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

- a -

• A : protocols::comparative_modeling::features , protocols::features
• AA : protocols::optimize_weights , core::chemical
• aa2idx() : core::scoring::saxs
• aa2name() : core::chemical
• aa2oneletter() : core::chemical
• aa_ala : core::chemical
• aa_arg : core::chemical
• aa_asn : core::chemical
• aa_asp : core::chemical
• aa_cmp : core::scoring
• aa_cys : core::chemical
• aa_from_name() : core::chemical
• aa_from_oneletter_code() : core::chemical
• aa_gln : core::chemical
• aa_glu : core::chemical
• aa_gly : core::chemical
• aa_his : core::chemical
• aa_ile : core::chemical
• aa_leu : core::chemical
• aa_lys : core::chemical
• aa_met : core::chemical
• aa_phe : core::chemical
• aa_pro : core::chemical
• aa_ser : core::chemical
• aa_thr : core::chemical
• aa_trp : core::chemical
• aa_tyr : core::chemical
• aa_unk : core::chemical
• aa_val : core::chemical
• aa_vrt : core::chemical
• Ab_TemplateInfoCOP : protocols::antibody2
• Ab_TemplateInfoOP : protocols::antibody2
• abego : core::scoring
• abego_index() : protocols::frag_picker::quota
• ABEGO_SS_MapCOP : protocols::frag_picker::quota
• ABEGO_SS_MapOP : protocols::frag_picker::quota
• ABEGO_SS_PoolCOP : protocols::frag_picker::quota
• ABEGO_SS_PoolOP : protocols::frag_picker::quota
• ABEGO_SS_ScoreCOP : protocols::frag_picker::scores
• ABEGO_SS_ScoreOP : protocols::frag_picker::scores
• ABEGOEvalAP : core::fragment::picking_old::vall::eval
• ABEGOEvalCAP : core::fragment::picking_old::vall::eval
• ABEGOEvalCOP : core::fragment::picking_old::vall::eval
• ABEGOEvalOP : core::fragment::picking_old::vall::eval
• ABEGOManagerCOP : core::util
• ABEGOManagerOP : core::util
• AbinitioMoverWeightAP : protocols::topology_broker::weights
• AbinitioMoverWeightCAP : protocols::topology_broker::weights
• AbinitioMoverWeightCOP : protocols::topology_broker::weights
• AbinitioMoverWeightOP : protocols::topology_broker::weights
• above : core::sequence
• AbrelaxMoverCOP : protocols::abinitio
• AbrelaxMoverOP : protocols::abinitio
• ABS : protocols::simple_filters
• AbstractArchiveBaseCOP : protocols::jd2::archive
• AbstractArchiveBaseOP : protocols::jd2::archive
• AbstractRotamerTrieCOP : core::conformation
• AbstractRotamerTrieOP : core::conformation
• accept : protocols::hotspot_hashing
• accept_reject : protocols::moves
• AccumulatorOP : core::scoring::packstat
• ACETYLATED_NTERMINUS : core::chemical
• ACETYLATION : core::chemical
• ActiveSiteGridCOP : protocols::match::downstream
• ActiveSiteGridOP : protocols::match::downstream
• AdaptiveScoreHistogramCOP : protocols::frag_picker::scores
• AdaptiveScoreHistogramOP : protocols::frag_picker::scores
• ADD : protocols::swa::monte_carlo
• add_atom() : core::kinematics
• add_atom_type_set_parameters_from_command_line() : core::chemical
• ADD_BATCH : protocols::jd2::archive
• add_chainbreaks_according_to_jumps() : protocols::toolbox::pose_manipulation
• add_claims_from_file() : protocols::topology_broker
• add_claims_from_stream() : protocols::topology_broker
• add_cmdline_claims() : protocols::topology_broker
• add_comment() : core::pose
• add_conformation_viewer() : protocols::viewer
• add_constraint_to_residue_constraints() : core::scoring::constraints
• add_constraints_from_cmdline() : core::scoring::constraints
• add_constraints_from_cmdline_to_pose() : core::scoring::constraints
• add_constraints_from_cmdline_to_scorefxn() : core::scoring::constraints
