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

- a -

• a() : core::pose::motif
• A : protocols::comparative_modeling::features , protocols::features
• A3B_HBS_POST : core::chemical
• A3B_HBS_PRE : core::chemical
• A3BHbsMoverCOP : protocols::simple_moves::a3b_hbs
• A3BHbsMoverOP : protocols::simple_moves::a3b_hbs
• A3BHbsPatcherCOP : protocols::simple_moves::a3b_hbs
• A3BHbsPatcherOP : protocols::simple_moves::a3b_hbs
• A3BHbsRandomSmallMoverCOP : protocols::simple_moves::a3b_hbs
• A3BHbsRandomSmallMoverOP : protocols::simple_moves::a3b_hbs
• A_MINOR : core::scoring::rna
• AA : core::chemical , core::enzymes
• aa : protocols::cluster::calibur
• AA : protocols::optimize_weights
• aa2idx() : core::energy_methods
• aa2name() : core::chemical
• aa2oneletter() : core::chemical
• aa2randomCodon() : core::chemical::NucleotideTools
• aa_ala : core::chemical
• aa_arg : core::chemical
• aa_asn : core::chemical
• aa_asp : core::chemical
• aa_b3a : core::chemical
• aa_b3c : core::chemical
• aa_b3cisACHC : core::chemical
• aa_b3cisACPC : core::chemical
• aa_b3d : core::chemical
• aa_b3e : core::chemical
• aa_b3f : core::chemical
• aa_b3g : core::chemical
• aa_b3h : core::chemical
• aa_b3i : core::chemical
• aa_b3k : core::chemical
• aa_b3l : core::chemical
• aa_b3m : core::chemical
• aa_b3n : core::chemical
• aa_b3p : core::chemical
• aa_b3q : core::chemical
• aa_b3r : core::chemical
• aa_b3s : core::chemical
• aa_b3t : core::chemical
• aa_b3transACPC : core::chemical
• aa_b3v : core::chemical
• aa_b3w : core::chemical
• aa_b3y : core::chemical
• aa_cmp : core::scoring
• aa_composition : core::scoring
• aa_cys : core::chemical
• aa_dal : core::chemical
• aa_dan : core::chemical
• aa_dar : core::chemical
• aa_das : core::chemical
• aa_dcs : core::chemical
• aa_dgn : core::chemical
• aa_dgu : core::chemical
• aa_dhi : core::chemical
• aa_dil : core::chemical
• aa_dle : core::chemical
• aa_dly : core::chemical
• aa_dme : core::chemical
• aa_dph : core::chemical
• aa_dpr : core::chemical
• aa_dse : core::chemical
• aa_dth : core::chemical
• aa_dtr : core::chemical
• aa_dty : core::chemical
• aa_dva : core::chemical
• aa_from_name() : core::chemical
• aa_from_one_or_three() : core::chemical
• aa_from_oneletter_code() : core::chemical
• aa_gln : core::chemical
• aa_glu : core::chemical
• aa_gly : core::chemical
• aa_h2o : core::chemical
• aa_his : core::chemical
• aa_ile : core::chemical
• aa_leu : core::chemical
• aa_lys : core::chemical
• aa_met : core::chemical
• aa_none : core::chemical
• aa_phe : core::chemical
• aa_pro : core::chemical
• aa_repeat : core::scoring
• aa_ser : core::chemical
• aa_thr : core::chemical
• aa_trp : core::chemical
• aa_trustworthiness() : core::scoring::motif
• aa_tyr : core::chemical
• aa_unk : core::chemical
• aa_unp : core::chemical
• aa_val : core::chemical
• AA_VariantsExceptions : core::chemical
• aa_vrt : core::chemical
• AACompositionConstraintCOP : core::scoring::aa_composition_energy
• AACompositionConstraintOP : core::scoring::aa_composition_energy
• AACompositionEnergyCreator_registrator : core::init
• AACompositionEnergyOP : core::energy_methods
• AACompositionEnergySetupCOP : core::scoring::aa_composition_energy
• AACompositionEnergySetupOP : core::scoring::aa_composition_energy
• AACompositionPropertiesSetCOP : core::scoring::aa_composition_energy
• AACompositionPropertiesSetOP : core::scoring::aa_composition_energy
• AAFrequencyCOP : protocols::denovo_design::task_operations
