Here is a list of all namespace members with links to the namespace documentation for each member:

- a -

• a : basic::options::OptionKeys::score::fiber_diffraction
• A() : ObjexxFCL::format
• a() : score::fiber_diffraction , test::T850_SubClassing
• a1 : test::Workshop3test
• a2 : test::Workshop3test
• aa : basic::options::OptionKeys::mh::match , mh::match
• aa1 : basic::options::OptionKeys::mh::filter , basic::options::OptionKeys::mh::match , mh::filter , mh::match
• aa2 : basic::options::OptionKeys::mh::filter , basic::options::OptionKeys::mh::match , mh::filter , mh::match
• aa_composition_setup_file : basic::options::OptionKeys::score , score
• aa_during_build : basic::options::OptionKeys::ufv , ufv
• aa_during_design_refine : basic::options::OptionKeys::ufv , ufv
• aa_repeat_energy_penalty_file : basic::options::OptionKeys::score , score
• AAs : app::delta_score_per_mutation
• ab : test::T400_Refinement
• ab_struct : test::G201_Module_Structure
• ABEGO : basic::options::OptionKeys::frags::ABEGO , frags::ABEGO
• abinitio() : abinitio , app::surface_docking::surface_docking
• ABINITIO : basic
• abinitio : basic::options::OptionKeys::abinitio
• abinitio_cycles : basic::options::OptionKeys::smhybrid , smhybrid
• abinitio_design : basic::options::OptionKeys::smhybrid , smhybrid
• about() : app::pyrosetta_toolkit::modules::help
• abrelax() : abrelax , basic::options::OptionKeys::abrelax
• abs() : ObjexxFCL
• abs_difference() : numeric
• accept_aborted_loops : basic::options::OptionKeys::loops , loops
• accumulate() : ObjexxFCL::internal::ObserverMediator
• ACHAR() : ObjexxFCL::Fortran
• action : basic::options::OptionKeys::evolution , evolution , toolbox::adjust_library_path
• activate_common_simple_type() : utility::tag
• active_site_definition_by_gridlig : basic::options::OptionKeys::match , match
• active_site_definition_by_residue : basic::options::OptionKeys::match , match
• acyclic() : ObjexxFCL::internal::ObserverMediator
• adapt_graft() : antibody::design , basic::options::OptionKeys::antibody::design
• add() : numeric
• add_anonymous_option() : basic::options
• add_atom_at_cen : basic::options::OptionKeys::smhybrid , smhybrid
• add_atom_type_set_parameters : basic::options::OptionKeys::chemical , chemical
• add_backrub_pivots() : antibody::design , basic::options::OptionKeys::antibody::design
• add_buffer_res : basic::options::OptionKeys::pepspec , pepspec
• add_cavities : basic::options::OptionKeys::smhybrid , smhybrid
• add_cid_to_database() : pyrosetta::toolbox::load_ligand , toolbox::load_ligand
• add_constraints : basic::options::OptionKeys::cyclization , cyclization
• add_constraints_to_pose_and_scorefunction() : app::pyrosetta_toolkit::modules::tools::input
• add_constructor() : yaml
• add_cst_loop : basic::options::OptionKeys::fold_from_loops , fold_from_loops
• add_delete_frequency : basic::options::OptionKeys::magnesium::montecarlo , basic::options::OptionKeys::stepwise::monte_carlo , magnesium::montecarlo , stepwise::monte_carlo
• add_esc_char() : utility::json_spirit
• add_esc_chars() : utility::json_spirit
• add_esp : basic::options::OptionKeys::fingerprint , fingerprint
• add_exit_callback() : utility
• add_extra_bodies() : apps::public1::scenarios::chemically_conjugated_docking
• add_extra_options() : src
• add_graft_log_to_pdb() : antibody::design , basic::options::OptionKeys::antibody::design
• add_implicit_resolver() : yaml
• add_metal_at_0 : basic::options::OptionKeys::smhybrid , smhybrid
• add_multi_constructor() : yaml
• add_multi_representer() : yaml
• add_non_init_chunks : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• add_option_to_map() : basic::resource_manager
• add_orbitals : basic::options::OptionKeys::in , in
