protocols::features::strand_assembly::SandwichFeatures Class Reference

#include <SandwichFeatures.hh>

Public Member Functions
	SandwichFeatures ()
	~SandwichFeatures ()
virtual std::string	type_name () const
virtual void	write_schema_to_db (utility::sql_database::sessionOP db_session) const
	generate the table schemas and write them to the database More...
void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
utility::vector1< std::string >	features_reporter_dependencies () const
	return the set of features reporters that are required to also already be extracted by the time this one is used. More...
virtual core::Size	report_features (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session)
	collect all the feature data for the pose More...
utility::vector1 < SandwichFragment >	get_full_strands (StructureID struct_id, utility::sql_database::sessionOP db_session)
	Select all strand segments reported by the ResidueSecondaryStructureFeatures and save them in a vector. More...
bool	check_whether_strand_i_is_in_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size segment_id)
utility::vector1 < SandwichFragment >	get_current_strands_in_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session)
utility::vector1 < SandwichFragment >	get_all_strands_in_sheet_i (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id)
utility::vector1< Size >	get_list_of_residues_in_sheet_i (utility::vector1< SandwichFragment > all_strands_in_sheet_i)
core::Size	get_max_sheet_id (StructureID struct_id, utility::sql_database::sessionOP db_session)
utility::vector1< core::Size >	get_chain_B_resNum (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
core::Size	get_num_of_sheets_that_surround_this_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id)
std::string	get_tag (StructureID struct_id, utility::sql_database::sessionOP db_session)
core::Size	get_num_strands_in_this_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id)
utility::vector1 < SandwichFragment >	get_full_strands_from_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id)
	Select all strand segments reported by the ResidueSecondaryStructureFeatures and save them in a vector. More...
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_sw_by_components_table (StructureID struct_id, utility::sql_database::sessionOP db_session)
core::Size	find_sheet (core::pose::Pose const &pose, SandwichFragment strand_i, SandwichFragment strand_j, bool antiparalell)
std::vector< core::Real >	cal_dis_angle_to_find_sheet (core::pose::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)
bool	see_whether_sheets_can_be_combined (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::Size i_sheet, core::Size j_sheet)
core::Size	update_sheet_id (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size new_sheet_id, core::Size old_sheet_id)
void	update_num_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)
void	update_sheet_antiparallel (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id, std::string antiparallel)
std::string	get_sheet_antiparallel_info (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id)
bool	change_sheet_id_if_possible (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose)
core::Real	check_sw_by_dis (core::pose::Pose const &pose, SandwichFragment strand_i, SandwichFragment strand_j, bool antiparalell)
std::string	see_whether_sheet_is_antiparallel (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::Size i_sheet)
bool	check_strand_too_closeness (core::pose::Pose const &pose, SandwichFragment strand_i, SandwichFragment strand_j)
core::Real	get_avg_dis_strands (core::pose::Pose const &pose, SandwichFragment strand_i, SandwichFragment strand_j)
core::Real	get_closest_distance_between_strands (core::pose::Pose const &pose, SandwichFragment strand_i, SandwichFragment strand_j)
core::Real	get_avg_dis_CA_CA (core::pose::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)
core::Size	round_to_Size (core::Real x)
float	round_to_float (float x)
core::Real	round_to_Real (core::Real x)
core::Real	calculate_dihedral_w_4_resnums (core::pose::Pose const &pose, core::Size res1_sheet_i, core::Size res2_sheet_i, core::Size res1_sheet_j, core::Size res2_sheet_j)
std::string	is_this_strand_at_edge (core::pose::Pose const &pose, StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id, core::Size residue_begin, 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)
bool	check_whether_this_sheet_is_too_short (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_i)
std::pair< int, int >	get_central_residues_in_each_of_two_edge_strands (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::Size sheet_i)
core::Real	get_shortest_among_4_vals (core::Real arr_dis_inter_sheet[])
int	judge_facing (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::Size sheet_i, core::Size sheet_j)
core::Size	write_to_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_PK_id_counter, core::Size sheet_id, core::Size segment_id)
core::Size	write_to_sw_can_by_sh (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_PK_id_counter, std::string tag, core::Size sw_can_by_sh_id_counter, core::Size sheet_id, core::Size num_strands_from_sheet)
void	report_number_of_electrostatic_interactions_of_residues (std::string tag, StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, std::string dssp_code, std::string heading_direction)
utility::vector1 < SandwichFragment >	prepare_to_fill_sw_by_components (StructureID struct_id, utility::sql_database::sessionOP db_session)
std::string	report_heading_directions_of_all_AA_in_a_strand (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::Size sw_can_by_sh_id, core::Size sheet_id, core::Size residue_begin, core::Size residue_end)
std::vector< Size >	get_cen_res_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< Size >	get_cen_residues_in_this_sheet (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sheet_id)
std::vector< core::Size >	count_AA (core::pose::Pose const &pose, core::Size residue_begin, core::Size residue_end)
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::string	see_edge_or_core (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size residue_num)
std::string	determine_core_heading_surface_heading_by_distance (core::pose::Pose const &pose_w_center_000, core::Size residue_num)
core::Size	fill_sw_by_components (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::Size sw_by_components_PK_id_counter, std::string tag, core::Size sw_can_by_sh_id, core::Size sheet_id, std::string sheet_antiparellel, core::Size sw_by_components_bs_id, std::string strand_is_at_edge, core::Size component_size, core::Size residue_begin, core::Size residue_end)
core::Size	update_sw_by_components_by_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)
utility::vector1< Size >	get_vec_sw_can_by_sh_id (StructureID struct_id, utility::sql_database::sessionOP db_session)
utility::vector1< Size >	get_vec_distinct_sheet_id (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
core::Size	get_size_sw_by_components_PK_id (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_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::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	update_sheet_connectivity (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::Size sw_by_components_PK_id_counter, std::string tag, core::Size sw_can_by_sh_id, std::string loop_kind, core::Size intra_sheet_con_id, core::Size inter_sheet_con_id, std::string LR, std::string cano_LR, std::string PA_by_preceding_E, std::string PA_by_following_E, std::string cano_PA, std::string heading_direction, std::string heading_parallel, std::string cano_parallel_EE, core::Size loop_size, core::Size start_res, core::Size end_res)