• AAFrequencyOP : protocols::denovo_design::task_operations
• AAMatrixCOP : protocols::mean_field
• AAMatrixOP : protocols::mean_field
• AAProbabilities : protocols::antibody , protocols::task_operations
• AARepeatEnergyCreator_registrator : core::init
• AARepeatEnergyOP : core::energy_methods
• Ab_TemplateInfoCOP : protocols::antibody
• Ab_TemplateInfoOP : protocols::antibody
• abego : core::scoring
• Abego : protocols::denovo_design::architects
• abego2secstruct : protocols::denovo_design::components
• abego3aa_to_index() : core::scoring
• ABEGO_index : core::scoring
• abego_index() : protocols::frag_picker::quota
• ABEGO_index_A : core::scoring
• ABEGO_index_B : core::scoring
• ABEGO_index_COUNT : core::scoring
• ABEGO_index_E : core::scoring
• ABEGO_index_G : core::scoring
• ABEGO_index_INVALID : core::scoring
• ABEGO_index_O : core::scoring
• ABEGO_index_START : core::scoring
• 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
• abego_str() : protocols::denovo_design
• abego_to_index() : core::scoring
• abego_vector() : protocols::denovo_design
• AbegoCOP : core::energy_methods
• AbegoEnergyCreator_registrator : core::init
• 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::sequence
• ABEGOManagerOP : core::sequence
• AbegoOP : core::energy_methods
• AbinitioMoverWeightAP : protocols::topology_broker::weights
• AbinitioMoverWeightCAP : protocols::topology_broker::weights
• AbinitioMoverWeightCOP : protocols::topology_broker::weights
• AbinitioMoverWeightOP : protocols::topology_broker::weights
• ABOVE : core::chemical::rna
• above : core::sequence
• AbrelaxMoverCOP : protocols::abinitio
• AbrelaxMoverOP : protocols::abinitio
• ABS : protocols::calc_taskop_filters
• AbscriptLoopCloserCMCOP : protocols::abinitio::abscript
• AbscriptLoopCloserCMOP : protocols::abinitio::abscript
• AbscriptMoverCOP : protocols::abinitio::abscript
• AbscriptMoverOP : protocols::abinitio::abscript
• AbscriptStageMoverCOP : protocols::abinitio::abscript
• AbscriptStageMoverOP : protocols::abinitio::abscript
• absfpart() : protocols::cryst
• absolute_vec() : protocols::features::strand_assembly
• AbstractArchiveBaseCOP : protocols::jd2::archive
• AbstractArchiveBaseOP : protocols::jd2::archive
• AbstractRotamerTrieCOP : core::conformation
• AbstractRotamerTrieOP : core::conformation
• Ac : core::chemical::element
• accept : protocols::hotspot_hashing
• accept_reject : protocols::moves
• AcceptanceCheckCOP : protocols::loop_modeling::utilities
• AcceptanceCheckOP : protocols::loop_modeling::utilities
• ACCEPTED : protocols::monte_carlo
• AcceptorAtomEIter : core::chemical
• AcceptorAtomGraph : core::chemical
• AcceptorAtomVIter : core::chemical
• AcceptorAtomVIterPair : core::chemical
• AcceptToBestMoverCOP : protocols::relax
• AcceptToBestMoverOP : protocols::relax
• accumulate_bur_rotamer_oversats() : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty
• accumulate_seqpos_oversats() : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty
• AccumulatorOP : core::scoring::packstat
• ACETYL_SUGAR : core::chemical
• ACETYLAMINO_SUGAR : core::chemical
• ACETYLATED_NTERMINUS : core::chemical
• ACETYLATED_NTERMINUS_VARIANT : core::chemical
• ACETYLATION : core::chemical
• ACHIRAL_BACKBONE : core::chemical
• ACHIRAL_SIDECHAIN : core::chemical
• activate_dof_deriv_terms_for_cart_min() : core::optimization
• ActiveSiteGridCOP : protocols::match::downstream
• ActiveSiteGridOP : protocols::match::downstream
• AdaptiveScoreHistogramCOP : protocols::frag_picker::scores
