]

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_
	)

References core::conformation::Residue::atom(), get_aro_residues_in_this_sheet(), get_num_strands_in_this_sheet(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::conformation::Atom::xyz().

Referenced by WriteToDB_shortest_dis_between_facing_aro_in_sw().

cal_shortest_dis_between_facing_aro_in_sw() [2/2]

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_
	)

calculate_dihedral_w_4_resnums()

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
	)

References core::conformation::Residue::atom(), get_shortest_among_4_vals(), core::pose::Pose::residue(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

Referenced by WriteToDB_dihedral_angle_between_core_strands_across_facing_sheets().

change_sheet_id_if_possible()

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_
	)

References get_max_sheet_id(), see_whether_sheets_can_be_combined(), and WriteToDB_sheet_id().

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

check_canonicalness_of_LR()

std::string protocols::features::strand_assembly::check_canonicalness_of_LR	(	core::Size	loop_size,
		bool	intra_sheet,
		string const &	LR
	)

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

check_canonicalness_of_PA()

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_
	)

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

check_canonicalness_of_parallel_EE()

std::string protocols::features::strand_assembly::check_canonicalness_of_parallel_EE	(	core::Size	loop_size,
		bool	intra_sheet,
		string const &	parallel_EE
	)

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

check_heading_direction()

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_
	)

References absolute_vec(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::residue_type(), TR(), and core::pose::Pose::xyz().

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

check_helix_existence()

bool protocols::features::strand_assembly::check_helix_existence

(

Pose const &

dssp_pose

)

References core::pose::Pose::secstruct(), and core::pose::Pose::size().

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

check_LR()

std::string protocols::features::strand_assembly::check_LR	(	Pose &	dssp_pose,
		core::Size	residue_begin,
		core::Size	residue_end
	)

References absolute_vec(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::residue_type(), and core::pose::Pose::xyz().

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

check_PA()

std::pair< std::string, std::string > protocols::features::strand_assembly::check_PA	(	Pose &	dssp_pose,
		core::Size	residue_begin,
		core::Size	residue_end
	)

References absolute_vec(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::residue_type(), and core::pose::Pose::xyz().

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

check_strand_too_closeness()

bool protocols::features::strand_assembly::check_strand_too_closeness	(	Pose const &	pose,
		SandwichFragment const &	strand_i,
		SandwichFragment const &	strand_j,
		Real	min_inter_sheet_dis_CA_CA_
	)

References core::conformation::Residue::atom(), protocols::features::strand_assembly::SandwichFragment::get_size(), protocols::features::strand_assembly::SandwichFragment::get_start(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

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

check_sw_by_dis()

core::Real protocols::features::strand_assembly::check_sw_by_dis	(	Pose const &	pose,
		SandwichFragment const &	strand_i,
		SandwichFragment const &	strand_j,
		bool	antiparallel,
		Real	min_sheet_dis_,
		Real	max_sheet_dis_
	)

References get_avg_dis_CA_CA(), protocols::features::strand_assembly::SandwichFragment::get_size(), protocols::features::strand_assembly::SandwichFragment::get_start(), and core::pose::Pose::size().

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

check_whether_hairpin_connects_short_strand() [1/2]

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
	)

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

check_whether_hairpin_connects_short_strand() [2/2]

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
	)

check_whether_same_direction_strands_connect_two_sheets_or_a_loop() [1/2]

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
	)

References absolute_vec(), and core::pose::Pose::xyz().

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

check_whether_same_direction_strands_connect_two_sheets_or_a_loop() [2/2]

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
	)

check_whether_sheets_are_connected_with_near_bb_atoms() [1/2]

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_
	)

References core::conformation::Residue::atom(), get_all_strands_in_sheet_i(), get_list_of_residues_in_sheet_i(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

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

check_whether_sheets_are_connected_with_near_bb_atoms() [2/2]

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_
	)

check_whether_strand_i_is_in_sheet() [1/2]

bool protocols::features::strand_assembly::check_whether_strand_i_is_in_sheet	(	StructureID	struct_id,
		sessionOP	db_session,
		core::Size	segment_id
	)

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

check_whether_strand_i_is_in_sheet() [2/2]

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
	)

check_whether_sw_by_sh_id_still_alive() [1/2]

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
	)

Referenced by WriteToDB_number_of_AAs_in_a_pair_of_edge_strands().

check_whether_sw_by_sh_id_still_alive() [2/2]

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
	)

check_whether_sw_is_not_connected_with_continuous_atoms() [1/2]

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
	)

References core::conformation::Residue::atom(), core::kinematics::distance(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

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

check_whether_sw_is_not_connected_with_continuous_atoms() [2/2]

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
	)

check_whether_this_pdb_should_be_excluded()

bool protocols::features::strand_assembly::check_whether_this_pdb_should_be_excluded

(

string const &

tag

)

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

check_whether_this_sheet_is_too_short()

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().

count_AA_w_direction() [1/2]

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
	)

References determine_core_heading_surface_heading_by_distance(), determine_heading_direction_by_vector(), core::chemical::ResidueTypeBase::name3(), and core::pose::Pose::residue_type().