• add_path_resolver() : yaml
• add_point() : PyMOLPyRosettaServer
• add_posn_iter_and_read_range_or_throw() : utility::json_spirit
• add_print_operators() : exclude
• add_proposal_density_factor : basic::options::OptionKeys::stepwise::monte_carlo , stepwise::monte_carlo
• add_relax_cycles : basic::options::OptionKeys::fold_from_loops , fold_from_loops
• add_relevant_include_for_decl() : binder
• add_relevant_includes() : binder
• add_representer() : yaml
• add_res_after : basic::options::OptionKeys::smhybrid , smhybrid
• add_res_before : basic::options::OptionKeys::smhybrid , smhybrid
• add_ss_after : basic::options::OptionKeys::smhybrid , smhybrid
• add_ss_before : basic::options::OptionKeys::smhybrid , smhybrid
• add_vectors() : PyMOLPyRosettaServer
• add_virt_root : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• addasa() : loadPDB
• addContacts() : calccontacts
• AddExpressionCOP : numeric::expression_parser
• AddExpressionOP : numeric::expression_parser
• addIndices() : loadPDB
• additional_objective_functions : basic::options::OptionKeys::lh , lh
• additional_packing_ligand_rb_confs : basic::options::OptionKeys::enzdes , enzdes
• addMax_radius() : calccontacts
• adducts : basic::options::OptionKeys::packing , packing
• ads : extract_scores_and_constraints
• ads_cycles : app::surface_docking::surface_docking
• ads_inner_cycles : app::surface_docking::surface_docking
• ads_outer_cycles : app::surface_docking::surface_docking
• ads_pdb : extract_scores_and_constraints
• agg_with_max : basic::options::OptionKeys::mh::harvest , mh::harvest
• AHD_cutoff : basic::options::OptionKeys::bunsat_calc2 , bunsat_calc2
• akash() : AnchoredDesign::akash , basic::options::OptionKeys::AnchoredDesign::akash
• ala : test::T100_Basic
• ala_scan : basic::options::OptionKeys::matdes::mutalyze , matdes::mutalyze
• ALIGN_CENTER : fmt
• ALIGN_DEFAULT : fmt
• ALIGN_LEFT : fmt
• ALIGN_NUMERIC : fmt
• align_pdb : basic::options::OptionKeys::stepwise , stepwise
• ALIGN_RIGHT : fmt
• align_rmsd_column : basic::options::OptionKeys::evaluation , evaluation
• align_rmsd_fns : basic::options::OptionKeys::evaluation , evaluation
• align_rmsd_format : basic::options::OptionKeys::evaluation , evaluation
• align_rmsd_target : basic::options::OptionKeys::evaluation , evaluation
• aligner : basic::options::OptionKeys::cm , cm
• alignment : basic::options::OptionKeys::in::file , basic::options::OptionKeys::out::file
• Alignment : fmt
• alignment() : in::file , out::file
• alignment2 : basic::options::OptionKeys::in::file , in::file
• alignment_res : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• alignVectorSets() : numeric
• ALL : app::pyrosetta_toolkit::modules::prettytable::prettytable
• all : basic::options::OptionKeys::out::path , out::path , utility::options::OptionKeys::options
• all_atom_mode_kink_constraint() : antibody , basic::options::OptionKeys::antibody
• all_hydration_frames : basic::options::OptionKeys::magnesium , magnesium
• allow_anchor_repack() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign
• allow_base_pair_only_centroid_screen : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• allow_bulge : basic::options::OptionKeys::rna::farna , rna::farna
• allow_bulge_at_chainbreak : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• allow_chain_boundary_jump_partner_right_at_fixed_BP : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• allow_complex_loop_graph : basic::options::OptionKeys::score , score
• allow_consecutive_bulges : basic::options::OptionKeys::rna::farna , rna::farna
• allow_fixed_res_at_moving_res : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• allow_flips : basic::options::OptionKeys::mp::dock , mp::dock