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)
core::Size	get_segment_id (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size all_strands_index)
core::Size	get_num_of_distinct_sheet_id (StructureID struct_id, utility::sql_database::sessionOP db_session)
core::Real	absolute_vec (numeric::xyzVector< core::Real > vector)
std::string	check_LR (core::pose::Pose &dssp_pose, core::Size preceding_E, core::Size following_E)
std::pair< std::string, std::string >	check_PA (core::pose::Pose &dssp_pose, core::Size residue_begin, core::Size residue_end)
std::string	check_heading_direction (core::pose::Pose &dssp_pose, core::Size preceding_E, core::Size following_E, std::string check_heading_direction_by_)
bool	check_helix_existence (core::pose::Pose const &pose)
std::string	check_canonicalness_of_LR (core::Size loop_size, bool intra_sheet, std::string LR)
std::string	check_canonicalness_of_PA (core::Size loop_size, bool intra_sheet, std::string PA_by_preceding_E, std::string PA_by_following_E, core::Real check_canonicalness_cutoff_)
std::string	check_canonicalness_of_parallel_EE (core::Size loop_size, bool intra_sheet, std::string parallel_EE)
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_hairpin_connects_short_strand (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size start_res, core::Size next_start_res)
void	add_AA_to_terminal_loops (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose &dssp_pose, core::Size sw_by_components_PK_id_counter, core::Size sw_can_by_sh_id, std::string tag, bool starting_loop, core::Size residue_begin, core::Size residue_end)
core::Size	add_starting_loop (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose &dssp_pose, core::Size sw_by_components_PK_id_counter, core::Size sw_can_by_sh_id, std::string tag)
core::Size	add_ending_loop (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose &dssp_pose, core::Size sw_by_components_PK_id_counter, core::Size sw_can_by_sh_id, std::string tag)
core::Size	add_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)
void	add_number_of_inward_pointing_W_in_sw (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
void	add_number_of_inward_pointing_LWY_in_core_strands_in_sw (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
core::Size	add_sw_res_size (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
core::Size	mark_sw_which_is_not_connected_with_continuous_atoms (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id, std::string sw_is_not_connected_with_continuous_atoms)
core::Size	add_num_strands_in_each_sw (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
core::Size	add_num_edge_strands_in_each_sw (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
core::Size	report_hydrophobic_ratio_net_charge (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
core::Size	report_dihedral_angle_between_core_strands_across_facing_sheets (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::Size sw_can_by_sh_id)
core::Size	report_avg_b_factor_CB_at_each_component (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::Pose const &pose, core::Size sw_can_by_sh_id)
core::Size	report_topology_candidate (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
bool	check_whether_this_pdb_should_be_excluded (std::string tag)
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::Real	cal_min_dis_between_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)
std::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, core::pose::Pose const &pose, core::Size sw_can_by_sh_id, core::Size sheet_id, core::Size residue_begin, core::Size residue_end)
core::Size	report_number_of_inward_pointing_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)
core::Size	report_number_of_inward_pointing_aro_AAs_in_a_pair_of_edge_strands (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id, core::Size current_bs_id, core::Size closest_bs_id)
core::Size	identify_sheet_id_by_residue_end (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size residue_end)
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)
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 dssp_code, std::string heading_direction)
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)
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)
utility::vector1< core::Size >	get_vector_AA_distribution_w_direction (StructureID struct_id, utility::sql_database::sessionOP db_session, std::string heading_direction, std::string strand_location)
utility::vector1< core::Size >	get_vector_AA_distribution_wo_direction (StructureID struct_id, utility::sql_database::sessionOP db_session, std::string loop_kind)
utility::vector1< core::Size >	get_vec_AA_kind (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size sw_can_by_sh_id)
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	report_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)
void	report_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 turn_type)
void	process_decoy (core::pose::Pose &dssp_pose, core::scoring::ScoreFunction const &) const
std::string	determine_heading_direction_by_vector (StructureID struct_id, utility::sql_database::sessionOP db_session, core::pose::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)
void	update_rkde_in_strands (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size RKDE_in_strands_PK_id_counter, std::string tag, core::Size sw_can_by_sh_id, core::Size residue_number, std::string residue_type, std::string heading_direction)
void	update_rkde (StructureID struct_id, utility::sql_database::sessionOP db_session, core::Size RKDE_PK_id_counter, std::string tag, core::Size residue_number, std::string residue_type)
Public Member Functions inherited from protocols::features::FeaturesReporter
	FeaturesReporter ()
virtual	~FeaturesReporter ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...
virtual std::string	schema () const
	return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator More...
core::Size	report_features (core::pose::Pose const &, StructureID, utility::sql_database::sessionOP)
	collect all the feature data for the pose. More...
virtual void	load_into_pose (utility::sql_database::sessionOP, StructureID, core::pose::Pose &)
virtual void	delete_record (StructureID, utility::sql_database::sessionOP)
void	set_relevant_residues_mode (RelevantResiduesMode::T setting)
RelevantResiduesMode::T	get_relevant_residues_mode () const
bool	check_relevant_residues (utility::vector1< bool > const &relevant_residues, core::Size res1) const
bool	check_relevant_residues (utility::vector1< bool > const &relevant_residues, core::Size res1, core::Size res2) const
bool	check_relevant_residues_range (utility::vector1< bool > const &relevant_residues, core::Size res1, core::Size res2) const
bool	check_relevant_residues (utility::vector1< bool > const &relevant_residues, utility::vector1< core::Size > const &residues) const

Private Member Functions
core::scoring::ScoreFunctionOP	generate_scorefxn (bool fullatom=false)
	create score-functions for centroid and fullatom level More...

