| abba_bins_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| add_cyclic_constraints(core::pose::PoseOP pose) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| add_n_methylation(core::pose::PoseOP pose, core::Size const cyclic_offset) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| align_and_calculate_rmsd(core::pose::PoseOP pose, core::pose::PoseCOP native_pose) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| allowed_canonicals_by_position_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| allowed_noncanonicals_by_position_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| already_completed_job_count_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| angle_length_relax_rounds() const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | inlineprivate |
| angle_length_relax_rounds_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| angle_relax_rounds() const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | inlineprivate |
| angle_relax_rounds_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| break_disulfides(core::pose::PoseOP pose, utility::vector1< std::pair< core::Size, core::Size > > const &disulfides) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| build_polymer(core::pose::PoseOP pose, utility::vector1< std::string > const &restypes) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| cartesian_relax_rounds() const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | inlineprivate |
| cartesian_relax_rounds_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| checkpoint(core::Size const curjob, core::Size const successes) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| checkpoint_filename_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| checkpoint_job_identifier_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| comp_file_contents_D_alpha_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| comp_file_contents_D_beta_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| comp_file_contents_L_alpha_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| comp_file_contents_L_beta_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| count_cis_peptide_bonds(core::pose::PoseCOP pose) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| count_sc_hbonds_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| current_position(core::Size const absolute_position, core::Size const permutation_offset, core::Size const nresidue) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | inlineprivate |
| custom_rama_table_defined(core::Size const absolute_position) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | inlineprivate |
| cyclic_permutations_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| D_alpha_comp_file_exists_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| D_beta_comp_file_exists_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| default_rama_table_type() const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | inlineprivate |
| default_rama_table_type_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| depermute(core::pose::PoseOP pose, core::Size const offset) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| depermute_disulfide_list(utility::vector1< std::pair< core::Size, core::Size > > const &old_disulfides, utility::vector1< std::pair< core::Size, core::Size > > &new_disulfides, core::Size const offset, core::Size const nres) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| design_filename_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| design_peptide_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| disable_cis_pro_sampling() | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| disable_total_energy_cutoff() | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| disulf_energy_cutoff_postrelax_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| disulf_energy_cutoff_prerelax_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| do_cyclic_permutation(utility::vector1< std::string > const &resnames, utility::vector1< std::string > &resnames_copy) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| do_final_fastrelax(core::pose::PoseOP pose, core::scoring::ScoreFunctionOP sfxn, core::Size const relax_rounds, bool const angle_min, bool const length_min, bool const cartesian_min) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| do_not_count_adjacent_res_hbonds_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| end_checkpointing() const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| erase_random_seed_info() const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| fast_relax_rounds_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| filter_oversaturated_hbond_acceptors_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| genkic_close(core::pose::PoseOP pose, core::scoring::ScoreFunctionOP sfxn_highhbond, core::scoring::ScoreFunctionOP sfxn_highhbond_cart, core::scoring::ScoreFunctionCOP sfxn_default, protocols::filters::CombinedFilterOP total_hbond, core::Size const cyclic_offset) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| genkic_closure_attempts_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| genkic_min_solution_count_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| get_nc_threeletter_codes(utility::vector1< std::string > const &fullnames) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| get_oneletter_codes(utility::vector1< std::string > const &fullnames) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| get_rama_table_type_from_name(std::string const &type_name) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| get_random_seed_info() const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| hbond_energy_cutoff_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| high_hbond_weight_multiplier_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| import_and_set_up_native(std::string const &native_file, core::pose::PoseOP native_pose, core::Size const expected_residue_count) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| initialize_checkpointing(core::Size &lastjob, core::Size &successes) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| initialize_from_options() | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| L_alpha_comp_file_exists_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| L_beta_comp_file_exists_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| link_all_cys_with_tbmb_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| min_final_hbonds_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| min_genkic_hbonds_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| my_rank_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| n_methyl_positions_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| native_exists_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| native_filename_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| native_pose_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| new_checkpoint_file() const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| nstruct_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| original_position(core::Size const curr_position, core::Size const permutation_offset, core::Size const nresidue) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | inlineprivate |
| out_filename_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| out_scorefilename_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| oversaturated_hbond_cutoff_energy_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| prevent_design_file_read_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| prohibit_D_at_negative_phi_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| prohibit_L_at_positive_phi_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| rama_cutoff_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| rama_table_type_by_res(core::Size const absolute_position) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | inlineprivate |