Referenced by WriteToDB_sandwich_by_AA_w_direction().

count_AA_w_direction() [2/2]

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
	)

count_AA_wo_direction()

std::vector< core::Size > protocols::features::strand_assembly::count_AA_wo_direction	(	Pose const &	pose,
		core::Size	residue_begin,
		core::Size	residue_end
	)

References core::chemical::ResidueTypeBase::name3(), and core::pose::Pose::residue_type().

Referenced by WriteToDB_AA_to_terminal_loops(), WriteToDB_sandwich(), and WriteToDB_sheet_connectivity().

delete_this_struct_id() [1/2]

Size protocols::features::strand_assembly::delete_this_struct_id	(	StructureID	struct_id,
		sessionOP	db_session
	)

References TR().

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

delete_this_struct_id() [2/2]

core::Size protocols::features::strand_assembly::delete_this_struct_id	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

delete_this_sw_can_by_sh_id_from_sw_by_comp() [1/2]

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
	)

References TR().

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

delete_this_sw_can_by_sh_id_from_sw_by_comp() [2/2]

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
	)

determine_core_heading_surface_heading_by_distance()

std::string protocols::features::strand_assembly::determine_core_heading_surface_heading_by_distance	(	Pose const &	pose_w_center_000,
		core::Size	ii
	)

References core::conformation::Residue::atom(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::conformation::Atom::xyz().

Referenced by count_AA_w_direction().

determine_heading_direction_by_vector()

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
	)

References absolute_vec(), core::conformation::Residue::atom(), core::kinematics::distance(), get_central_residues_in_other_sheet(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), round_to_Size(), core::conformation::Atom::xyz(), and core::pose::Pose::xyz().

Referenced by count_AA_w_direction(), prepare_and_write_number_of_electrostatic_interactions_of_residues_to_files(), report_heading_directions_of_all_AA_in_a_strand(), write_resfile_to_a_file(), and write_resfile_to_a_file_when_seq_rec_is_bad().

find_sheet()

core::Size protocols::features::strand_assembly::find_sheet	(	Pose const &	pose,
		SandwichFragment const &	strand_i,
		SandwichFragment const &	strand_j,
		bool	antiparallel,
		Real	min_CA_CA_dis_,
		Real	max_CA_CA_dis_,
		Real	min_C_O_N_angle_,
		bool	care_smaller_sheet
	)

References core::conformation::Residue::atom(), cal_dis_angle_to_find_sheet(), protocols::features::strand_assembly::SandwichFragment::get_end(), protocols::features::strand_assembly::SandwichFragment::get_size(), protocols::features::strand_assembly::SandwichFragment::get_start(), core::pose::Pose::residue(), TR(), and core::conformation::Atom::xyz().

Referenced by protocols::features::strand_assembly::SandwichFeatures::report_features(), protocols::legacy_sewing::see_whether_model_is_H_bonded_by_terminal_strands(), see_whether_sheet_is_antiparallel(), and see_whether_sheets_can_be_combined().

get_all_residues_in_this_sheet() [1/2]

vector<core::Size> protocols::features::strand_assembly::get_all_residues_in_this_sheet	(	StructureID	struct_id,
		sessionOP	db_session,
		core::Size	sheet_id
	)

References core::scoring::pair, and query_begin_end().

Referenced by cal_min_dis_between_two_sheets_by_all_res().

get_all_residues_in_this_sheet() [2/2]

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
	)

get_all_strands_in_sheet_i() [1/2]

utility::vector1<SandwichFragment> protocols::features::strand_assembly::get_all_strands_in_sheet_i	(	StructureID	struct_id,
		sessionOP	db_session,
		core::Size	sheet_id
	)

Referenced by check_whether_sheets_are_connected_with_near_bb_atoms(), get_start_end_res_num_in_the_longest_strand(), and WriteToDB_dihedral_angle_between_core_strands_across_facing_sheets().

get_all_strands_in_sheet_i() [2/2]

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
	)

get_aro_residues_in_this_sheet() [1/2]

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
	)

References core::chemical::ResidueTypeBase::name3(), and core::pose::Pose::residue_type().