Private Attributes
core::Size	min_num_strands_to_deal_
core::Size	max_num_strands_to_deal_
core::Size	min_res_in_strand_
core::Real	min_CA_CA_dis_
core::Real	max_CA_CA_dis_
core::Real	min_O_N_dis_
core::Real	max_O_N_dis_
core::Real	min_C_O_N_angle_
core::Real	min_sheet_dis_
core::Real	max_sheet_dis_
core::Real	max_sheet_angle_with_cen_res_in_smaller_sheet_and_two_terminal_res_in_larger_sheet_
core::Real	min_sheet_angle_by_four_term_cen_res_
core::Real	max_sheet_angle_by_four_term_cen_res_
core::Real	min_sheet_torsion_cen_res_
core::Real	max_sheet_torsion_cen_res_
core::Size	min_num_strands_in_sheet_
core::Real	min_inter_sheet_dis_CA_CA_
core::Real	max_inter_sheet_dis_CA_CA_
bool	extract_sandwich_
bool	write_chain_B_resnum_
bool	no_helix_in_pdb_
core::Size	max_H_in_extracted_sw_loop_
core::Size	max_E_in_extracted_sw_loop_
bool	exclude_sandwich_that_is_linked_w_same_direction_strand_
core::Real	max_inter_strand_angle_to_not_be_same_direction_strands_
core::Real	max_abs_inter_strand_dihedral_to_not_be_same_direction_strands_
bool	write_phi_psi_of_all_
bool	write_phi_psi_of_E_
bool	write_resfile_
bool	write_p_aa_pp_files_
bool	write_rama_at_AA_to_files_
bool	write_heading_directions_of_all_AA_in_a_strand_
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_
bool	write_beta_sheet_capping_info_
core::Size	max_starting_loop_size_
core::Size	max_ending_loop_size_
core::Size	max_num_sw_per_pdb_
std::string	check_N_to_C_direction_by_
bool	do_not_connect_sheets_by_loops_
core::Real	check_canonicalness_cutoff_
bool	count_AA_with_direction_
core::Real	inter_sheet_distance_to_see_whether_a_sheet_is_surrounded_by_other_sheets_
bool	exclude_desinated_pdbs_
bool	exclude_sandwich_that_has_near_backbone_atoms_between_sheets_
core::Real	min_N_O_dis_between_two_sheets_
core::Real	min_N_H_O_angle_between_two_sheets_
core::Real	allowed_deviation_for_turn_type_id_
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::Real	distance_cutoff_for_electrostatic_interactions_
core::Real	CB_b_factor_cutoff_for_electrostatic_interactions_
core::Size	primary_seq_distance_cutoff_for_electrostatic_interactions_
bool	write_all_info_files_
bool	write_AA_kind_files_
bool	write_AA_distribution_files_w_direction_
bool	write_AA_distribution_files_wo_direction_

Additional Inherited Members
Protected Member Functions inherited from protocols::features::FeaturesReporter
std::string	find_tag (core::pose::Pose const &pose) const
void	delete_records_from_table (std::string const &table_name, StructureID struct_id, utility::sql_database::sessionOP db_session)
	a helper function for deleting data associated with a given structure from feature database WARNING table_name must be sanitized! More...
Protected Attributes inherited from protocols::features::FeaturesReporter
RelevantResiduesMode::T	relevant_residues_mode_

Constructor & Destructor Documentation

protocols::features::strand_assembly::SandwichFeatures::SandwichFeatures

(

)

protocols::features::strand_assembly::SandwichFeatures::~SandwichFeatures

(

)

Member Function Documentation

Real protocols::features::strand_assembly::SandwichFeatures::absolute_vec

(

numeric::xyzVector< core::Real >

vector

)

void protocols::features::strand_assembly::SandwichFeatures::add_AA_to_terminal_loops	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::pose::Pose &	dssp_pose,
		core::Size	sw_by_components_PK_id_counter,
		core::Size	sw_can_by_sh_id,
		std::string	tag,
		bool	starting_loop,
		core::Size	residue_begin,
		core::Size	residue_end
	)

References protocols::simple_moves::insert, basic::database::safely_prepare_statement(), and basic::database::safely_write_to_database().

Size protocols::features::strand_assembly::SandwichFeatures::add_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
	)

References basic::database::safely_prepare_statement(), basic::database::safely_write_to_database(), core::pose::Pose::secstruct(), and core::pose::Pose::total_residue().

Size protocols::features::strand_assembly::SandwichFeatures::add_ending_loop	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::pose::Pose &	dssp_pose,
		core::Size	sw_by_components_PK_id_counter,
		core::Size	sw_can_by_sh_id,
		std::string	tag
	)

References core::conformation::Residue::atom(), numeric::xyzVector< class >::distance(), core::pose::Pose::residue(), basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), core::pose::Pose::secstruct(), core::pose::Pose::total_residue(), and core::conformation::Atom::xyz().

