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

- a -

• aa1 : basic::options::OptionKeys::mh::filter , mh::filter
• aa2 : basic::options::OptionKeys::mh::filter , mh::filter
• aa_during_build : basic::options::OptionKeys::ufv , ufv
• aa_during_design_refine : basic::options::OptionKeys::ufv , ufv
• ab_dock_chains() : antibody::design , basic::options::OptionKeys::antibody::design
• ABEGO() : basic::options::OptionKeys::frags::ABEGO , frags::ABEGO
• abinitio() : abinitio
• ABINITIO : basic
• abinitio : basic::options::OptionKeys::abinitio
• abinitio_cycles : basic::options::OptionKeys::smhybrid , smhybrid
• abinitio_design : basic::options::OptionKeys::smhybrid , smhybrid
• abrelax() : abrelax , basic::options::OptionKeys::abrelax
• abs_difference() : numeric
• accept_aborted_loops : basic::options::OptionKeys::loops , loops
• access_ptr_bool : utility::pointer
• access_ptr_char : utility::pointer
• access_ptr_double : utility::pointer
• access_ptr_float : utility::pointer
• access_ptr_int : utility::pointer
• access_ptr_long : utility::pointer
• access_ptr_longdouble : utility::pointer
• access_ptr_schar : utility::pointer
• access_ptr_short : utility::pointer
• access_ptr_size_t : utility::pointer
• access_ptr_uchar : utility::pointer
• access_ptr_uint : utility::pointer
• access_ptr_ulong : utility::pointer
• access_ptr_ushort : utility::pointer
• action : basic::options::OptionKeys::evolution , evolution
• active_site_definition_by_gridlig : basic::options::OptionKeys::match , match
• active_site_definition_by_residue : basic::options::OptionKeys::match , match
• add() : numeric
• add_atom_at_cen : basic::options::OptionKeys::smhybrid , smhybrid
• add_atom_type_set_parameters() : basic::options::OptionKeys::chemical , chemical
• add_buffer_res : basic::options::OptionKeys::pepspec , pepspec
• add_cavities : basic::options::OptionKeys::smhybrid , smhybrid
• add_cst_loop : basic::options::OptionKeys::fold_from_loops , fold_from_loops
• add_delete_frequency : basic::options::OptionKeys::stepwise::monte_carlo , stepwise::monte_carlo
• add_esc_char() : utility::json_spirit
• add_esc_chars() : utility::json_spirit
• add_exit_callback() : utility
• add_metal_at_0 : basic::options::OptionKeys::smhybrid , smhybrid
• add_non_init_chunks : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• add_orbitals : basic::options::OptionKeys::in , in
• add_posn_iter_and_read_range_or_throw() : utility::json_spirit
• add_relax_cycles : basic::options::OptionKeys::fold_from_loops , fold_from_loops
• add_res_after : basic::options::OptionKeys::smhybrid , smhybrid
• add_res_before : basic::options::OptionKeys::smhybrid , smhybrid
• add_spaces_left_align() : utility
• add_spaces_right_align() : utility
• add_ss_after : basic::options::OptionKeys::smhybrid , smhybrid
• add_ss_before : basic::options::OptionKeys::smhybrid , smhybrid
• add_virt_root : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• AddExpressionCOP : numeric::expression_parser
• AddExpressionOP : numeric::expression_parser
• additional_packing_ligand_rb_confs : basic::options::OptionKeys::enzdes , enzdes
• adducts : basic::options::OptionKeys::packing , packing
• AHD_cutoff : basic::options::OptionKeys::bunsat_calc2 , bunsat_calc2
• akash() : AnchoredDesign::akash , basic::options::OptionKeys::AnchoredDesign::akash
• ala_scan : basic::options::OptionKeys::matdes::mutalyze , matdes::mutalyze
• align_pdb : basic::options::OptionKeys::stepwise , stepwise
• 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 , in::file , out::file
• alignment2 : basic::options::OptionKeys::in::file , in::file
• alignment_from_chunk_mapping : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• alignment_from_template_seqpos : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• alignment_res : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• alignVectorSets() : numeric
• all : basic::options::OptionKeys::out::path , out::path , utility::options::OptionKeys::options
• allow_anchor_repack() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign
• allow_base_pair_only_centroid_screen : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• 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_fixed_res_at_moving_res : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• 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_lig_move : basic::options::OptionKeys::loops , loops
• 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_takeoff_torsion_move : basic::options::OptionKeys::loops , loops
• allow_variable_bond_geometry : basic::options::OptionKeys::stepwise::monte_carlo , stepwise::monte_carlo
• allow_virtual_side_chains : basic::options::OptionKeys::stepwise::protein , stepwise::protein
• allowed_closure_attempts : basic::options::OptionKeys::remodel::RemodelLoopMover , remodel::RemodelLoopMover
• allowed_pdb : basic::options::OptionKeys::frags , frags
• aln_format : basic::options::OptionKeys::cm , cm
• aln_length_filter : basic::options::OptionKeys::cm , cm
• aln_length_filter_quantile : basic::options::OptionKeys::cm , cm
• alternative_closure_protocol : basic::options::OptionKeys::loops , loops
• 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
• analytic_etable_evaluation : basic::options::OptionKeys::score , score
• 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_type : basic::options::OptionKeys::pepspec , pepspec
• anchor_via_constraints() : AnchoredDesign::testing , basic::options::OptionKeys::AnchoredDesign::testing
• anchored_foldtree : basic::options::OptionKeys::membrane_new , membrane_new
• AnchoredDesign() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign
• angle : basic::options::OptionKeys::hotspot , basic::options::OptionKeys::matdes , hotspot , matdes
• angle_degrees() : numeric
• angle_degrees_double() : numeric
• angle_in_range() : basic
• 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 , frags
• annotate_ring_edges() : utility::graph
• antibody() : antibody , basic::options::OptionKeys::antibody
• antibody_database() : antibody::design , basic::options::OptionKeys::antibody::design
• apbs_debug : basic::options::OptionKeys::pb_potential , pb_potential
• apbs_path : basic::options::OptionKeys::pb_potential , pb_potential
• append_double() : utility::json_spirit
• append_esc_char_and_incr_iter() : utility::json_spirit
• APPLY_BB_MOVE : basic
• 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
• 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
• argmax() : utility
• argmin() : utility
• 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
• assembly() : assembly , basic::options::OptionKeys::assembly
• assign_ss : basic::options::OptionKeys::rescore , rescore
• ASTPrinterCOP : numeric::expression_parser
• ASTPrinterOP : numeric::expression_parser
• ASTVisitorCOP : numeric::expression_parser
• ASTVisitorOP : numeric::expression_parser
• atom_mask() : basic::options::OptionKeys::edensity , edensity
• atom_mask_min : basic::options::OptionKeys::edensity , edensity
• atom_names() : basic::options::OptionKeys::james , james
• 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
• atomic_burial_cutoff : basic::options::OptionKeys::pose_metrics , pose_metrics
• atr_rep_screen : 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
• auto_frag_insertion_weight : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• auto_setup_metals() : basic::options::OptionKeys::in , in
• auto_tune : basic::options::OptionKeys::cluster , cluster
• average_link_clustering() : numeric