• add_constraints_from_file() : protocols::dna
• add_coordinate_constraints() : core::scoring::constraints , protocols::protein_interface_design::movers , protocols::seeded_abinitio
• add_coordinate_constraints_to_pose() : protocols::loops , protocols::relax
• add_cutpoint_variants() : core::util , protocols::forge::methods , protocols::loops
• add_daemon : protocols::pack_daemon
• add_dens_scores_from_cmdline_to_scorefxn() : core::scoring::electron_density
• add_dist_constraints() : protocols::seeded_abinitio
• add_edges() : protocols::forge::methods
• add_fa_constraints_from_cmdline() : core::scoring::constraints
• add_fa_constraints_from_cmdline_to_pose() : core::scoring::constraints
• add_fa_constraints_from_cmdline_to_scorefxn() : core::scoring::constraints
• Add_harmonic_chainbreak_constraint() : protocols::swa::rna
• add_hbs_constraint() : protocols::simple_moves::hbs
• add_hydrogen_tracer() : protocols::ligand_docking
• add_hydrogens_tracer() : protocols::ligand_docking
• add_job_data_to_ss() : protocols::jd2
• add_ligand_conditionally() : protocols::ligand_docking
• add_loop() : protocols::loops
• add_loop_flank_residues_bb_to_movemap() : protocols::loops
• add_lower_terminus_type_to_conformation_residue() : core::conformation
• add_lower_terminus_type_to_pose_residue() : core::pose
• add_monte_carlo_silent_viewer() : protocols::viewer
• add_monte_carlo_viewer() : protocols::viewer
• add_motif_bb_constraints() : protocols::motifs
• add_motif_sc_constraints() : protocols::motifs
• ADD_NEW : protocols::enzdes
• add_non_protein_cst() : protocols::hybridization
• add_oop_constraint() : protocols::simple_moves::oop
• ADD_PREGENERATED : protocols::enzdes
• add_relevant_restypes_to_subset() : protocols::toolbox::match_enzdes_util
• add_rna_chi_rotamers() : core::pack::rotamer_set
• add_score_line_string() : core::pose
• add_single_cutpoint_variant() : protocols::loops
• add_strand_pairs_cst() : protocols::hybridization
• add_to_individual_sol_energies() : core::scoring::geometric_solvation
• add_upper_terminus_type_to_conformation_residue() : core::conformation
• add_upper_terminus_type_to_pose_residue() : core::pose
• add_variant_type_to_conformation_residue() : core::conformation
• add_variant_type_to_pose_residue() : core::pose
• add_variant_type_to_residue() : core::pose
• add_vec() : protocols::toolbox
• add_vertex() : protocols::forge::methods
• Add_virtual_O2Star_hydrogen() : protocols::swa::rna
• add_virtual_residue_to_cterm() : protocols::relax
• AddAssemblyConstraintsCOP : protocols::domain_assembly
• AddAssemblyConstraintsOP : protocols::domain_assembly
• AddBehaviorRLTCreator_registrator : core
• AddBehaviorRLTOP : core::pack::task::operation
• ADDED_STRUCTURE_AS_INTENDED : protocols::optimize_weights
• ADDED_STRUCTURE_OPPOSITE_AS_INTENDED : protocols::optimize_weights
• AddHydrogenCOP : protocols::ligand_docking
• AddHydrogenOP : protocols::ligand_docking
• AddHydrogensCOP : protocols::ligand_docking
• AddHydrogensOP : protocols::ligand_docking
• AddLigandMotifRotamersCOP : protocols::enzdes
• AddLigandMotifRotamersOP : protocols::enzdes
• AddOrDeleteChoice : protocols::swa::monte_carlo
• AddPyMolObserver() : protocols::moves
• Address : protocols::canonical_sampling::mc_convergence_checks
• AddRigidBodyLigandConfsCOP : protocols::enzdes
• AddRigidBodyLigandConfsOP : protocols::enzdes
• addScoresForLoopParts() : protocols::loops