Size protocols::features::strand_assembly::SandwichFeatures::add_num_edge_strands_in_each_sw	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	sw_can_by_sh_id
	)

References basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), and basic::database::safely_write_to_database().

Size protocols::features::strand_assembly::SandwichFeatures::add_num_strands_in_each_sw	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	sw_can_by_sh_id
	)

References basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), and basic::database::safely_write_to_database().

void protocols::features::strand_assembly::SandwichFeatures::add_number_of_inward_pointing_LWY_in_core_strands_in_sw	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	sw_can_by_sh_id
	)

References basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), and basic::database::safely_write_to_database().

void protocols::features::strand_assembly::SandwichFeatures::add_number_of_inward_pointing_W_in_sw	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	sw_can_by_sh_id
	)

References basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), and basic::database::safely_write_to_database().

Size protocols::features::strand_assembly::SandwichFeatures::add_starting_loop	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::pose::Pose &	dssp_pose,
		core::Size	sw_by_components_PK_id_counter,
		core::Size	sw_can_by_sh_id,
		std::string	tag
	)

References core::conformation::Residue::atom(), numeric::xyzVector< class >::distance(), core::pose::Pose::residue(), basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), core::pose::Pose::secstruct(), and core::conformation::Atom::xyz().

Size protocols::features::strand_assembly::SandwichFeatures::add_sw_res_size	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	sw_can_by_sh_id
	)

References basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), and basic::database::safely_write_to_database().

vector< Real > protocols::features::strand_assembly::SandwichFeatures::cal_dis_angle_to_find_sheet	(	core::pose::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 numeric::angle_degrees(), core::conformation::Residue::atom(), numeric::xyzVector< class >::distance(), core::pose::Pose::residue(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

Real protocols::features::strand_assembly::SandwichFeatures::cal_min_dis_between_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
	)

References core::conformation::Residue::atom(), numeric::xyzVector< class >::distance(), distance(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Size protocols::features::strand_assembly::SandwichFeatures::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
	)

References protocols::features::TR.

Real protocols::features::strand_assembly::SandwichFeatures::calculate_dihedral_w_4_resnums	(	core::pose::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(), numeric::dihedral_degrees(), numeric::xyzVector< class >::distance(), core::pose::Pose::residue(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

bool protocols::features::strand_assembly::SandwichFeatures::change_sheet_id_if_possible	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::pose::Pose const &	pose
	)

References j.

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

string protocols::features::strand_assembly::SandwichFeatures::check_canonicalness_of_PA	(	core::Size	loop_size,
		bool	intra_sheet,
		std::string	PA_by_preceding_E,
		std::string	PA_by_following_E,
		core::Real	check_canonicalness_cutoff_
	)

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

string protocols::features::strand_assembly::SandwichFeatures::check_heading_direction	(	core::pose::Pose &	dssp_pose,
		core::Size	preceding_E,
		core::Size	following_E,
		std::string	check_heading_direction_by_
	)

References dot_product(), core::chemical::ResidueType::name3(), core::pose::Pose::residue_type(), protocols::features::TR, and core::pose::Pose::xyz().

bool protocols::features::strand_assembly::SandwichFeatures::check_helix_existence

(

core::pose::Pose const &

pose

)

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

string protocols::features::strand_assembly::SandwichFeatures::check_LR	(	core::pose::Pose &	dssp_pose,
		core::Size	preceding_E,
		core::Size	following_E
	)

References cross_product(), dot_product(), core::chemical::ResidueType::name3(), core::pose::Pose::residue_type(), and core::pose::Pose::xyz().

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

References dot_product(), core::chemical::ResidueType::name3(), core::pose::Pose::residue_type(), and core::pose::Pose::xyz().

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

References core::conformation::Residue::atom(), numeric::xyzVector< class >::distance(), protocols::features::strand_assembly::SandwichFragment::get_size(), protocols::features::strand_assembly::SandwichFragment::get_start(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Real protocols::features::strand_assembly::SandwichFeatures::check_sw_by_dis	(	core::pose::Pose const &	pose,
		SandwichFragment	strand_i,
		SandwichFragment	strand_j,
		bool	antiparalell
	)

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

bool protocols::features::strand_assembly::SandwichFeatures::check_whether_hairpin_connects_short_strand	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	start_res,
		core::Size	next_start_res
	)

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

bool protocols::features::strand_assembly::SandwichFeatures::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
	)

References dot_product(), basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), and core::pose::Pose::xyz().

bool protocols::features::strand_assembly::SandwichFeatures::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
	)

References numeric::angle_degrees(), core::conformation::Residue::atom(), numeric::xyzVector< class >::distance(), j, core::chemical::ResidueType::name3(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

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

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

bool protocols::features::strand_assembly::SandwichFeatures::check_whether_sw_by_sh_id_still_alive	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	sw_can_by_sh_id
	)

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

string protocols::features::strand_assembly::SandwichFeatures::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
	)

References core::conformation::Residue::atom(), distance(), numeric::xyzVector< class >::distance(), core::pose::Pose::residue(), basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), and core::conformation::Atom::xyz().

bool protocols::features::strand_assembly::SandwichFeatures::check_whether_this_pdb_should_be_excluded

(

std::string

tag

)

bool protocols::features::strand_assembly::SandwichFeatures::check_whether_this_sheet_is_too_short	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	sheet_i
	)

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

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

vector< Size > protocols::features::strand_assembly::SandwichFeatures::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
	)

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

Size protocols::features::strand_assembly::SandwichFeatures::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
	)

References basic::database::safely_prepare_statement(), basic::database::safely_write_to_database(), and protocols::features::TR.