Referenced by cal_shortest_dis_between_facing_aro_in_sw().

get_aro_residues_in_this_sheet() [2/2]

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
	)

get_avg_dis_CA_CA()

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_
	)

References core::conformation::Residue::atom(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by check_sw_by_dis().

get_avg_dis_strands()

core::Real protocols::features::strand_assembly::get_avg_dis_strands	(	Pose const &	pose,
		SandwichFragment const &	strand_i,
		SandwichFragment const &	strand_j
	)

References core::conformation::Residue::atom(), protocols::features::strand_assembly::SandwichFragment::get_size(), protocols::features::strand_assembly::SandwichFragment::get_start(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by get_current_bs_id_and_closest_edge_bs_id_in_different_sheet(), protocols::features::strand_assembly::SandwichFeatures::report_features(), and see_whether_sheet_is_antiparallel().

get_central_residues_in_each_of_two_edge_strands()

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_
	)

References core::conformation::Residue::atom(), get_full_strands_from_sheet(), is_this_strand_at_edge(), core::pose::Pose::residue(), round_to_Size(), and core::conformation::Atom::xyz().

Referenced by judge_facing().

get_central_residues_in_other_sheet() [1/2]

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
	)

References round_to_Size().

Referenced by determine_heading_direction_by_vector().

get_central_residues_in_other_sheet() [2/2]

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
	)

get_central_residues_in_this_sheet() [1/2]

vector<core::Size> protocols::features::strand_assembly::get_central_residues_in_this_sheet	(	StructureID	struct_id,
		sessionOP	db_session,
		core::Size	sheet_id
	)

References core::scoring::pair, query_begin_end(), and round_to_Size().

Referenced by cal_min_avg_dis_between_two_sheets_by_cen_res().

get_central_residues_in_this_sheet() [2/2]

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
	)

get_chain_B_resNum() [1/2]

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
	)

References get_vec_distinct_sheet_id().

Referenced by write_chain_B_resNum_to_a_file().

get_chain_B_resNum() [2/2]

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
	)

get_closest_distance_between_strands()

core::Real protocols::features::strand_assembly::get_closest_distance_between_strands	(	Pose const &	pose,
		SandwichFragment const &	strand_i,
		SandwichFragment const &	strand_j
	)

References core::conformation::Residue::atom(), protocols::features::strand_assembly::SandwichFragment::get_size(), protocols::features::strand_assembly::SandwichFragment::get_start(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by is_this_strand_at_edge().

get_current_bs_id_and_closest_edge_bs_id_in_different_sheet()

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
	)

References get_avg_dis_strands().

Referenced by WriteToDB_number_of_AAs_in_a_pair_of_edge_strands().

get_current_strands_in_sheet() [1/2]

utility::vector1<SandwichFragment> protocols::features::strand_assembly::get_current_strands_in_sheet	(	StructureID	struct_id,
		sessionOP	db_session
	)

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

get_current_strands_in_sheet() [2/2]

utility::vector1<SandwichFragment> protocols::features::strand_assembly::get_current_strands_in_sheet	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

get_distinct_sheet_id_from_sheet_table() [1/2]

utility::vector1<core::Size> protocols::features::strand_assembly::get_distinct_sheet_id_from_sheet_table	(	StructureID	struct_id,
		sessionOP	db_session
	)

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

get_distinct_sheet_id_from_sheet_table() [2/2]

utility::vector1<core::Size> protocols::features::strand_assembly::get_distinct_sheet_id_from_sheet_table	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

get_distinct_sw_id_from_sandwich_table() [1/2]

utility::vector1<core::Size> protocols::features::strand_assembly::get_distinct_sw_id_from_sandwich_table	(	StructureID	struct_id,
		sessionOP	db_session
	)

Referenced by write_number_of_electrostatic_interactions_of_residues_to_files().

get_distinct_sw_id_from_sandwich_table() [2/2]

utility::vector1<core::Size> protocols::features::strand_assembly::get_distinct_sw_id_from_sandwich_table	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

get_full_strands() [1/2]

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().

get_full_strands() [2/2]

utility::vector1<SandwichFragment> protocols::features::strand_assembly::get_full_strands	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

get_full_strands_from_sheet() [1/2]

utility::vector1<SandwichFragment> protocols::features::strand_assembly::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.

Referenced by check_whether_this_sheet_is_too_short(), get_central_residues_in_each_of_two_edge_strands(), is_this_strand_at_edge(), protocols::features::strand_assembly::SandwichFeatures::report_features(), see_whether_sheet_is_antiparallel(), and see_whether_sheets_can_be_combined().

get_full_strands_from_sheet() [2/2]

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
	)

get_list_of_residues_in_sheet_i()

utility::vector1< core::Size > protocols::features::strand_assembly::get_list_of_residues_in_sheet_i

(

utility::vector1< SandwichFragment >

all_strands_in_sheet_i

)

Referenced by check_whether_sheets_are_connected_with_near_bb_atoms().

get_max_sheet_id() [1/2]

Size protocols::features::strand_assembly::get_max_sheet_id	(	StructureID	struct_id,
		sessionOP	db_session
	)

Referenced by change_sheet_id_if_possible(), and protocols::features::strand_assembly::SandwichFeatures::report_features().

