| add_chunk_filter(VallChunkFilterOP filter) | protocols::frag_picker::FragmentPicker | inline |
| add_query_ss(std::string, std::string) | protocols::frag_picker::FragmentPicker | |
| add_scoring_method(scores::FragmentScoringMethodOP scoring_term, core::Real weight, core::Size index=1) | protocols::frag_picker::FragmentPicker | inline |
| atom_pair_constraint_contact_map_ | protocols::frag_picker::FragmentPicker | private |
| bounded_protocol() | protocols::frag_picker::FragmentPicker | |
| candidates_sink_ | protocols::frag_picker::FragmentPicker | private |
| candidates_sinks_ | protocols::frag_picker::FragmentPicker | private |
| chunks_ | protocols::frag_picker::FragmentPicker | private |
| contact_types_ | protocols::frag_picker::FragmentPicker | private |
| contacts_dist_cutoff_squared_ | protocols::frag_picker::FragmentPicker | private |
| contacts_dist_cutoffs_squared_ | protocols::frag_picker::FragmentPicker | private |
| contacts_min_seq_sep_ | protocols::frag_picker::FragmentPicker | private |
| count_query_ss() | protocols::frag_picker::FragmentPicker | inline |
| create_scores(std::string file_name) | protocols::frag_picker::FragmentPicker | inline |
| filters_ | protocols::frag_picker::FragmentPicker | private |
| frag_sizes_ | protocols::frag_picker::FragmentPicker | |
| fragment_contacts(core::Size const fragment_size, utility::vector1< Candidates > const &fragment_set) | protocols::frag_picker::FragmentPicker | |
| FragmentPicker() | protocols::frag_picker::FragmentPicker | inline |
| FragmentPicker(std::string fragment_score_manager_type) | protocols::frag_picker::FragmentPicker | inline |
| get_candidates_collector(core::Size frag_size, core::Size index=1) | protocols::frag_picker::FragmentPicker | inline |
| get_final_fragments(core::Size qPos, core::Size frag_size, Candidates &out) | protocols::frag_picker::FragmentPicker | |
| get_final_fragments(core::Size qPos, Candidates &out) | protocols::frag_picker::FragmentPicker | |
| get_frag_sizes() const | protocols::frag_picker::FragmentPicker | |
| get_n_candidates() const | protocols::frag_picker::FragmentPicker | |
| get_n_frags() const | protocols::frag_picker::FragmentPicker | |
| get_picked_positions() const | protocols::frag_picker::FragmentPicker | |
| get_query_phi_prediction() | protocols::frag_picker::FragmentPicker | inline |
| get_query_phi_prediction_conf() | protocols::frag_picker::FragmentPicker | inline |
| get_query_psi_prediction() | protocols::frag_picker::FragmentPicker | inline |
| get_query_psi_prediction_conf() | protocols::frag_picker::FragmentPicker | inline |
| get_query_residue_depth() | protocols::frag_picker::FragmentPicker | inline |
| get_query_sa_prediction() | protocols::frag_picker::FragmentPicker | inline |
| get_query_seq() | protocols::frag_picker::FragmentPicker | inline |
| get_query_seq_string() | protocols::frag_picker::FragmentPicker | inline |
| get_query_ss(std::string prediction_name) | protocols::frag_picker::FragmentPicker | inline |
| get_query_ss_string(std::string prediction_name) | protocols::frag_picker::FragmentPicker | inline |
| get_score_manager(core::Size index=1) | protocols::frag_picker::FragmentPicker | inline |
| get_self_ptr() const | protocols::frag_picker::FragmentPicker | inline |
| get_self_ptr() | protocols::frag_picker::FragmentPicker | inline |
| get_self_weak_ptr() const | protocols::frag_picker::FragmentPicker | inline |
| get_self_weak_ptr() | protocols::frag_picker::FragmentPicker | inline |
| get_vall() | protocols::frag_picker::FragmentPicker | inline |
| getFragSet(int residueInPose_) | protocols::frag_picker::FragmentPicker | |
| is_valid_chunk(VallChunkOP chunk) | protocols::frag_picker::FragmentPicker | |
| is_valid_chunk(core::Size const frag_len, VallChunkOP chunk) | protocols::frag_picker::FragmentPicker | |
| keep_all_protocol() | protocols::frag_picker::FragmentPicker | |
| log_200_ | protocols::frag_picker::FragmentPicker | static |
| log_25_ | protocols::frag_picker::FragmentPicker | static |
| max_frag_len() | protocols::frag_picker::FragmentPicker | inline |
| max_frag_size_ | protocols::frag_picker::FragmentPicker | private |
| max_threads_ | protocols::frag_picker::FragmentPicker | private |
| n_candidates_ | protocols::frag_picker::FragmentPicker | |
| n_frags_ | protocols::frag_picker::FragmentPicker | |
| nonlocal_min_contacts_per_res_ | protocols::frag_picker::FragmentPicker | private |
| nonlocal_pairs(core::Size const fragment_size, utility::vector1< Candidates > const &fragment_set) | protocols::frag_picker::FragmentPicker | |
| nonlocal_pairs_at_positions(utility::vector1< core::Size > const &positions, core::Size const &fragment_size, utility::vector1< bool > const &skip, utility::vector1< Candidates > const &fragment_set, utility::vector1< nonlocal::NonlocalPairOP > &pairs) | protocols::frag_picker::FragmentPicker | |
| output_fragments(core::Size const fragment_size, utility::vector1< Candidates > const &final_fragments) | protocols::frag_picker::FragmentPicker | |