string protocols::features::strand_assembly::SandwichFeatures::determine_core_heading_surface_heading_by_distance	(	core::pose::Pose const &	pose_w_center_000,
		core::Size	residue_num
	)

References core::conformation::Residue::atom(), numeric::xyzVector< class >::distance(), core::chemical::ResidueType::name3(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::conformation::Atom::xyz().

string protocols::features::strand_assembly::SandwichFeatures::determine_heading_direction_by_vector	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::pose::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 core::conformation::Residue::atom(), numeric::xyzVector< class >::distance(), distance(), dot_product(), core::chemical::ResidueType::name3(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::conformation::Atom::xyz(), and core::pose::Pose::xyz().

utility::vector1< std::string > protocols::features::strand_assembly::SandwichFeatures::features_reporter_dependencies ( ) const

virtual

return the set of features reporters that are required to also already be extracted by the time this one is used.

Reimplemented from protocols::features::FeaturesReporter.

Size protocols::features::strand_assembly::SandwichFeatures::fill_sw_by_components	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::pose::Pose const &	pose,
		core::Size	sw_by_components_PK_id_counter,
		std::string	tag,
		core::Size	sw_can_by_sh_id,
		core::Size	sheet_id,
		std::string	sheet_antiparellel,
		core::Size	sw_by_components_bs_id,
		std::string	strand_is_at_edge,
		core::Size	component_size,
		core::Size	residue_begin,
		core::Size	residue_end
	)

References protocols::simple_moves::insert, basic::database::safely_prepare_statement(), and basic::database::safely_write_to_database().

Size protocols::features::strand_assembly::SandwichFeatures::find_sheet	(	core::pose::Pose const &	pose,
		SandwichFragment	strand_i,
		SandwichFragment	strand_j,
		bool	antiparalell
	)

References core::conformation::Residue::atom(), numeric::xyzVector< class >::distance(), 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(), and core::conformation::Atom::xyz().

core::scoring::ScoreFunctionOP protocols::features::strand_assembly::SandwichFeatures::generate_scorefxn ( bool  fullatom = false )

private

create score-functions for centroid and fullatom level

References core::scoring::ScoreFunctionFactory::create_score_function(), and core::scoring::getScoreFunction().

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

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

Real protocols::features::strand_assembly::SandwichFeatures::get_avg_dis_CA_CA	(	core::pose::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
	)

References core::conformation::Residue::atom(), numeric::xyzVector< class >::distance(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

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

References core::conformation::Residue::atom(), numeric::xyzVector< class >::distance(), protocols::features::strand_assembly::SandwichFragment::get_size(), protocols::features::strand_assembly::SandwichFragment::get_start(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

vector< Size > protocols::features::strand_assembly::SandwichFeatures::get_cen_res_in_other_sheet	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	sw_can_by_sh_id,
		core::Size	sheet_id
	)

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

vector< Size > protocols::features::strand_assembly::SandwichFeatures::get_cen_residues_in_this_sheet	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	sheet_id
	)

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

std::pair< int, int > protocols::features::strand_assembly::SandwichFeatures::get_central_residues_in_each_of_two_edge_strands	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::pose::Pose const &	pose,
		core::Size	sheet_i
	)

References core::conformation::Residue::atom(), numeric::xyzVector< class >::distance(), j, core::pose::Pose::residue(), and core::conformation::Atom::xyz().

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

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

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

References core::conformation::Residue::atom(), numeric::xyzVector< class >::distance(), protocols::features::strand_assembly::SandwichFragment::get_size(), protocols::features::strand_assembly::SandwichFragment::get_start(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

std::pair< Size, Size > protocols::features::strand_assembly::SandwichFeatures::get_current_bs_id_and_closest_edge_bs_id_in_different_sheet	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::pose::Pose const &	pose,
		core::Size	sw_can_by_sh_id,
		core::Size	sheet_id,
		core::Size	residue_begin,
		core::Size	residue_end
	)

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

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

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

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

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

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

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

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

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

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

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

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

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

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

(

utility::vector1< SandwichFragment >

all_strands_in_sheet_i

)

References j.

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

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

std::pair< Size, Size > protocols::features::strand_assembly::SandwichFeatures::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
	)

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

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

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

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

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

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

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

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

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

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

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

Real protocols::features::strand_assembly::SandwichFeatures::get_shortest_among_4_vals

(

core::Real

arr_dis_inter_sheet[]

)

Size protocols::features::strand_assembly::SandwichFeatures::get_size_sw_by_components_PK_id	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	sw_can_by_sh_id
	)

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

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

std::pair< Size, Size > protocols::features::strand_assembly::SandwichFeatures::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
	)

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

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

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

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

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

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

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

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

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

utility::vector1< Size > protocols::features::strand_assembly::SandwichFeatures::get_vector_AA_distribution_w_direction	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		std::string	heading_direction,
		std::string	strand_location
	)

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

utility::vector1< Size > protocols::features::strand_assembly::SandwichFeatures::get_vector_AA_distribution_wo_direction	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		std::string	loop_kind
	)

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

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

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

string protocols::features::strand_assembly::SandwichFeatures::is_this_strand_at_edge	(	core::pose::Pose const &	pose,
		StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	sheet_id,
		core::Size	residue_begin,
		core::Size	residue_end
	)

References core::conformation::Residue::atom(), numeric::xyzVector< class >::distance(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

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

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

int protocols::features::strand_assembly::SandwichFeatures::judge_facing	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::pose::Pose const &	pose,
		core::Size	sheet_i,
		core::Size	sheet_j
	)

References numeric::angle_degrees(), core::conformation::Residue::atom(), numeric::dihedral_degrees(), numeric::xyzVector< class >::distance(), core::pose::Pose::residue(), core::conformation::Atom::xyz(), core::conformation::Residue::xyz(), and protocols::kinmatch::xyz().