get_max_sheet_id() [2/2]

core::Size protocols::features::strand_assembly::get_max_sheet_id	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

get_next_starting_res_for_connecting_strands() [1/2]

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
	)

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

get_next_starting_res_for_connecting_strands() [2/2]

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
	)

get_num_of_distinct_sheet_id() [1/2]

Size protocols::features::strand_assembly::get_num_of_distinct_sheet_id	(	StructureID	struct_id,
		sessionOP	db_session
	)

get_num_of_distinct_sheet_id() [2/2]

core::Size protocols::features::strand_assembly::get_num_of_distinct_sheet_id	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

get_num_of_sheets_that_surround_this_sheet() [1/2]

Size protocols::features::strand_assembly::get_num_of_sheets_that_surround_this_sheet	(	StructureID	struct_id,
		sessionOP	db_session,
		core::Size	sheet_id
	)

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

get_num_of_sheets_that_surround_this_sheet() [2/2]

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
	)

get_num_strands_in_this_sheet() [1/2]

Size protocols::features::strand_assembly::get_num_strands_in_this_sheet	(	StructureID	struct_id,
		sessionOP	db_session,
		core::Size	sheet_id
	)

References protocols::denovo_design::components::num_strands().

Referenced by cal_min_avg_dis_between_sheets_by_cen_res(), cal_min_dis_between_sheets_by_all_res(), cal_num_of_sheets_that_surround_this_sheet(), cal_shortest_dis_between_facing_aro_in_sw(), and protocols::features::strand_assembly::SandwichFeatures::report_features().

get_num_strands_in_this_sheet() [2/2]

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
	)

get_segment_id() [1/2]

Size protocols::features::strand_assembly::get_segment_id	(	StructureID	struct_id,
		sessionOP	db_session,
		core::Size	all_strands_index
	)

Referenced by protocols::sewing::data_storage::HashedSmartAssembly::add_segment(), protocols::sewing::data_storage::SmartAssembly::reconstitute_assembly_from_string(), and protocols::features::strand_assembly::SandwichFeatures::report_features().

get_segment_id() [2/2]

core::Size protocols::features::strand_assembly::get_segment_id	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	all_strands_index
	)

get_sheet_antiparallel_info() [1/2]

string protocols::features::strand_assembly::get_sheet_antiparallel_info	(	StructureID	struct_id,
		sessionOP	db_session,
		core::Size	sheet_id
	)

Referenced by Run_WriteToDB_sandwich(), and write_phi_psi_of_each_residue_to_a_file().

get_sheet_antiparallel_info() [2/2]

std::string protocols::features::strand_assembly::get_sheet_antiparallel_info	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	sheet_id
	)

get_shortest_among_4_vals()

core::Real protocols::features::strand_assembly::get_shortest_among_4_vals

(

const Real

arr_dis_inter_sheet[]

)

Referenced by calculate_dihedral_w_4_resnums(), and judge_facing().

get_size_sandwich_PK_id() [1/2]

Size protocols::features::strand_assembly::get_size_sandwich_PK_id	(	StructureID	struct_id,
		sessionOP	db_session,
		core::Size	sw_can_by_sh_id
	)

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

get_size_sandwich_PK_id() [2/2]

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
	)

get_start_end_res_num_in_the_longest_strand() [1/2]

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().

get_start_end_res_num_in_the_longest_strand() [2/2]

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
	)

get_starting_res_for_connecting_strands() [1/2]

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
	)

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

get_starting_res_for_connecting_strands() [2/2]

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
	)

get_tag() [1/2]

string protocols::features::strand_assembly::get_tag	(	StructureID	struct_id,
		sessionOP	db_session
	)

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

get_tag() [2/2]

std::string protocols::features::strand_assembly::get_tag	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

get_vec_AA_kind() [1/2]

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().

get_vec_AA_kind() [2/2]

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
	)

get_vec_distinct_sheet_id() [1/2]

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
	)

Referenced by get_chain_B_resNum(), and WriteToDB_dihedral_angle_between_core_strands_across_facing_sheets().

get_vec_distinct_sheet_id() [2/2]

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
	)

get_vec_of_sw_can_by_sh_id() [1/2]

utility::vector1<core::Size> protocols::features::strand_assembly::get_vec_of_sw_can_by_sh_id	(	StructureID	struct_id,
		sessionOP	db_session
	)

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

get_vec_of_sw_can_by_sh_id() [2/2]

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
	)

get_vector_of_loop_AA_distribution() [1/2]

utility::vector1<core::Size> protocols::features::strand_assembly::get_vector_of_loop_AA_distribution	(	StructureID	struct_id,
		sessionOP	db_session,
		string	loop_kind
	)

Referenced by write_AA_distribution_without_direction_to_a_file().

get_vector_of_loop_AA_distribution() [2/2]