| rama_table_type_by_res_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| rand_checkpoint_file_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| re_append_tbmb_residues(core::pose::PoseCOP pose, core::pose::PoseOP newpose, core::Size const offset) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| read_sequence(std::string const &seqfile, utility::vector1< std::string > &resnames) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| rebuild_disulfides(core::pose::PoseOP pose, utility::vector1< std::pair< core::Size, core::Size > > const &disulfides) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| register_options() | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | static |
| required_symmetry_angle_threshold_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| required_symmetry_mirroring_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| required_symmetry_perturbation_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| required_symmetry_repeats_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| run() const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| sample_cis_pro() const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | inlineprivate |
| sample_cis_pro_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| sample_cis_pro_frequency() const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | inlineprivate |
| sample_cis_pro_frequency_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| scorefxn_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| sequence_file_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| sequence_length() const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | inlineprivate |
| sequence_length_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | mutableprivate |
| sequence_string_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| set_abba_bins_binfile_contents(std::string const &contents_in) | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| set_allowed_residues_by_position(std::map< core::Size, utility::vector1< std::string > > const &allowed_canonicals, std::map< core::Size, utility::vector1< std::string > > const &allowed_noncanonicals) | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| set_already_completed_job_count(core::Size const count_in) | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| set_angle_length_relax_rounds(core::Size const rounds_in) | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| set_angle_relax_rounds(core::Size const rounds_in) | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| set_cartesian_relax_rounds(core::Size const rounds_in) | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| set_D_alpha_compfile_contents(std::string const &contents_in) | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| set_D_beta_compfile_contents(std::string const &contents_in) | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| set_default_rama_table_type(std::string const &type_name) | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| set_L_alpha_compfile_contents(std::string const &contents_in) | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| set_L_beta_compfile_contents(std::string const &contents_in) | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| set_mainchain_torsions(core::pose::PoseOP pose, core::Size const cyclic_offset) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| set_my_rank(int const rank_in) | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| set_native(core::pose::PoseCOP native) | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| set_nstruct(core::Size const nstruct_in) | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| set_rama_table_type_by_res(utility::vector1< std::string > const &type_name_vector) | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| set_sample_cis_pro_frequency(core::Real const &freq_in) | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| set_scorefxn(core::scoring::ScoreFunctionCOP sfxn_in) | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| set_sequence(std::string const &seq) | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| set_silentstructure_outputlist(utility::vector1< core::io::silent::SilentStructOP > *silentlist, utility::vector1< SimpleCycpepPredictApplication_MPI_JobResultsSummaryOP > *summarylist) | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| set_suppress_checkpoints(bool const suppress_checkpoints) | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| set_total_energy_cutoff(core::Real const &value_in) | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| set_up_design_taskoperations(protocols::denovo_design::movers::FastDesignOP fdes, core::Size const cyclic_offset, core::Size const nres) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| set_up_hbond_filter(protocols::filters::CombinedFilterOP total_hbond, core::Size const nres, core::scoring::ScoreFunctionOP sfxn, core::Real const &min_hbonds) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| set_up_native(core::pose::PoseOP native_pose, core::Size const expected_residue_count) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| set_up_termini_mover(protocols::cyclic_peptide::DeclareBondOP termini, core::pose::PoseCOP pose, bool const native=false, core::Size const last_res=0) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| set_use_rama_prepro_for_sampling(bool const setting) | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| silent_out_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| silentlist_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| silentlist_out_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| SimpleCycpepPredictApplication(bool const allow_file_read=true) | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| SimpleCycpepPredictApplication(SimpleCycpepPredictApplication const &src) | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
| store_disulfides(core::pose::PoseCOP pose, utility::vector1< std::pair< core::Size, core::Size > > &old_disulfides) const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| store_random_seed_info() const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| summarylist_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| suppress_checkpoints_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| tbmb_constraints_energy_filter_multiplier_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| tbmb_positions_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | mutableprivate |
| tbmb_sidechain_distance_filter_multiplier_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| total_energy_cutoff_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| try_all_disulfides_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| use_aa_comp_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| use_rama_filter() const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | inlineprivate |
| use_rama_filter_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| use_rama_prepro_for_sampling() const | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | inlineprivate |
| use_rama_prepro_for_sampling_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| use_tbmb_filters_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| use_total_energy_cutoff_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| user_set_alpha_dihedrals_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| user_set_dihedral_perturbation_ | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | private |
| ~SimpleCycpepPredictApplication() override | protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication | |
1.8.7