• AddSearchPatternRotSetOpCOP : protocols::hotspot_hashing
• AddSearchPatternRotSetOpOP : protocols::hotspot_hashing
• AddStatus : protocols::optimize_weights
• ADDUCT : core::chemical
• AdductMap : core::chemical
• AdductOP : core::chemical
• addVirtualResAsRoot() : core::pose
• adjust_des_residues() : protocols::seeded_abinitio
• adjust_mm_to_length() : protocols::seeded_abinitio
• adjust_residues() : protocols::seeded_abinitio
• adjust_single_residues() : protocols::seeded_abinitio
• advance_euler_angles() : protocols::match
• advance_to_neighbor_bin() : protocols::match
• AHO : protocols::antibody2
• alapose() : protocols::kinmatch
• align_naive() : core::sequence
• align_poses() : protocols::swa::rna
• align_poses_naive() : core::sequence
• align_RG() : core::sequence
• Align_RmsdEvaluatorCOP : protocols::comparative_modeling
• Align_RmsdEvaluatorOP : protocols::comparative_modeling
• Align_RotamerEvaluatorCOP : protocols::comparative_modeling
• Align_RotamerEvaluatorOP : protocols::comparative_modeling
• align_to_native() : protocols::antibody2
• AlignerCOP : core::sequence
• AlignerOP : core::sequence
• AlignEvaluatorCOP : protocols::evaluation
• AlignEvaluatorOP : protocols::evaluation
• alignment_from_cmd_line() : protocols::comparative_modeling
• alignment_from_pose() : core::sequence
• alignment_into_pose() : core::sequence
• alignment_probabilities() : protocols::medal
• AlignmentClusterCOP : protocols::comparative_modeling
• AlignmentClusteringCOP : protocols::comparative_modeling
• AlignmentClusteringOP : protocols::comparative_modeling
• AlignmentClusterOP : protocols::comparative_modeling
• alignments_from_cmd_line() : protocols::comparative_modeling
• AlignmentSetCOP : protocols::comparative_modeling
• AlignmentSetOP : protocols::comparative_modeling
• AlignMove : core::sequence
• AlignOption : protocols::hybridization
• AlignPoseToInvrotTreeMoverCOP : protocols::toolbox::match_enzdes_util
• AlignPoseToInvrotTreeMoverOP : protocols::toolbox::match_enzdes_util
• ALL : protocols::sic_dock , protocols::swa::rna
• all_atom_rmsd() : core::scoring
• all_chunks : protocols::hybridization
• ALL_STAGES : protocols::abinitio
• all_stats : protocols::moves
• all_visited() : core::graph
• all_water_weights_iterator : core::scoring::geometric_solvation
• allifnone() : protocols::kinmatch
• allocate_matrix() : protocols::frag_picker::scores
• AllowedSeqposForGeomCstCOP : protocols::toolbox::match_enzdes_util
• AllowedSeqposForGeomCstOP : protocols::toolbox::match_enzdes_util
• AllowInsertOP : protocols::toolbox
• AllowPdbIdFilterCOP : protocols::frag_picker
• AllowPdbIdFilterOP : protocols::frag_picker
• AllResFilterCreator_registrator : core
• ALPHA : core::scoring::dna , core::scoring::rna
• ALREADY_SYMMETRIZED : core::pack::task
• ALWAYS_CLEAR : protocols::forge::components::VLB_VallMemoryUsage
• AmberPeriodicFuncCOP : core::scoring::constraints
• AmberPeriodicFuncOP : core::scoring::constraints
• AmbiguousConstraintCOP : core::scoring::constraints
• AmbiguousConstraintCreator_registrator : core
• AmbiguousConstraintOP : core::scoring::constraints
• AmbiguousMultiConstraintCOP : protocols::constraints_additional
• AmbiguousMultiConstraintOP : protocols::constraints_additional
• AmbiguousNMRConstraintCOP : core::scoring::constraints
• AmbiguousNMRConstraintCreator_registrator : core
• AmbiguousNMRConstraintOP : core::scoring::constraints
