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

#include <SandwichFeatures.hh>

Inheritance diagram for protocols::features::strand_assembly::SandwichFeatures:
Inheritance graph
[legend]

Public Member Functions

 SandwichFeatures ()
 
 ~SandwichFeatures () override
 
void write_schema_to_db (utility::sql_database::sessionOP db_session) const override
 generate the table schemas and write them to the database More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 
utility::vector1< std::string > features_reporter_dependencies () const override
 return the set of features reporters that are required to also already be extracted by the time this one is used. More...
 
core::Size report_features (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session) override
 collect all the feature data for the pose More...
 
std::string type_name () const override
 
- Public Member Functions inherited from protocols::features::FeaturesReporter
 FeaturesReporter ()
 
 ~FeaturesReporter () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. 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
 

Static Public Member Functions

static std::string class_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 

Private Member Functions

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

Private Attributes

core::Real allowed_deviation_for_turn_type_id_
 
core::Real CB_b_factor_cutoff_for_electrostatic_interactions_
 
bool chance_of_being_canonical_sw
 
std::string check_N_to_C_direction_by_
 
core::Real check_canonicalness_cutoff_
 
bool count_AA_with_direction_
 
core::Real distance_cutoff_for_electrostatic_interactions_
 
bool do_not_connect_sheets_by_loops_
 
bool do_not_write_resfile_of_sandwich_that_has_non_canonical_LR_
 
bool exclude_sandwich_that_is_linked_w_same_direction_strand_
 
bool exclude_sandwich_that_has_non_canonical_LR_
 
bool exclude_sandwich_that_has_non_canonical_properties_
 
bool exclude_sandwich_that_has_non_canonical_shortest_dis_between_facing_aro_in_sw_
 
bool exclude_sandwich_with_SS_bond_
 
bool exclude_desinated_pdbs_
 
bool exclude_sandwich_that_is_suspected_to_have_not_facing_2_sheets_
 
bool exclude_sandwich_that_has_near_backbone_atoms_between_sheets_
 
bool extract_sandwich_
 
core::Real inter_sheet_distance_to_see_whether_a_sheet_is_surrounded_by_other_sheets_
 
core::Real min_CA_CA_dis_
 
core::Real max_CA_CA_dis_
 
core::Size min_num_strands_to_deal_
 
core::Size max_num_strands_to_deal_
 
core::Size min_res_in_strand_
 
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_
 
core::Size max_H_in_extracted_sw_loop_
 
core::Size max_E_in_extracted_sw_loop_
 
core::Real max_abs_inter_strand_dihedral_to_not_be_same_direction_strands_
 
core::Real max_inter_strand_angle_to_not_be_same_direction_strands_
 
core::Size max_starting_loop_size_
 
core::Size max_ending_loop_size_
 
core::Size max_num_sw_per_pdb_
 
core::Real min_N_O_dis_between_two_sheets_
 
core::Real min_N_H_O_angle_between_two_sheets_
 
core::Size min_primary_seq_distance_diff_for_electrostatic_interactions_
 
bool no_helix_in_pdb_
 
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_
 
bool unit_test_pass_identifier
 
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_
 
bool write_all_info_files_
 
bool write_AA_kind_files_
 
bool write_beta_sheet_capping_info_
 
bool write_chain_B_resnum_
 
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_heading_directions_of_all_AA_in_a_strand_
 
bool write_loop_AA_distribution_files_
 
bool write_p_aa_pp_files_
 
bool write_phi_psi_of_all_
 
bool write_phi_psi_of_E_
 
bool write_rama_at_AA_to_files_
 
bool write_resfile_
 
bool write_resfile_NOT_FWY_on_surface_
 
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_
 
bool write_resfile_when_seq_rec_is_bad_
 
bool write_strand_AA_distribution_files_
 

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 ( )
override

Member Function Documentation

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

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.

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::get_score_function().

void protocols::features::strand_assembly::SandwichFeatures::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &   
)
overridevirtual
void protocols::features::strand_assembly::SandwichFeatures::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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 
)
overridevirtual

collect all the feature data for the pose

Implements protocols::features::FeaturesReporter.