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
	)

get_vector_of_strand_AA_distribution() [1/2]

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
	)

Referenced by write_AA_distribution_with_direction_to_a_file().

get_vector_of_strand_AA_distribution() [2/2]

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
	)

identify_sheet_id_by_residue_end() [1/2]

Size protocols::features::strand_assembly::identify_sheet_id_by_residue_end	(	StructureID	struct_id,
		sessionOP	db_session,
		core::Size	residue_end
	)

Referenced by WriteToDB_sheet_connectivity().

identify_sheet_id_by_residue_end() [2/2]

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
	)

is_this_strand_at_edge()

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_
	)

References core::conformation::Residue::atom(), get_closest_distance_between_strands(), get_full_strands_from_sheet(), core::pose::Pose::residue(), round_to_Size(), and core::conformation::Atom::xyz().

Referenced by get_central_residues_in_each_of_two_edge_strands(), Run_WriteToDB_sandwich(), see_whether_sheet_is_antiparallel(), write_phi_psi_of_each_residue_to_a_file(), and WriteToDB_number_of_AAs_in_a_pair_of_edge_strands().

is_this_strand_at_edge_by_looking_db() [1/2]

string protocols::features::strand_assembly::is_this_strand_at_edge_by_looking_db	(	StructureID	struct_id,
		sessionOP	db_session,
		core::Size	residue_begin
	)

Referenced by WriteToDB_dihedral_angle_between_core_strands_across_facing_sheets().

is_this_strand_at_edge_by_looking_db() [2/2]

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
	)

judge_facing()

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_
	)

References core::conformation::Residue::atom(), check_whether_this_sheet_is_too_short(), get_central_residues_in_each_of_two_edge_strands(), get_shortest_among_4_vals(), get_start_end_res_num_in_the_longest_strand(), core::pose::Pose::residue(), round_to_Size(), TR(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

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

prepare_and_write_number_of_electrostatic_interactions_of_residues_to_files() [1/2]

core::Size protocols::features::strand_assembly::prepare_and_write_number_of_electrostatic_interactions_of_residues_to_files	(	std::string const &	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
	)

prepare_and_write_number_of_electrostatic_interactions_of_residues_to_files() [2/2]

core::Size protocols::features::strand_assembly::prepare_and_write_number_of_electrostatic_interactions_of_residues_to_files	(	string const &	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
	)

References determine_heading_direction_by_vector(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::residue_type(), core::pose::Pose::size(), write_number_of_electrostatic_interactions_of_residues_to_files(), WriteToDB_rkde(), and WriteToDB_rkde_in_strands().

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

prepare_WriteToDB_sandwich() [1/2]

utility::vector1<SandwichFragment> protocols::features::strand_assembly::prepare_WriteToDB_sandwich	(	StructureID	struct_id,
		sessionOP	db_session
	)

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

prepare_WriteToDB_sandwich() [2/2]

utility::vector1<SandwichFragment> protocols::features::strand_assembly::prepare_WriteToDB_sandwich	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

process_decoy()

void protocols::features::strand_assembly::process_decoy	(	Pose &	dssp_pose,
		core::scoring::ScoreFunction const &	scorefxn
	)

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

query_begin_end()

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
	)

Referenced by get_all_residues_in_this_sheet(), and get_central_residues_in_this_sheet().

report_heading_directions_of_all_AA_in_a_strand()

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
	)

References determine_heading_direction_by_vector().

Referenced by write_heading_direction_of_all_AA_in_a_strand_to_a_file().

retrieve_residue_num_of_rkde() [1/2]

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
	)

Referenced by write_number_of_electrostatic_interactions_of_residues_to_files().

retrieve_residue_num_of_rkde() [2/2]

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
	)

round_to_float()

float protocols::features::strand_assembly::round_to_float

(

float

x

)

Referenced by write_number_of_electrostatic_interactions_of_residues_to_files().

round_to_Real()

core::Real protocols::features::strand_assembly::round_to_Real

(

Real

x

)

Referenced by write_p_aa_pp_of_AAs_to_a_file(), write_phi_psi_of_each_residue_to_a_file(), write_rama_of_AAs_to_a_file(), WriteToDB_dihedral_angle_between_core_strands_across_facing_sheets(), WriteToDB_dssp_ratio_in_sw(), WriteToDB_min_avg_dis_between_sheets_by_cen_res(), WriteToDB_min_dis_between_sheets_by_all_res(), WriteToDB_ratio_of_core_heading_FWY_in_sw(), and WriteToDB_shortest_dis_between_facing_aro_in_sw().

round_to_Size()

core::Size protocols::features::strand_assembly::round_to_Size

(

Real

x

)

Referenced by determine_heading_direction_by_vector(), get_central_residues_in_each_of_two_edge_strands(), get_central_residues_in_other_sheet(), get_central_residues_in_this_sheet(), is_this_strand_at_edge(), judge_facing(), see_whether_sheet_is_antiparallel(), and write_AA_kind_to_a_file().