• AmbiguousNMRDistanceConstraintCOP : core::scoring::constraints
• AmbiguousNMRDistanceConstraintCreator_registrator : core
• AmbiguousNMRDistanceConstraintOP : core::scoring::constraints
• Analyze_base_bin_map() : protocols::swa::rna
• anchor_num : protocols::protein_interface_design::movers
• ANCHOR_TARGET() : protocols::anchored_design
• AnchorCOP : protocols::anchored_design
• AnchoredDesignMoverOP : protocols::anchored_design
• AnchoredGraftMoverAP : protocols::grafting
• AnchoredGraftMoverCAP : protocols::grafting
• AnchoredGraftMoverCOP : protocols::grafting
• AnchoredGraftMoverOP : protocols::grafting
• AnchoredPerturbMoverOP : protocols::anchored_design
• AnchoredRefineMoverOP : protocols::anchored_design
• AnchorMoversDataCOP : protocols::anchored_design
• AnchorMoversDataOP : protocols::anchored_design
• AnchorOP : protocols::anchored_design
• AND : protocols::filters
• ANDNOT : protocols::filters
• Angle : core
• angle_between() : protocols::rigid
• angle_constraint : core::scoring
• angle_diff() : protocols::MakeRotLib
• angleA : protocols::jumping
• angleB : protocols::jumping
• AngleConstraintCOP : core::scoring::constraints
• AngleConstraintCreator_registrator : core
• AngleConstraintOP : core::scoring::constraints
• angles() : core::scoring::packstat::old , core::scoring , core::scoring::packstat::old
• AngleVector : core::pack::dunbrack
• annotated_atom_graph_from_conformation() : core::conformation
• annotated_to_oneletter_sequence() : core::pose
• AnnotatedFragDataCOP : core::fragment
• AnnotatedFragDataOP : core::fragment
• ANTI : protocols::swa::rna
• AntibodyCDRNameEnum : protocols::antibody2
• AntibodyInfoCOP : protocols::antibody2
• AntibodyInfoOP : protocols::antibody2
• AntibodyModelerCOP : protocols
• AntibodyModelerOP : protocols
• AntibodyModelerProtocolCOP : protocols::antibody2
• AntibodyModelerProtocolOP : protocols::antibody2
• AntibodyNumberingEnum : protocols::antibody2
• any_atoms_within_cutoff() : core::pack::task::operation::util
• AnyResFilterCreator_registrator : core
• APBSConfigAP : core::scoring
• APBSConfigCAP : core::scoring
• APBSConfigCOP : core::scoring
• APBSConfigOP : core::scoring
• APBSResultAP : core::scoring
• APBSResultCAP : core::scoring
• APBSResultCOP : core::scoring
• APBSResultOP : core::scoring
• APBSWrapperAP : core::scoring
• APBSWrapperCAP : core::scoring
• APBSWrapperCOP : core::scoring
• APBSWrapperOP : core::scoring
• APClusterCOP : protocols::cluster
• APClusterOP : protocols::cluster
• append : protocols::simple_moves
• append_automorphic_rmsd() : protocols::ligand_docking
• append_interface_deltas() : protocols::ligand_docking
• append_ligand_grid_scores() : protocols::ligand_docking
• append_ligand_RMSD() : protocols::ligand_docking
• append_ligand_travel() : protocols::ligand_docking
• append_multi_residue_ligand_RMSD() : protocols::ligand_docking
• append_radius_of_gyration() : protocols::ligand_docking
• append_rsd_by_jump_near_atom() : protocols::toolbox::pose_metric_calculators
• AppendRotamerCreator_registrator : core
• AppendRotamerOP : core::pack::task::operation
• AppendRotamerSetCreator_registrator : core
• AppendRotamerSetOP : core::pack::task::operation
• apply_adducts_to_residue() : core::chemical
• apply_best_scoring_fragdata() : core::fragment
• apply_full_to_sub_mapping() : protocols::swa::rna
• apply_ideal_c2endo_sugar_coords() : core::scoring::rna
• apply_ideal_coordinates_for_alternative_pucker() : protocols::simple_moves