Size protocols::features::strand_assembly::SandwichFeatures::mark_sw_which_is_not_connected_with_continuous_atoms	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	sw_can_by_sh_id,
		std::string	sw_is_not_connected_with_continuous_atoms
	)

References basic::database::safely_prepare_statement(), and basic::database::safely_write_to_database().

void protocols::features::strand_assembly::SandwichFeatures::parse_my_tag ( utility::tag::TagCOP  tag, basic::datacache::DataMap &  , protocols::filters::Filters_map const &  , protocols::moves::Movers_map const &  , core::pose::Pose const &    )

virtual

Reimplemented from protocols::features::FeaturesReporter.

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

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

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

Size protocols::features::strand_assembly::SandwichFeatures::report_avg_b_factor_CB_at_each_component	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::pose::Pose const &	pose,
		core::Size	sw_can_by_sh_id
	)

References protocols::simple_moves::insert, core::pose::Pose::pdb_info(), protocols::noesy_assign::round(), basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), and basic::database::safely_write_to_database().

Size protocols::features::strand_assembly::SandwichFeatures::report_dihedral_angle_between_core_strands_across_facing_sheets	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::pose::Pose const &	pose,
		core::Size	sw_can_by_sh_id
	)

References dihedral(), protocols::simple_moves::insert, j, basic::database::safely_prepare_statement(), and basic::database::safely_write_to_database().

core::Size protocols::features::strand_assembly::SandwichFeatures::report_features ( core::pose::Pose const &  pose, utility::vector1< bool > const &  relevant_residues, StructureID  struct_id, utility::sql_database::sessionOP  db_session  )

virtual

collect all the feature data for the pose

Implements protocols::features::FeaturesReporter.

References core::pose::Pose::center(), dssp, core::pose::Pose::energies(), core::scoring::dssp::Dssp::insert_ss_into_pose(), core::pose::Pose::is_fullatom(), j, core::chemical::ResidueType::name3(), core::scoring::p_aa_pp, core::pose::Pose::phi(), protocols::stepwise::sampling::protein::phi(), core::pose::Pose::psi(), protocols::stepwise::sampling::protein::psi(), core::scoring::rama, core::scoring::Energies::residue_total_energies(), core::pose::Pose::residue_type(), core::pose::Pose::secstruct(), core::scoring::Energies::show_total_headers(), sum(), tag, core::pose::Pose::total_residue(), and protocols::features::TR.

string protocols::features::strand_assembly::SandwichFeatures::report_heading_directions_of_all_AA_in_a_strand	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::pose::Pose const &	pose,
		core::Size	sw_can_by_sh_id,
		core::Size	sheet_id,
		core::Size	residue_begin,
		core::Size	residue_end
	)

Size protocols::features::strand_assembly::SandwichFeatures::report_hydrophobic_ratio_net_charge	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	sw_can_by_sh_id
	)

References protocols::simple_moves::insert, basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), and basic::database::safely_write_to_database().

void protocols::features::strand_assembly::SandwichFeatures::report_number_of_electrostatic_interactions_of_residues	(	std::string	tag,
		StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::pose::Pose const &	pose,
		std::string	dssp_code,
		std::string	heading_direction
	)

References core::conformation::Residue::atom(), cutoff, numeric::xyzVector< class >::distance(), core::chemical::ResidueType::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::features::TR, numeric::xyzVector< class >::x(), core::conformation::Atom::xyz(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Size protocols::features::strand_assembly::SandwichFeatures::report_number_of_inward_pointing_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
	)

References protocols::simple_moves::insert, basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), and basic::database::safely_write_to_database().

Size protocols::features::strand_assembly::SandwichFeatures::report_number_of_inward_pointing_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
	)

References protocols::simple_moves::insert, basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), and basic::database::safely_write_to_database().

Size protocols::features::strand_assembly::SandwichFeatures::report_topology_candidate	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	sw_can_by_sh_id
	)

References protocols::simple_moves::insert, basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), and basic::database::safely_write_to_database().

void protocols::features::strand_assembly::SandwichFeatures::report_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	turn_type
	)

References core::chemical::ResidueType::name3(), core::pose::Pose::residue_type(), basic::database::safely_prepare_statement(), basic::database::safely_write_to_database(), and protocols::features::TR.

string protocols::features::strand_assembly::SandwichFeatures::report_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
	)

References core::pose::Pose::phi(), core::pose::Pose::psi(), basic::database::safely_prepare_statement(), and basic::database::safely_write_to_database().

utility::vector1< int > protocols::features::strand_assembly::SandwichFeatures::retrieve_residue_num_of_rkde	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	sw_can_by_sh_id,
		std::string	dssp_code,
		std::string	heading_direction
	)

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

float protocols::features::strand_assembly::SandwichFeatures::round_to_float

(

float

x

)

Real protocols::features::strand_assembly::SandwichFeatures::round_to_Real

(

core::Real

x

)

Size protocols::features::strand_assembly::SandwichFeatures::round_to_Size

(

core::Real

x

)

string protocols::features::strand_assembly::SandwichFeatures::see_edge_or_core	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	residue_num
	)

References basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

string protocols::features::strand_assembly::SandwichFeatures::see_whether_sheet_is_antiparallel	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::pose::Pose const &	pose,
		core::Size	i_sheet
	)