• allow_fragment_moves_in_bps : basic::options::OptionKeys::rna::farna , rna::farna
• allow_gly : basic::options::OptionKeys::hotspot , hotspot
• allow_internal_hinge_moves : basic::options::OptionKeys::stepwise::monte_carlo , stepwise::monte_carlo
• allow_internal_local_moves : basic::options::OptionKeys::stepwise::monte_carlo , stepwise::monte_carlo
• allow_jump_in_numbering : basic::options::OptionKeys::full_model , full_model
• allow_lig_move : basic::options::OptionKeys::loops , loops
• allow_omega_mismatches_for_north_clusters() : antibody , basic::options::OptionKeys::antibody
• allow_omega_move : basic::options::OptionKeys::loops , loops
• allow_proline : basic::options::OptionKeys::hotspot , hotspot
• allow_rare_aro_chi : basic::options::OptionKeys::remodel::design , remodel::design
• allow_skip_bulge : basic::options::OptionKeys::stepwise::monte_carlo , stepwise::monte_carlo
• allow_split_off : basic::options::OptionKeys::stepwise::monte_carlo , stepwise::monte_carlo
• allow_submotif_split : basic::options::OptionKeys::stepwise::monte_carlo , stepwise::monte_carlo
• allow_takeoff_torsion_move : basic::options::OptionKeys::loops , loops
• allow_variable_bond_geometry : basic::options::OptionKeys::stepwise::monte_carlo , stepwise::monte_carlo
• allow_virtual_o2prime_hydrogens : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• allow_virtual_side_chains : basic::options::OptionKeys::stepwise::protein , stepwise::protein
• allowed_bulge_res : basic::options::OptionKeys::rna::farna , rna::farna
• allowed_closure_attempts : basic::options::OptionKeys::remodel::RemodelLoopMover , remodel::RemodelLoopMover
• allowed_pdb : basic::options::OptionKeys::frags , frags
• allowed_residues_by_position : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• aln_format : basic::options::OptionKeys::cm , cm
• aln_length_filter : basic::options::OptionKeys::cm , cm
• aln_length_filter_quantile : basic::options::OptionKeys::cm , cm
• ALPHA() : numeric::crick_equations
• alpha_increment : basic::options::OptionKeys::sample_around , sample_around
• ALPHANUMERICS() : utility
• alter_spec_disruption_mode : protocols::pmut_scan
• alternate_3_letter_codes : basic::options::OptionKeys::in , in
• alternative_closure_protocol : basic::options::OptionKeys::loops , loops
• altpos : clean_pdb_keep_ligand
• always_remodel_full_loop : basic::options::OptionKeys::loops , loops
• ambig_talos_cs_A : basic::options::OptionKeys::in::file , in::file
• ambig_talos_cs_B : basic::options::OptionKeys::in::file , in::file
• amino_acids : amino_acids
• AminoAcidTable() : PDBInfo
• analytic_etable_evaluation : basic::options::OptionKeys::score , score
• analyze_interface() : app::pyrosetta_toolkit::modules::tools::analysis
• analyze_loops() : app::pyrosetta_toolkit::modules::tools::analysis
• analyze_packing() : app::pyrosetta_toolkit::modules::tools::analysis
• analyze_vip() : app::pyrosetta_toolkit::modules::tools::analysis
• analyzer : app::pyrosetta_toolkit::modules::ScoreAnalysis
• anchor() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign
• anchor_noise_constraints_mode() : AnchoredDesign::testing , basic::options::OptionKeys::AnchoredDesign::testing
• anchor_offset : basic::options::OptionKeys::ms , ms
• anchor_pdb : basic::options::OptionKeys::AnchoredPDBCreator
• anchor_type : basic::options::OptionKeys::pepspec , pepspec
• anchor_via_constraints() : AnchoredDesign::testing , basic::options::OptionKeys::AnchoredDesign::testing
• AnchoredDesign() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign
• angle : basic::options::OptionKeys::hotspot , basic::options::OptionKeys::matdes , Equations , hotspot , matdes , PhiPsi
• angle_cutoff : basic::options::OptionKeys::mp::lipid_acc , mp::lipid_acc
• angle_degrees() : numeric