Run_WriteToDB_sandwich() [1/2]

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
	)

Run_WriteToDB_sandwich() [2/2]

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
	)

References get_sheet_antiparallel_info(), is_this_strand_at_edge(), and WriteToDB_sandwich().

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

see_edge_or_core_or_loop_or_short_edge() [1/2]

string protocols::features::strand_assembly::see_edge_or_core_or_loop_or_short_edge	(	StructureID	struct_id,
		sessionOP	db_session,
		core::Size	residue_num
	)

Referenced by write_resfile_to_a_file(), and write_resfile_to_a_file_when_seq_rec_is_bad().

see_edge_or_core_or_loop_or_short_edge() [2/2]

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
	)

see_whether_sheet_is_antiparallel()

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_
	)

References core::conformation::Residue::atom(), find_sheet(), get_avg_dis_strands(), get_full_strands_from_sheet(), is_this_strand_at_edge(), core::pose::Pose::residue(), round_to_Size(), and core::conformation::Atom::xyz().

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

see_whether_sheets_can_be_combined()

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_
	)

References find_sheet(), and get_full_strands_from_sheet().

Referenced by change_sheet_id_if_possible().

see_whether_this_sw_has_SS_bond() [1/2]

bool protocols::features::strand_assembly::see_whether_this_sw_has_SS_bond	(	StructureID	struct_id,
		sessionOP	db_session
	)

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

see_whether_this_sw_has_SS_bond() [2/2]

bool protocols::features::strand_assembly::see_whether_this_sw_has_SS_bond	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

TR() [1/5]

static basic::Tracer protocols::features::strand_assembly::TR ( "protocols.features.strand_assembly.CheckForSandwichFeatures"  )

static

Referenced by cal_num_of_sheets_that_surround_this_sheet(), check_heading_direction(), delete_this_struct_id(), delete_this_sw_can_by_sh_id_from_sw_by_comp(), find_sheet(), judge_facing(), protocols::features::strand_assembly::SandwichFeatures::report_features(), protocols::features::strand_assembly::StrandBundleFeatures::report_features(), write_number_of_electrostatic_interactions_of_residues_to_files(), and WriteToDB_shortest_dis_between_facing_aro_in_sw().

TR() [2/5]

static basic::Tracer protocols::features::strand_assembly::TR ( "protocols.features.strand_assembly.SandwichFeatures"  )

static

TR() [3/5]

static basic::Tracer protocols::features::strand_assembly::TR ( "protocols.features.strand_assembly.StrandBundleFeatures"  )

static

TR() [4/5]

static basic::Tracer protocols::features::strand_assembly::TR ( "protocols.features.strand_assembly.WriteToDBFromSandwichFeatures"  )

static

TR() [5/5]

static basic::Tracer protocols::features::strand_assembly::TR ( "protocols.features.strand_assembly.WriteToFileFromSandwichFeatures"  )

static

write_AA_distribution_with_direction_to_a_file()

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
	)

References get_vector_of_strand_AA_distribution().

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

write_AA_distribution_without_direction_to_a_file()

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
	)

References get_vector_of_loop_AA_distribution().

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

write_AA_kind_to_a_file()

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
	)

References get_vec_AA_kind(), and round_to_Size().

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

write_beta_sheet_capping_info_to_a_file()

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_
	)

References core::chemical::ResidueTypeBase::name3(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

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

write_chain_B_resNum_to_a_file() [1/2]

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
	)

write_chain_B_resNum_to_a_file() [2/2]

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
	)

References get_chain_B_resNum().

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

write_heading_direction_of_all_AA_in_a_strand_to_a_file() [1/2]

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
	)

write_heading_direction_of_all_AA_in_a_strand_to_a_file() [2/2]

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
	)

References report_heading_directions_of_all_AA_in_a_strand().

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

write_number_of_electrostatic_interactions_of_residues_to_files() [1/2]

core::Size protocols::features::strand_assembly::write_number_of_electrostatic_interactions_of_residues_to_files	(	std::string const &	tag,
		StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::pose::Pose const &	pose,
		std::string const &	dssp_code,
		std::string const &	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_
	)

write_number_of_electrostatic_interactions_of_residues_to_files() [2/2]

core::Size protocols::features::strand_assembly::write_number_of_electrostatic_interactions_of_residues_to_files	(	string const &	tag,
		StructureID	struct_id,
		sessionOP	db_session,
		Pose const &	pose,
		string const &	dssp_code,
		string const &	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_
	)

References core::conformation::Residue::atom(), get_distinct_sw_id_from_sandwich_table(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), retrieve_residue_num_of_rkde(), round_to_float(), TR(), and core::conformation::Atom::xyz().

