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WriteToDBFromSandwichFeatures.cc File Reference

Write to a DB after SandwichFeatures. More...

#include <protocols/features/strand_assembly/WriteToDBFromSandwichFeatures.hh>

Namespaces

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

Functions

static basic::Tracer protocols::features::strand_assembly::TR ("protocols.features.strand_assembly.WriteToDBFromSandwichFeatures")
 
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_)
 
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)
 
Size protocols::features::strand_assembly::delete_this_struct_id (StructureID struct_id, sessionOP db_session)
 
utility::vector1
< SandwichFragment > 
protocols::features::strand_assembly::prepare_WriteToDB_sandwich (StructureID struct_id, sessionOP db_session)
 
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)
 
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_)
 
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)
 
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)
 
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)
 
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)
 
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)
 
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_)
 
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)
 
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)
 
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_)
 
Size protocols::features::strand_assembly::WriteToDB_number_of_core_heading_LWY_in_core_strands_in_sw (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id)
 
void protocols::features::strand_assembly::WriteToDB_number_of_core_heading_FWY_in_sw (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id)
 
void protocols::features::strand_assembly::WriteToDB_number_of_core_heading_W_in_sw (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id)
 
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)
 
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)
 
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)
 
Size protocols::features::strand_assembly::WriteToDB_number_strands_in_each_sw (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id)
 
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_)
 
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)
 
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)
 
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)
 
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)
 
Size protocols::features::strand_assembly::WriteToDB_sheet_antiparallel (StructureID struct_id, sessionOP db_session, core::Size sheet_id, string const &antiparallel)
 
Size protocols::features::strand_assembly::WriteToDB_sheet_id (StructureID struct_id, sessionOP db_session, core::Size new_sheet_id, core::Size old_sheet_id)
 
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)
 
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_)
 
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_)
 
Size protocols::features::strand_assembly::WriteToDB_sw_res_size (StructureID struct_id, sessionOP db_session, core::Size sw_can_by_sh_id)
 
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)
 
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)
 
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)
 
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)
 
Size protocols::features::strand_assembly::WriteToDB_topology_candidate (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
 
void protocols::features::strand_assembly::WriteToDB_turn_AA (Pose const &pose, core::Size sw_can_by_sh_id, core::Size i, StructureID struct_id, sessionOP db_session, string const &turn_type)
 
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_)
 
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)
 

Detailed Description

Write to a DB after SandwichFeatures.

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