• angle_degrees_double() : numeric
• angle_in_range() : basic
• angle_max : basic::options::OptionKeys::mp::quickrelax , basic::options::OptionKeys::relax::range , mp::quickrelax , relax::range
• angle_of() : numeric
• angle_p1_deriv() : numeric::deriv
• angle_p1_p2_p3_deriv() : numeric::deriv
• angle_p2_deriv() : numeric::deriv
• angle_radians() : numeric
• angle_radians_double() : numeric
• angle_res : basic::options::OptionKeys::hotspot , hotspot
• AngleUnit : numeric::conversions
• annealer : basic::options::OptionKeys::flexpack::annealer , basic::options::OptionKeys::rotamerdump , flexpack::annealer , rotamerdump
• annotate : basic::options::OptionKeys::frags , exclude , frags
• annotate_ring_edges() : utility::graph
• ansi_colors : app::pyrosetta_toolkit::window_modules::interactive_terminal::interactive_terminal
• anti_parallel_vector() : app::surface_docking::surf_param
• anti_polar_weight : basic::options::OptionKeys::mh::score , mh::score
• antibody() : antibody , basic::options::OptionKeys::antibody
• antibody_database() : antibody::design , basic::options::OptionKeys::antibody::design
• ANY_OPTION : utility::options
• ANY_VECTOR_OPTION : utility::options
• apbs_debug : basic::options::OptionKeys::pb_potential , pb_potential
• apbs_path : basic::options::OptionKeys::pb_potential , pb_potential
• apc : test::T250_Constraints
• APDBC_cycles : basic::options::OptionKeys::AnchoredPDBCreator
• append_constraints() : app::surface_docking::append_data
• append_data() : app::surface_docking::surface_docking
• append_double() : utility::json_spirit
• append_esc_char_and_incr_iter() : utility::json_spirit
• append_hbonds() : app::surface_docking::append_data
• append_name_and_attributes_to_complex_type() : utility::tag
• append_rc : setup_pyrosetta
• append_required_name_and_attributes_to_complex_type() : utility::tag
• append_rmsd() : app::surface_docking::append_data
• append_scores() : app::surface_docking::append_data
• append_surf_ads : app::surface_docking::surface_docking
• append_surf_sol : app::surface_docking::surface_docking
• APPLY_BB_MOVE : basic
• apply_constraints() : app::surface_docking::constraints
• apply_disulf() : app::surface_docking::constraints
• APPLY_MOVE : basic
• APPLY_SC_MOVE : basic
• approximate_decoy_entropy : basic::options::OptionKeys::optE , optE
• arccos() : numeric
• archive() : archive , basic::options::OptionKeys::archive , basic::options::OptionKeys::run , run
• ARCHIVE_BLOCK_FILE : basic
• ARCHIVE_CRITICAL_JOBSCOMPLETE : basic
• ARCHIVE_EVAL_DECOYS : basic
• ARCHIVE_EVALUATORS : basic
• ARCHIVE_FILL_POSE : basic
• ARCHIVE_GEN_BATCH : basic
• ARCHIVE_JOBSCOMPLETE : basic
• ARCHIVE_READ_DECOYS : basic
• ARCHIVE_SCORE_POSE : basic
• ARCHIVE_SYNC_BATCHES : basic
• are_coplanar() : numeric::geometry
• arg() : fmt
• arg_greatest_several() : utility
• arg_least_several() : utility
• arg_max() : utility
• arg_min() : utility
• arg_sweep_cutoff : basic::options::OptionKeys::enzdes , enzdes
• arg_sweep_interface : basic::options::OptionKeys::enzdes , enzdes
• arglist : contacts
• argmax() : utility
• argmin() : utility
• args : app::delta_score_per_mutation , app::pyrosetta_toolkit::modules::DesignBreakdown , app::surface_docking::surface_docking , loops_kic
• ArithmeticASTExpressionCOP : numeric::expression_parser
• ArithmeticASTExpressionOP : numeric::expression_parser
• ArithmeticASTFactorCOP : numeric::expression_parser
• ArithmeticASTFactorOP : numeric::expression_parser
• ArithmeticASTFunctionCOP : numeric::expression_parser
• ArithmeticASTFunctionOP : numeric::expression_parser
• ArithmeticASTNodeCOP : numeric::expression_parser
• ArithmeticASTNodeOP : numeric::expression_parser
• ArithmeticASTRestExpressionCOP : numeric::expression_parser