Referenced by prepare_and_write_number_of_electrostatic_interactions_of_residues_to_files().

write_p_aa_pp_of_AAs_to_a_file()

core::Size protocols::features::strand_assembly::write_p_aa_pp_of_AAs_to_a_file	(	string	tag,
		Pose &	dssp_pose
	)

References core::pose::Pose::energies(), core::chemical::ResidueTypeBase::name3(), core::scoring::p_aa_pp, core::scoring::Energies::residue_total_energies(), core::pose::Pose::residue_type(), round_to_Real(), and core::pose::Pose::size().

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

write_phi_psi_of_each_residue_to_a_file() [1/2]

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_
	)

write_phi_psi_of_each_residue_to_a_file() [2/2]

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_
	)

References get_sheet_antiparallel_info(), is_this_strand_at_edge(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue_type(), round_to_Real(), core::pose::Pose::secstruct(), and core::pose::Pose::size().

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

write_rama_of_AAs_to_a_file()

core::Size protocols::features::strand_assembly::write_rama_of_AAs_to_a_file	(	string	tag,
		Pose &	dssp_pose
	)

References core::pose::Pose::energies(), core::chemical::ResidueTypeBase::name3(), core::scoring::rama, core::scoring::Energies::residue_total_energies(), core::pose::Pose::residue_type(), round_to_Real(), and core::pose::Pose::size().

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

write_resfile_to_a_file()

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_
	)

References determine_heading_direction_by_vector(), see_edge_or_core_or_loop_or_short_edge(), and core::pose::Pose::size().

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

write_resfile_to_a_file_when_seq_rec_is_bad()

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_
	)

References determine_heading_direction_by_vector(), see_edge_or_core_or_loop_or_short_edge(), and core::pose::Pose::size().

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

WriteToDB_AA_to_terminal_loops() [1/2]

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
	)

References count_AA_wo_direction().

Referenced by WriteToDB_ending_loop(), and WriteToDB_starting_loop().

WriteToDB_AA_to_terminal_loops() [2/2]

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
	)

WriteToDB_avg_b_factor_CB_at_each_component()

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
	)

References core::pose::Pose::pdb_info(), and protocols::noesy_assign::round().

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

WriteToDB_dihedral_angle_between_core_strands_across_facing_sheets()

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
	)

References calculate_dihedral_w_4_resnums(), get_all_strands_in_sheet_i(), get_vec_distinct_sheet_id(), is_this_strand_at_edge_by_looking_db(), and round_to_Real().

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

WriteToDB_dssp_ratio_in_sw() [1/2]

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
	)

References round_to_Real(), core::pose::Pose::secstruct(), and core::pose::Pose::size().

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

WriteToDB_dssp_ratio_in_sw() [2/2]

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
	)

WriteToDB_ending_loop() [1/2]

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_
	)

References core::conformation::Residue::atom(), core::pose::Pose::residue(), core::pose::Pose::secstruct(), core::pose::Pose::size(), WriteToDB_AA_to_terminal_loops(), and core::conformation::Atom::xyz().

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

WriteToDB_ending_loop() [2/2]

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_
	)

WriteToDB_hydrophobic_ratio_net_charge()

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
	)

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

WriteToDB_long_strand_id_in_each_sw() [1/2]

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
	)

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

WriteToDB_long_strand_id_in_each_sw() [2/2]

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
	)

WriteToDB_min_avg_dis_between_sheets_by_cen_res()

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_
	)

References cal_min_avg_dis_between_sheets_by_cen_res(), and round_to_Real().

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

WriteToDB_min_dis_between_sheets_by_all_res()

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
	)

References cal_min_dis_between_sheets_by_all_res(), and round_to_Real().

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

WriteToDB_number_of_AAs_in_a_pair_of_edge_strands() [1/2]

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_
	)

References check_whether_sw_by_sh_id_still_alive(), get_current_bs_id_and_closest_edge_bs_id_in_different_sheet(), is_this_strand_at_edge(), WriteToDB_number_of_core_heading_aro_AAs_in_a_pair_of_edge_strands(), and WriteToDB_number_of_core_heading_charged_AAs_in_a_pair_of_edge_strands().

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

WriteToDB_number_of_AAs_in_a_pair_of_edge_strands() [2/2]

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_
	)

WriteToDB_number_of_core_heading_aro_AAs_in_a_pair_of_edge_strands()

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
	)

Referenced by WriteToDB_number_of_AAs_in_a_pair_of_edge_strands().

WriteToDB_number_of_core_heading_charged_AAs_in_a_pair_of_edge_strands()

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
	)

Referenced by WriteToDB_number_of_AAs_in_a_pair_of_edge_strands().

