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Rosetta Protocols
2014.35
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#include <SandwichFeatures.hh>
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core::scoring::ScoreFunctionOP | generate_scorefxn (bool fullatom=false) |
create score-functions for centroid and fullatom level More... | |
Additional Inherited Members | |
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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... | |
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RelevantResiduesMode::T | relevant_residues_mode_ |
protocols::features::strand_assembly::SandwichFeatures::SandwichFeatures | ( | ) |
protocols::features::strand_assembly::SandwichFeatures::~SandwichFeatures | ( | ) |
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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.
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create score-functions for centroid and fullatom level
References core::scoring::ScoreFunctionFactory::create_score_function(), and core::scoring::get_score_function().
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Reimplemented from protocols::features::FeaturesReporter.
void protocols::features::strand_assembly::SandwichFeatures::process_decoy | ( | core::pose::Pose & | dssp_pose, |
core::scoring::ScoreFunction const & | scorefxn | ||
) | const |
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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_sheet_antiparallel_info(), 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(), protocols::features::strand_assembly::is_this_strand_at_edge(), protocols::features::strand_assembly::judge_facing(), core::chemical::ResidueType::name3(), core::pose::Pose::phi(), protocols::features::strand_assembly::prepare_and_write_number_of_electrostatic_interactions_of_residues_to_files(), protocols::features::strand_assembly::prepare_WriteToDB_sandwich(), core::pose::Pose::psi(), core::pose::Pose::residue_type(), core::pose::Pose::secstruct(), protocols::features::strand_assembly::see_whether_sheet_is_antiparallel(), protocols::features::strand_assembly::see_whether_this_sw_has_SS_bond(), sum(), tag, core::pose::Pose::total_residue(), 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_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_prolines_that_seem_to_prevent_aggregation(), protocols::features::strand_assembly::WriteToDB_ratio_of_core_heading_FWY_in_sw(), protocols::features::strand_assembly::WriteToDB_sandwich(), 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().
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Reimplemented from protocols::features::FeaturesReporter.
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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(), C, D, protocols::features::E, F, protocols::comparative_modeling::features::G, H, I, K, protocols::features::L, N, S, sheet, tag, V, W, basic::database::schema_generator::Schema::write(), and Y.
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