• apply_lk_ball_fraction_weight_for_hbonds() : core::scoring::methods
• apply_non_main_chain_sugar_coords() : core::scoring::rna
• apply_protonated_H1_adenosine_variant_type() : protocols::swa::rna
• apply_rotamer() : protocols::swa::rna
• apply_rotate() : protocols::ligand_docking
• apply_sequence_mapping() : protocols::loops
• apply_sub_to_full_mapping() : protocols::swa::rna
• apply_transformation() : protocols::hybridization
• apply_virtual_rna_residue_variant_type() : protocols::swa::rna
• ApplyRandomStoredRBConfCOP : protocols::enzdes
• ApplyRandomStoredRBConfOP : protocols::enzdes
• Arc : core::scoring::packstat
• ArchiveBaseCOP : protocols::jd2::archive
• ArchiveBaseOP : protocols::jd2::archive
• ArchiveManagerAP : protocols::jd2::archive
• ArchiveManagerCAP : protocols::jd2::archive
• ArchiveManagerCOP : protocols::jd2::archive
• ArchiveManagerOP : protocols::jd2::archive
• ArcIter : core::scoring::packstat
• Arcs : core::scoring::packstat
• are_seqs_different() : protocols::vip
• AreaAccumulatorOP : core::scoring::packstat
• argrot_dna_dis2() : protocols::dna
• AroBonds : core::chemical::sdf
• AromaticBond : core::chemical
• Aroop : protocols::antibody2
• as_set() : protocols::medal
• asp_corrections() : protocols::MakeRotLib
• assemble_remark_line() : protocols::toolbox::match_enzdes_util
• AssembleLinkerMoverCOP : protocols::domain_assembly
• AssembleLinkerMoverOP : protocols::domain_assembly
• assert_can_append() : protocols::swa::rna
• assert_can_prepend() : protocols::swa::rna
• assert_phosphate_nomenclature_matches_mini() : protocols::rna
• assign_abase_derivs() : core::scoring::hbonds
• assign_random_continuous_rotamer() : core::pack
• assign_random_rotamers() : core::pack
• assign_ss_dssp() : protocols::jumping
• AssignToClustersMoverCOP : protocols::cluster
• AssignToClustersMoverOP : protocols::cluster
• AsymFoldandDockClaimerAP : protocols::topology_broker
• AsymFoldandDockClaimerCAP : protocols::topology_broker
• AsymFoldandDockClaimerCOP : protocols::topology_broker
• AsymFoldandDockClaimerOP : protocols::topology_broker
• AsymFoldandDockMoveRbJumpMoverCOP : protocols::simple_moves::asym_fold_and_dock
• AsymFoldandDockMoveRbJumpMoverOP : protocols::simple_moves::asym_fold_and_dock
• at() : core::io::serialization
• atom_graph_from_conformation() : core::conformation
• atom_id_from_icoor_line() : core::chemical
• atom_id_to_named_atom_id() : core::pose , core::conformation
• atom_is_acceptor() : protocols::rna
• atom_is_aro() : core::scoring::hackelec
• atom_is_aro2() : core::scoring::hackelec
• atom_is_polar() : protocols::rna
• atom_map_valid_size() : protocols::hybridization
• atom_pair_constraint : core::scoring
• ATOM_RADIUS : core::scoring::sc
• atom_specific_rms() : protocols::motifs
• atom_square_deviation() : protocols::swa::rna
• atom_tracer() : protocols::ligand_docking
• atom_tree_dfunc() : core::optimization::symmetry , core::optimization
• ATOM_TREE_FILE : protocols::jd2::JobInputterInputSource
• atom_tree_get_atompairE_deriv() : core::optimization , core::optimization::symmetry
• AtomAngleSecMatchRPECOP : protocols::match::downstream
• AtomAngleSecMatchRPEOP : protocols::match::downstream
• AtomAP : core::kinematics::tree
• AtomAtomPairFeaturesCOP : protocols::features
• AtomAtomPairFeaturesOP : protocols::features
• AtomBasedConstraintsScoreCOP : protocols::frag_picker::scores