WriteToDB_number_of_core_heading_FWY_in_sw() [1/2]

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
	)

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

WriteToDB_number_of_core_heading_FWY_in_sw() [2/2]

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
	)

WriteToDB_number_of_core_heading_LWY_in_core_strands_in_sw() [1/2]

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
	)

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

WriteToDB_number_of_core_heading_LWY_in_core_strands_in_sw() [2/2]

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
	)

WriteToDB_number_of_core_heading_W_in_sw() [1/2]

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
	)

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

WriteToDB_number_of_core_heading_W_in_sw() [2/2]

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
	)

WriteToDB_number_of_edge_strands_in_each_sw() [1/2]

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
	)

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

WriteToDB_number_of_edge_strands_in_each_sw() [2/2]

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
	)

WriteToDB_number_of_sheets_that_surround_this_sheet() [1/2]

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
	)

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

WriteToDB_number_of_sheets_that_surround_this_sheet() [2/2]

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
	)

WriteToDB_number_strands_in_each_sw() [1/2]

Size protocols::features::strand_assembly::WriteToDB_number_strands_in_each_sw	(	StructureID	struct_id,
		sessionOP	db_session,
		core::Size	sw_can_by_sh_id
	)

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

WriteToDB_number_strands_in_each_sw() [2/2]

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
	)

WriteToDB_prolines_that_seem_to_prevent_aggregation() [1/2]

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_
	)

WriteToDB_prolines_that_seem_to_prevent_aggregation() [2/2]

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_
	)

WriteToDB_ratio_of_core_heading_FWY_in_sw() [1/2]

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
	)

References round_to_Real(), and core::pose::Pose::size().

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

WriteToDB_ratio_of_core_heading_FWY_in_sw() [2/2]

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
	)

WriteToDB_rkde() [1/2]

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
	)

Referenced by prepare_and_write_number_of_electrostatic_interactions_of_residues_to_files().

WriteToDB_rkde() [2/2]

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
	)

WriteToDB_rkde_in_strands() [1/2]

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
	)

Referenced by prepare_and_write_number_of_electrostatic_interactions_of_residues_to_files().

WriteToDB_rkde_in_strands() [2/2]

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
	)

WriteToDB_sandwich()

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
	)

References count_AA_wo_direction().

Referenced by Run_WriteToDB_sandwich().

WriteToDB_sandwich_by_AA_w_direction()

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
	)

References count_AA_w_direction().

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

WriteToDB_sheet()

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
	)

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

WriteToDB_sheet_antiparallel() [1/2]

Size protocols::features::strand_assembly::WriteToDB_sheet_antiparallel	(	StructureID	struct_id,
		sessionOP	db_session,
		core::Size	sheet_id,
		string const &	antiparallel
	)

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

WriteToDB_sheet_antiparallel() [2/2]

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
	)

WriteToDB_sheet_connectivity() [1/2]

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
	)

References count_AA_wo_direction(), and identify_sheet_id_by_residue_end().

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

WriteToDB_sheet_connectivity() [2/2]

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
	)

WriteToDB_sheet_id() [1/2]

Size protocols::features::strand_assembly::WriteToDB_sheet_id	(	StructureID	struct_id,
		sessionOP	db_session,
		core::Size	new_sheet_id,
		core::Size	old_sheet_id
	)

Referenced by change_sheet_id_if_possible().

WriteToDB_sheet_id() [2/2]

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
	)

WriteToDB_shortest_dis_between_facing_aro_in_sw()

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_
	)

References cal_shortest_dis_between_facing_aro_in_sw(), round_to_Real(), and TR().

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

WriteToDB_starting_loop() [1/2]

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_
	)

References core::conformation::Residue::atom(), core::pose::Pose::residue(), core::pose::Pose::secstruct(), WriteToDB_AA_to_terminal_loops(), and core::conformation::Atom::xyz().

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

WriteToDB_starting_loop() [2/2]

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_
	)

WriteToDB_sw_can_by_sh()

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
	)

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

WriteToDB_sw_res_size() [1/2]

Size protocols::features::strand_assembly::WriteToDB_sw_res_size	(	StructureID	struct_id,
		sessionOP	db_session,
		core::Size	sw_can_by_sh_id
	)

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

WriteToDB_sw_res_size() [2/2]

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
	)

WriteToDB_topology_candidate()

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
	)

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

WriteToDB_turn_AA() [1/2]

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
	)

WriteToDB_turn_AA() [2/2]

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
	)

References core::chemical::ResidueTypeBase::name3(), and core::pose::Pose::residue_type().

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

WriteToDB_turn_type() [1/2]

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_
	)

WriteToDB_turn_type() [2/2]

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_
	)

References core::pose::Pose::phi(), and core::pose::Pose::psi().

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

WriteToDB_whether_sw_is_not_connected_with_continuous_atoms() [1/2]

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
	)

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

WriteToDB_whether_sw_is_not_connected_with_continuous_atoms() [2/2]

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
	)