References core::conformation::Residue::atom(), numeric::xyzVector< class >::distance(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

bool protocols::features::strand_assembly::SandwichFeatures::see_whether_sheets_can_be_combined	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::pose::Pose const &	pose,
		core::Size	i_sheet,
		core::Size	j_sheet
	)

References j.

virtual std::string protocols::features::strand_assembly::SandwichFeatures::type_name ( ) const

inlinevirtual

Reimplemented from protocols::features::FeaturesReporter.

void protocols::features::strand_assembly::SandwichFeatures::update_num_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
	)

References basic::database::safely_prepare_statement(), and basic::database::safely_write_to_database().

void protocols::features::strand_assembly::SandwichFeatures::update_rkde	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	RKDE_PK_id_counter,
		std::string	tag,
		core::Size	residue_number,
		std::string	residue_type
	)

References protocols::simple_moves::insert, basic::database::safely_prepare_statement(), and basic::database::safely_write_to_database().

void protocols::features::strand_assembly::SandwichFeatures::update_rkde_in_strands	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	RKDE_in_strands_PK_id_counter,
		std::string	tag,
		core::Size	sw_can_by_sh_id,
		core::Size	residue_number,
		std::string	residue_type,
		std::string	heading_direction
	)

References protocols::simple_moves::insert, basic::database::safely_prepare_statement(), and basic::database::safely_write_to_database().

void protocols::features::strand_assembly::SandwichFeatures::update_sheet_antiparallel	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	sheet_id,
		std::string	antiparallel
	)

References basic::database::safely_prepare_statement(), and basic::database::safely_write_to_database().

Size protocols::features::strand_assembly::SandwichFeatures::update_sheet_connectivity	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::pose::Pose const &	pose,
		core::Size	sw_by_components_PK_id_counter,
		std::string	tag,
		core::Size	sw_can_by_sh_id,
		std::string	loop_kind,
		core::Size	intra_sheet_con_id,
		core::Size	inter_sheet_con_id,
		std::string	LR,
		std::string	cano_LR,
		std::string	PA_by_preceding_E,
		std::string	PA_by_following_E,
		std::string	cano_PA,
		std::string	heading_direction,
		std::string	heading_parallel,
		std::string	cano_parallel_EE,
		core::Size	loop_size,
		core::Size	start_res,
		core::Size	end_res
	)

References protocols::simple_moves::insert, basic::database::safely_prepare_statement(), and basic::database::safely_write_to_database().

Size protocols::features::strand_assembly::SandwichFeatures::update_sheet_id	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	new_sheet_id,
		core::Size	old_sheet_id
	)

References basic::database::safely_prepare_statement(), and basic::database::safely_write_to_database().

Size protocols::features::strand_assembly::SandwichFeatures::update_sw_by_components_by_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
	)

References protocols::simple_moves::insert, basic::database::safely_prepare_statement(), and basic::database::safely_write_to_database().

void protocols::features::strand_assembly::SandwichFeatures::write_schema_to_db ( utility::sql_database::sessionOP  db_session ) const

virtual

generate the table schemas and write them to the database

Implements protocols::features::FeaturesReporter.

References basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_foreign_key(), D, protocols::features::E, protocols::comparative_modeling::features::G, protocols::abinitio::abscript::I, protocols::features::L, protocols::forge::build::SegmentInsertConnectionScheme::N, sheet, tag, and basic::database::schema_generator::Schema::write().

Size protocols::features::strand_assembly::SandwichFeatures::write_to_sheet	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	sheet_PK_id_counter,
		core::Size	sheet_id,
		core::Size	segment_id
	)

References basic::database::safely_prepare_statement(), and basic::database::safely_write_to_database().

Size protocols::features::strand_assembly::SandwichFeatures::write_to_sw_can_by_sh	(	StructureID	struct_id,
		utility::sql_database::sessionOP	db_session,
		core::Size	sw_can_by_sh_PK_id_counter,
		std::string	tag,
		core::Size	sw_can_by_sh_id_counter,
		core::Size	sheet_id,
		core::Size	num_strands_from_sheet
	)

References basic::database::safely_prepare_statement(), and basic::database::safely_write_to_database().

Member Data Documentation

core::Real protocols::features::strand_assembly::SandwichFeatures::allowed_deviation_for_turn_type_id_

private

core::Real protocols::features::strand_assembly::SandwichFeatures::CB_b_factor_cutoff_for_electrostatic_interactions_

private

core::Real protocols::features::strand_assembly::SandwichFeatures::check_canonicalness_cutoff_

private

std::string protocols::features::strand_assembly::SandwichFeatures::check_N_to_C_direction_by_

private

bool protocols::features::strand_assembly::SandwichFeatures::count_AA_with_direction_

private

core::Real protocols::features::strand_assembly::SandwichFeatures::distance_cutoff_for_electrostatic_interactions_

private

bool protocols::features::strand_assembly::SandwichFeatures::do_not_connect_sheets_by_loops_

private

bool protocols::features::strand_assembly::SandwichFeatures::exclude_desinated_pdbs_

private

bool protocols::features::strand_assembly::SandwichFeatures::exclude_sandwich_that_has_near_backbone_atoms_between_sheets_

private

bool protocols::features::strand_assembly::SandwichFeatures::exclude_sandwich_that_is_linked_w_same_direction_strand_

private

bool protocols::features::strand_assembly::SandwichFeatures::extract_sandwich_

private

core::Real protocols::features::strand_assembly::SandwichFeatures::inter_sheet_distance_to_see_whether_a_sheet_is_surrounded_by_other_sheets_