• AtomBasedConstraintsScoreOP : protocols::frag_picker::scores
• AtomCAP : core::kinematics::tree
• AtomChain : core::io::pdb
• AtomCOP : core::kinematics::tree , core::chemical
• AtomCOPs : core::chemical
• AtomDihedralSecMatchRPECOP : protocols::match::downstream
• AtomDihedralSecMatchRPEOP : protocols::match::downstream
• AtomDistanceSecMatchRPECOP : protocols::match::downstream
• AtomDistanceSecMatchRPEOP : protocols::match::downstream
• AtomDOFChangeSet : core::kinematics
• AtomGeometrySecMatchRPECOP : protocols::match::downstream
• AtomGeometrySecMatchRPEOP : protocols::match::downstream
• AtomGraph : core::conformation
• AtomGraphOP : core::conformation
• AtomGrps : protocols::noesy_assign
• AtomID_Mask : core::id
• AtomIndices : core::chemical
• AtomInResidueAtomInResiduePairFeaturesCOP : protocols::features
• AtomInResidueAtomInResiduePairFeaturesOP : protocols::features
• atomitem : core::scoring::rna::chemical_shift
• AtomNeighbors : core::scoring
• AtomOP : core::chemical , core::kinematics::tree
• AtomOPs : core::chemical
• AtomPairConstraintCOP : core::scoring::constraints
• AtomPairConstraintCreator_registrator : core
• AtomPairConstraintOP : core::scoring::constraints
• AtomPairConstraintsDataCOP : protocols::frag_picker::scores
• AtomPairConstraintsDataOP : protocols::frag_picker::scores
• AtomPairConstraintsScoreCOP : protocols::frag_picker::scores
• AtomPairConstraintsScoreOP : protocols::frag_picker::scores
• AtomPairEnergyTable : core::scoring
• AtomPairFuncListCOP : core::scoring::custom_pair_distance
• AtomPairFuncListOP : core::scoring::custom_pair_distance
• AtomPointer1D : core::kinematics
• AtomPointer2D : core::kinematics
• Atoms : core::conformation
• atoms_interact() : core::scoring::methods
• AtomTreeAP : core::kinematics
• AtomTreeCAP : core::kinematics
• AtomTreeCollectionCOP : core::pack::scmin
• AtomTreeCollectionOP : core::pack::scmin
• AtomTreeCOP : core::kinematics
• AtomTreeDiffCOP : core::import_pose::atom_tree_diffs
• AtomTreeDiffJobInputterOP : protocols::jd2
• AtomTreeDiffJobOutputterCOP : protocols::jd2
• AtomTreeDiffJobOutputterOP : protocols::jd2
• AtomTreeDiffOP : core::import_pose::atom_tree_diffs
• AtomTreeMinimizerCOP : core::optimization
• AtomTreeMinimizerOP : core::optimization
• AtomTreeOP : core::kinematics
• AtomTreeSCMinMinimizerMapCOP : core::pack::scmin
• AtomTreeSCMinMinimizerMapOP : core::pack::scmin
• AtomTypeDatabaseIOCOP : core::chemical
• AtomTypeIndex : core::chemical
• AtomTypeSetAP : core::chemical
• AtomTypeSetCAP : core::chemical
• AtomTypeSetOP : core::chemical
• AtomTypesFeaturesCOP : protocols::features
• AtomTypesFeaturesOP : protocols::features
• AtomVDWCOP : core::scoring
• AtomVDWOP : core::scoring
• attach_debugger() : protocols::optimize_weights
• ATTEN_2 : core::scoring::sc
• ATTEN_6 : core::scoring::sc
• ATTEN_BLOCKER : core::scoring::sc
• ATTEN_BURIED_FLAGGED : core::scoring::sc
• AUTOMATIC : core::conformation
• automorphic_rmsd() : core::scoring
• AutomorphismIteratorCOP : core::chemical
• AutomorphismIteratorOP : core::chemical
• AverageDegreeCountFilterCOP : protocols::protein_interface_design::filters
• AverageDegreeCountFilterOP : protocols::protein_interface_design::filters
• AverageDegreeFilterCOP : protocols::protein_interface_design::filters
• AverageDegreeFilterOP : protocols::protein_interface_design::filters
• avg_ca_position() : protocols::nonlocal
• avg_cluster_cen_dist() : protocols::MakeRotLib