| output_pair_counts(core::Size const fragment_size, core::Size const neighbors, std::map< std::pair< core::Real, ContactType >, ContactCountsOP > contact_counts) | protocols::frag_picker::FragmentPicker | private |
| parse_command_line() | protocols::frag_picker::FragmentPicker | |
| parse_quota_command_line() | protocols::frag_picker::FragmentPicker | |
| pick_candidates() | protocols::frag_picker::FragmentPicker | |
| pick_candidates(core::Size i_pos, core::Size frag_len) | protocols::frag_picker::FragmentPicker | |
| pick_chunk_candidates(utility::vector1< VallChunkOP > const &chunks, core::Size const &index) | protocols::frag_picker::FragmentPicker | |
| prefix_ | protocols::frag_picker::FragmentPicker | |
| query_phi_prediction_ | protocols::frag_picker::FragmentPicker | private |
| query_phi_prediction_conf_ | protocols::frag_picker::FragmentPicker | private |
| query_positions_ | protocols::frag_picker::FragmentPicker | private |
| query_profile_ | protocols::frag_picker::FragmentPicker | private |
| query_psi_prediction_ | protocols::frag_picker::FragmentPicker | private |
| query_psi_prediction_conf_ | protocols::frag_picker::FragmentPicker | private |
| query_residue_depth_ | protocols::frag_picker::FragmentPicker | private |
| query_sa_prediction_ | protocols::frag_picker::FragmentPicker | private |
| query_seq_as_string_ | protocols::frag_picker::FragmentPicker | private |
| query_ss_as_string_ | protocols::frag_picker::FragmentPicker | private |
| query_ss_profile_ | protocols::frag_picker::FragmentPicker | private |
| quota_protocol() | protocols::frag_picker::FragmentPicker | |
| read_depth(std::string const &file_name) | protocols::frag_picker::FragmentPicker | |
| read_psipred_ss2(std::string const &, std::string) | protocols::frag_picker::FragmentPicker | |
| read_spine_x(std::string const &file_name) | protocols::frag_picker::FragmentPicker | |
| read_ss_file(std::string const &, std::string) | protocols::frag_picker::FragmentPicker | |
| read_ss_files(utility::vector1< std::string > sec_str_input) | protocols::frag_picker::FragmentPicker | |
| read_talos_ss(std::string const &, std::string) | protocols::frag_picker::FragmentPicker | |
| read_vall(std::string const &fn) | protocols::frag_picker::FragmentPicker | |
| read_vall(utility::vector1< std::string > const &fns) | protocols::frag_picker::FragmentPicker | |
| save_candidates() | protocols::frag_picker::FragmentPicker | |
| save_fragments() | protocols::frag_picker::FragmentPicker | |
| scores_ | protocols::frag_picker::FragmentPicker | private |
| selector_ | protocols::frag_picker::FragmentPicker | |
| set_candidates_collector(core::Size frag_size, CandidatesCollectorOP sink, core::Size index=1) | protocols::frag_picker::FragmentPicker | inline |
| set_frag_sizes(utility::vector1< core::Size > size, bool clear) | protocols::frag_picker::FragmentPicker | |
| set_n_candidates(core::Size n_candidates) | protocols::frag_picker::FragmentPicker | |
| set_n_frags(core::Size n_frags) | protocols::frag_picker::FragmentPicker | |
| set_picked_positions(core::Size, core::Size) | protocols::frag_picker::FragmentPicker | |
| set_picked_positions(utility::vector1< core::Size >) | protocols::frag_picker::FragmentPicker | |
| set_query_phi(utility::vector1< core::Real > &query_phi) | protocols::frag_picker::FragmentPicker | |
| set_query_phi_conf(utility::vector1< core::Real > &query_phi_conf) | protocols::frag_picker::FragmentPicker | |
| set_query_profile(core::sequence::SequenceProfileOP profile) | protocols::frag_picker::FragmentPicker | inline |
| set_query_psi(utility::vector1< core::Real > &query_psi) | protocols::frag_picker::FragmentPicker | |
| set_query_psi_conf(utility::vector1< core::Real > &query_psi_conf) | protocols::frag_picker::FragmentPicker | |
| set_query_sa(utility::vector1< core::Real > &query_sa) | protocols::frag_picker::FragmentPicker | |
| set_query_seq(core::sequence::SequenceProfileOP query_sequence) | protocols::frag_picker::FragmentPicker | |
| set_query_seq(std::string &query_sequence) | protocols::frag_picker::FragmentPicker | |
| set_selector(FragmentSelectingRuleOP selector) | protocols::frag_picker::FragmentPicker | inline |
| set_up_quota_nnmake_style() | protocols::frag_picker::FragmentPicker | |
| set_up_ss_abego_quota() | protocols::frag_picker::FragmentPicker | |
| set_vall(VallProviderOP vall_chunks) | protocols::frag_picker::FragmentPicker | inline |
| show_scoring_methods(std::ostream &out, core::Size index=1) | protocols::frag_picker::FragmentPicker | inline |
| sidechain_contact_dist_cutoff_ | protocols::frag_picker::FragmentPicker | private |
| size_of_query() | protocols::frag_picker::FragmentPicker | inline |
| total_score(scores::FragmentScoreMapOP f, core::Size index=1) | protocols::frag_picker::FragmentPicker | |
| ~FragmentPicker() override | protocols::frag_picker::FragmentPicker | |
1.8.7