• ArithmeticASTRestExpressionOP : numeric::expression_parser
• ArithmeticASTRestTermCOP : numeric::expression_parser
• ArithmeticASTRestTermOP : numeric::expression_parser
• ArithmeticASTTermCOP : numeric::expression_parser
• ArithmeticASTTermOP : numeric::expression_parser
• ArithmeticASTValueCOP : numeric::expression_parser
• ArithmeticASTValueOP : numeric::expression_parser
• ArithmeticScannerCOP : numeric::expression_parser
• ArithmeticScannerOP : numeric::expression_parser
• armijo_min_stepsize : basic::options::OptionKeys::optimization , optimization
• aromatic_motifs : basic::options::OptionKeys::motifs , motifs
• Array : utility::json_spirit
• array_type : utility::json_spirit
• ArrayWriter : fmt
• ask_append_rc() : setup_pyrosetta
• asp_hack : mrlo
• aspartimide_penalty_value : basic::options::OptionKeys::score , score
• assembly() : assembly , basic::options::OptionKeys::assembly
• assembly_type : basic::options::OptionKeys::sewing , sewing
• assign_gasteiger_atom_types : basic::options::OptionKeys::in::file , in::file
• assign_ss : basic::options::OptionKeys::rescore , rescore
• ASTPrinterCOP : numeric::expression_parser
• ASTPrinterOP : numeric::expression_parser
• ASTVisitorCOP : numeric::expression_parser
• ASTVisitorOP : numeric::expression_parser
• at5C : test::T100_Basic
• at5CA : test::T100_Basic
• at5N : test::T100_Basic
• atom1 : test::T220_AtomAtomPairEnergies
• atom2 : test::T220_AtomAtomPairEnergies
• atom_mask : basic::options::OptionKeys::edensity , edensity
• atom_mask_min : basic::options::OptionKeys::edensity , edensity
• atom_names : basic::options::OptionKeys::james , james
• atom_pair_cst_weight() : antibody::design , basic::options::OptionKeys::antibody::design
• atom_radius_buffer : basic::options::OptionKeys::fingerprint , fingerprint
• atom_radius_scale : basic::options::OptionKeys::fingerprint , fingerprint
• atom_scores : basic::options::OptionKeys::holes , holes
• atom_tree_diff : basic::options::OptionKeys::in::file , basic::options::OptionKeys::out::file , in::file , out::file
• atom_tree_diff_bb : basic::options::OptionKeys::out::file , out::file
• atom_tree_diff_bl : basic::options::OptionKeys::out::file , out::file
• atom_tree_diff_sc : basic::options::OptionKeys::out::file , out::file
• ATOM_TREE_UPDATE_INTERNAL_COORDS : basic
• ATOM_TREE_UPDATE_XYZ_COORDS : basic
• atomC : test::T100_Basic
• atomCA : test::T100_Basic
• atomic_burial_cutoff : basic::options::OptionKeys::pose_metrics , pose_metrics
• atomN : test::T100_Basic
• ATOMS : PDBInfo
• atr_rep_screen : basic::options::OptionKeys::stepwise , stepwise
• atr_rep_screen_for_docking : basic::options::OptionKeys::stepwise , stepwise
• attach_as_sc : basic::options::OptionKeys::smhybrid , smhybrid
• attach_as_sc_sub : basic::options::OptionKeys::smhybrid , smhybrid
• attach_atom : basic::options::OptionKeys::smhybrid , smhybrid
• attach_rsd : basic::options::OptionKeys::smhybrid , smhybrid
• attached_pdb : basic::options::OptionKeys::ufv::insert , ufv::insert
• attempt_pyrimidine_flip : basic::options::OptionKeys::rna::farna::erraser , rna::farna::erraser
• AttributeList : utility::tag
• author : app::pyrosetta_toolkit::modules::prettytable::setup
• author_email : app::pyrosetta_toolkit::modules::prettytable::setup
• auto_frag_insertion_weight : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• auto_generate_kink_constraint() : antibody , basic::options::OptionKeys::antibody
• auto_setup_metals : basic::options::OptionKeys::in , in
• auto_tune : basic::options::OptionKeys::cluster , cluster
• autofilter : basic::options::OptionKeys::rna::farna , rna::farna
• AvNAPSA_negative : local
• AvNAPSA_positive : local
• axisangle_to_rot() : loadPDB