private

core::Real protocols::features::strand_assembly::SandwichFeatures::max_abs_inter_strand_dihedral_to_not_be_same_direction_strands_

private

core::Real protocols::features::strand_assembly::SandwichFeatures::max_CA_CA_dis_

private

core::Size protocols::features::strand_assembly::SandwichFeatures::max_E_in_extracted_sw_loop_

private

core::Size protocols::features::strand_assembly::SandwichFeatures::max_ending_loop_size_

private

core::Size protocols::features::strand_assembly::SandwichFeatures::max_H_in_extracted_sw_loop_

private

core::Real protocols::features::strand_assembly::SandwichFeatures::max_inter_sheet_dis_CA_CA_

private

core::Real protocols::features::strand_assembly::SandwichFeatures::max_inter_strand_angle_to_not_be_same_direction_strands_

private

core::Size protocols::features::strand_assembly::SandwichFeatures::max_num_strands_to_deal_

private

core::Size protocols::features::strand_assembly::SandwichFeatures::max_num_sw_per_pdb_

private

core::Real protocols::features::strand_assembly::SandwichFeatures::max_O_N_dis_

private

core::Real protocols::features::strand_assembly::SandwichFeatures::max_sheet_angle_by_four_term_cen_res_

private

core::Real protocols::features::strand_assembly::SandwichFeatures::max_sheet_angle_with_cen_res_in_smaller_sheet_and_two_terminal_res_in_larger_sheet_

private

core::Real protocols::features::strand_assembly::SandwichFeatures::max_sheet_dis_

private

core::Real protocols::features::strand_assembly::SandwichFeatures::max_sheet_torsion_cen_res_

private

core::Size protocols::features::strand_assembly::SandwichFeatures::max_starting_loop_size_

private

core::Real protocols::features::strand_assembly::SandwichFeatures::min_C_O_N_angle_

private

core::Real protocols::features::strand_assembly::SandwichFeatures::min_CA_CA_dis_

private

core::Real protocols::features::strand_assembly::SandwichFeatures::min_inter_sheet_dis_CA_CA_

private

core::Real protocols::features::strand_assembly::SandwichFeatures::min_N_H_O_angle_between_two_sheets_

private

core::Real protocols::features::strand_assembly::SandwichFeatures::min_N_O_dis_between_two_sheets_

private

core::Size protocols::features::strand_assembly::SandwichFeatures::min_num_strands_in_sheet_

private

core::Size protocols::features::strand_assembly::SandwichFeatures::min_num_strands_to_deal_

private

core::Real protocols::features::strand_assembly::SandwichFeatures::min_O_N_dis_

private

core::Size protocols::features::strand_assembly::SandwichFeatures::min_res_in_strand_

private

core::Real protocols::features::strand_assembly::SandwichFeatures::min_sheet_angle_by_four_term_cen_res_

private

core::Real protocols::features::strand_assembly::SandwichFeatures::min_sheet_dis_

private

core::Real protocols::features::strand_assembly::SandwichFeatures::min_sheet_torsion_cen_res_

private

bool protocols::features::strand_assembly::SandwichFeatures::no_helix_in_pdb_

private

int protocols::features::strand_assembly::SandwichFeatures::primary_seq_distance_cutoff_for_beta_sheet_capping_after_C_term_capping_

private

int protocols::features::strand_assembly::SandwichFeatures::primary_seq_distance_cutoff_for_beta_sheet_capping_after_N_term_capping_

private

int protocols::features::strand_assembly::SandwichFeatures::primary_seq_distance_cutoff_for_beta_sheet_capping_before_C_term_capping_

private

int protocols::features::strand_assembly::SandwichFeatures::primary_seq_distance_cutoff_for_beta_sheet_capping_before_N_term_capping_

private

core::Size protocols::features::strand_assembly::SandwichFeatures::primary_seq_distance_cutoff_for_electrostatic_interactions_

private

bool protocols::features::strand_assembly::SandwichFeatures::write_AA_distribution_files_w_direction_

private

bool protocols::features::strand_assembly::SandwichFeatures::write_AA_distribution_files_wo_direction_

private

bool protocols::features::strand_assembly::SandwichFeatures::write_AA_kind_files_

private

bool protocols::features::strand_assembly::SandwichFeatures::write_all_info_files_

private

bool protocols::features::strand_assembly::SandwichFeatures::write_beta_sheet_capping_info_

private

bool protocols::features::strand_assembly::SandwichFeatures::write_chain_B_resnum_

private

bool protocols::features::strand_assembly::SandwichFeatures::write_electrostatic_interactions_of_all_residues_

private

bool protocols::features::strand_assembly::SandwichFeatures::write_electrostatic_interactions_of_all_residues_in_a_strand_

private

bool protocols::features::strand_assembly::SandwichFeatures::write_electrostatic_interactions_of_surface_residues_in_a_strand_

private

bool protocols::features::strand_assembly::SandwichFeatures::write_heading_directions_of_all_AA_in_a_strand_

private

bool protocols::features::strand_assembly::SandwichFeatures::write_p_aa_pp_files_

private

bool protocols::features::strand_assembly::SandwichFeatures::write_phi_psi_of_all_

private

bool protocols::features::strand_assembly::SandwichFeatures::write_phi_psi_of_E_

private

bool protocols::features::strand_assembly::SandwichFeatures::write_rama_at_AA_to_files_

private

bool protocols::features::strand_assembly::SandwichFeatures::write_resfile_

private

---

The documentation for this class was generated from the following files:

• symlinks/rosetta/src/protocols/features/strand_assembly/SandwichFeatures.hh
• symlinks/rosetta/src/protocols/features/strand_assembly/SandwichFeatures.cc