References protocols::features::strand_assembly::cal_num_of_sheets_that_surround_this_sheet(), core::pose::Pose::center(), protocols::features::strand_assembly::change_sheet_id_if_possible(), protocols::features::strand_assembly::check_canonicalness_of_LR(), protocols::features::strand_assembly::check_canonicalness_of_PA(), protocols::features::strand_assembly::check_canonicalness_of_parallel_EE(), protocols::features::strand_assembly::check_heading_direction(), protocols::features::strand_assembly::check_helix_existence(), protocols::features::strand_assembly::check_LR(), protocols::features::strand_assembly::check_PA(), protocols::features::strand_assembly::check_strand_too_closeness(), protocols::features::strand_assembly::check_sw_by_dis(), protocols::features::strand_assembly::check_whether_hairpin_connects_short_strand(), protocols::features::strand_assembly::check_whether_same_direction_strands_connect_two_sheets_or_a_loop(), protocols::features::strand_assembly::check_whether_sheets_are_connected_with_near_bb_atoms(), protocols::features::strand_assembly::check_whether_strand_i_is_in_sheet(), protocols::features::strand_assembly::check_whether_sw_is_not_connected_with_continuous_atoms(), protocols::features::strand_assembly::check_whether_this_pdb_should_be_excluded(), protocols::features::strand_assembly::delete_this_struct_id(), protocols::features::strand_assembly::delete_this_sw_can_by_sh_id_from_sw_by_comp(), protocols::simple_filters::dssp(), core::scoring::dssp::Dssp::dssp_reduced(), protocols::features::strand_assembly::find_sheet(), protocols::features::strand_assembly::get_avg_dis_strands(), protocols::features::strand_assembly::get_current_strands_in_sheet(), protocols::features::strand_assembly::get_distinct_sheet_id_from_sheet_table(), protocols::features::strand_assembly::get_full_strands(), protocols::features::strand_assembly::get_full_strands_from_sheet(), protocols::features::strand_assembly::get_max_sheet_id(), protocols::features::strand_assembly::get_next_starting_res_for_connecting_strands(), protocols::features::strand_assembly::get_num_of_sheets_that_surround_this_sheet(), protocols::features::strand_assembly::get_num_strands_in_this_sheet(), protocols::features::strand_assembly::get_segment_id(), protocols::features::strand_assembly::get_size_sandwich_PK_id(), protocols::features::strand_assembly::get_starting_res_for_connecting_strands(), protocols::features::strand_assembly::get_tag(), protocols::features::strand_assembly::get_vec_of_sw_can_by_sh_id(), core::scoring::dssp::Dssp::insert_ss_into_pose(), core::pose::Pose::is_fullatom(), protocols::features::strand_assembly::judge_facing(), protocols::features::strand_assembly::prepare_and_write_number_of_electrostatic_interactions_of_residues_to_files(), protocols::features::strand_assembly::prepare_WriteToDB_sandwich(), protocols::features::strand_assembly::process_decoy(), protocols::features::strand_assembly::Run_WriteToDB_sandwich(), core::pose::Pose::secstruct(), protocols::features::strand_assembly::see_whether_sheet_is_antiparallel(), protocols::features::strand_assembly::see_whether_this_sw_has_SS_bond(), core::pose::Pose::size(), core::simple_metrics::metrics::sum, protocols::features::strand_assembly::TR(), protocols::features::strand_assembly::write_AA_distribution_with_direction_to_a_file(), protocols::features::strand_assembly::write_AA_distribution_without_direction_to_a_file(), protocols::features::strand_assembly::write_AA_kind_to_a_file(), protocols::features::strand_assembly::write_beta_sheet_capping_info_to_a_file(), protocols::features::strand_assembly::write_chain_B_resNum_to_a_file(), protocols::features::strand_assembly::write_heading_direction_of_all_AA_in_a_strand_to_a_file(), protocols::features::strand_assembly::write_p_aa_pp_of_AAs_to_a_file(), protocols::features::strand_assembly::write_phi_psi_of_each_residue_to_a_file(), protocols::features::strand_assembly::write_rama_of_AAs_to_a_file(), protocols::features::strand_assembly::write_resfile_to_a_file(), protocols::features::strand_assembly::write_resfile_to_a_file_when_seq_rec_is_bad(), protocols::features::strand_assembly::WriteToDB_avg_b_factor_CB_at_each_component(), protocols::features::strand_assembly::WriteToDB_dihedral_angle_between_core_strands_across_facing_sheets(), protocols::features::strand_assembly::WriteToDB_dssp_ratio_in_sw(), protocols::features::strand_assembly::WriteToDB_ending_loop(), protocols::features::strand_assembly::WriteToDB_hydrophobic_ratio_net_charge(), protocols::features::strand_assembly::WriteToDB_long_strand_id_in_each_sw(), protocols::features::strand_assembly::WriteToDB_min_avg_dis_between_sheets_by_cen_res(), protocols::features::strand_assembly::WriteToDB_min_dis_between_sheets_by_all_res(), protocols::features::strand_assembly::WriteToDB_number_of_AAs_in_a_pair_of_edge_strands(), protocols::features::strand_assembly::WriteToDB_number_of_core_heading_FWY_in_sw(), protocols::features::strand_assembly::WriteToDB_number_of_core_heading_LWY_in_core_strands_in_sw(), protocols::features::strand_assembly::WriteToDB_number_of_core_heading_W_in_sw(), protocols::features::strand_assembly::WriteToDB_number_of_edge_strands_in_each_sw(), protocols::features::strand_assembly::WriteToDB_number_of_sheets_that_surround_this_sheet(), protocols::features::strand_assembly::WriteToDB_number_strands_in_each_sw(), protocols::features::strand_assembly::WriteToDB_ratio_of_core_heading_FWY_in_sw(), protocols::features::strand_assembly::WriteToDB_sandwich_by_AA_w_direction(), protocols::features::strand_assembly::WriteToDB_sheet(), protocols::features::strand_assembly::WriteToDB_sheet_antiparallel(), protocols::features::strand_assembly::WriteToDB_sheet_connectivity(), protocols::features::strand_assembly::WriteToDB_shortest_dis_between_facing_aro_in_sw(), protocols::features::strand_assembly::WriteToDB_starting_loop(), protocols::features::strand_assembly::WriteToDB_sw_can_by_sh(), protocols::features::strand_assembly::WriteToDB_sw_res_size(), protocols::features::strand_assembly::WriteToDB_topology_candidate(), protocols::features::strand_assembly::WriteToDB_turn_AA(), protocols::features::strand_assembly::WriteToDB_turn_type(), and protocols::features::strand_assembly::WriteToDB_whether_sw_is_not_connected_with_continuous_atoms().

std::string protocols::features::strand_assembly::SandwichFeatures::type_name ( ) const
overridevirtual
void protocols::features::strand_assembly::SandwichFeatures::write_schema_to_db ( utility::sql_database::sessionOP  db_session) const
overridevirtual

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
bool protocols::features::strand_assembly::SandwichFeatures::chance_of_being_canonical_sw
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::do_not_write_resfile_of_sandwich_that_has_non_canonical_LR_
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_has_non_canonical_LR_
private
bool protocols::features::strand_assembly::SandwichFeatures::exclude_sandwich_that_has_non_canonical_properties_
private
bool protocols::features::strand_assembly::SandwichFeatures::exclude_sandwich_that_has_non_canonical_shortest_dis_between_facing_aro_in_sw_
private
bool protocols::features::strand_assembly::SandwichFeatures::exclude_sandwich_that_is_linked_w_same_direction_strand_
private
bool protocols::features::strand_assembly::SandwichFeatures::exclude_sandwich_that_is_suspected_to_have_not_facing_2_sheets_
private
bool protocols::features::strand_assembly::SandwichFeatures::exclude_sandwich_with_SS_bond_
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_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::Size protocols::features::strand_assembly::SandwichFeatures::min_primary_seq_distance_diff_for_electrostatic_interactions_
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
bool protocols::features::strand_assembly::SandwichFeatures::unit_test_pass_identifier
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_loop_AA_distribution_files_
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
bool protocols::features::strand_assembly::SandwichFeatures::write_resfile_NOT_FWY_on_surface_
private
bool protocols::features::strand_assembly::SandwichFeatures::write_resfile_to_minimize_too_many_core_heading_FWY_on_core_strands_
private
bool protocols::features::strand_assembly::SandwichFeatures::write_resfile_to_minimize_too_many_core_heading_FWY_on_edge_strands_
private
bool protocols::features::strand_assembly::SandwichFeatures::write_resfile_to_minimize_too_much_hydrophobic_surface_
private
bool protocols::features::strand_assembly::SandwichFeatures::write_resfile_when_seq_rec_is_bad_
private
bool protocols::features::strand_assembly::SandwichFeatures::write_strand_AA_distribution_files_
private
core::Real protocols::features::strand_assembly::SandwichFeatures::wt_for_pro_in_1st_inter_sheet_loop_
private
core::Real protocols::features::strand_assembly::SandwichFeatures::wt_for_pro_in_3rd_inter_sheet_loop_
private
core::Real protocols::features::strand_assembly::SandwichFeatures::wt_for_pro_in_starting_loop_
private

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