• AdaptiveScoreHistogramOP : protocols::frag_picker::scores
• add() : protocols::mean_field
• ADD : protocols::stepwise::monte_carlo::mover
• add_a3b_hbs_constraint() : core::pose::ncbb
• add_another_virtual_res() : protocols::toolbox::sample_around
• add_anti_chi_constraints() : core::pose::rna
• add_atom() : core::kinematics
• add_atom_type_set_parameters_from_command_line() : core::chemical
• add_atom_types_from_command_line() : core::chemical
• add_attributes_for_common_options() : protocols::ncbb
• add_attributes_for_helix_params() : protocols::helical_bundle
• add_attributes_for_make_bundle_minorhelix_defaults() : protocols::helical_bundle
• add_attributes_for_make_bundle_other_defaults() : protocols::helical_bundle
• add_attributes_for_make_bundle_symmetry() : protocols::helical_bundle
• add_attributes_for_minor_helix_params() : protocols::helical_bundle
• add_attributes_for_other_helix_params() : protocols::helical_bundle
• ADD_BATCH : protocols::jd2::archive
• add_bckg() : core::scoring::epr_deer
• add_block_stack_variants() : core::import_pose
• add_bond_information() : core::io::mmtf
• add_bonds_to_sd() : core::io::mmtf
• add_chain_from_pose() : protocols::denovo_design
• add_chainbreaks_according_to_jumps() : protocols::toolbox::pose_manipulation
• add_chi_constraints() : core::pose::rna
• add_claims_from_file() : protocols::topology_broker
• add_claims_from_stream() : protocols::topology_broker
• add_clashes_to_shell() : core::pack::task::residue_selector
• add_cluster_comments_to_pose() : protocols::antibody::clusters
• 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() : protocols::hybridization
• 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_constraints_to_metal() : core::util
• add_coordinate_constraint_func_atoms() : protocols::relax
• add_coordinate_constraints() : core::scoring::constraints , protocols::protein_interface_design::movers , protocols::seeded_abinitio
• add_coordinate_constraints_to_pose() : protocols::loops , protocols::relax
• add_covalent_linkage() : core::util
• add_covalent_linkage_helper() : core::util
• add_covalent_linkages_to_metal() : core::util
• add_current_job_data_to_ss() : protocols::jd2
• add_custom_variant_type_to_pose_residue() : core::pose
• add_cutpoint_closed() : core::import_pose
• add_cutpoint_variants() : protocols::forge::methods , protocols::loops
• add_cutpoint_variants_for_ccd() : protocols::grafting
• add_cutpoints() : protocols::denovo_design
• add_daemon : protocols::pack_daemon
• add_dens_scores_from_cmdline_to_scorefxn() : core::scoring::electron_density
• add_dist_constraints() : protocols::seeded_abinitio
• ADD_EDGE : protocols::legacy_sewing
• add_edges() : protocols::forge::methods
• add_extra_bodies() : protocols::chemically_conjugated_docking
• add_extra_data() : core::io::mmtf
• 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_fade_chain_break_constraint_across_gap() : protocols::stepwise::modeler::rna
• add_generic_hbs_constraint() : core::pose::ncbb
• add_glycan_links_to_map() : core::io
• add_harmonic_chain_break_constraint() : protocols::stepwise::modeler::rna
• add_harmonic_dihedral_cst_general() : protocols::antibody::constraints
• add_hbs_constraint() : core::pose::ncbb
• add_hydrogen_tracer() : protocols::ligand_docking
• add_hydrogens_tracer() : protocols::ligand_docking
• add_if_not_empty() : core::io::mmtf
• add_init_dev_penalty() : protocols::mpi_refinement
• add_job_data_to_ss() : protocols::jd2
• add_ligand_conditionally() : protocols::ligand_docking
• add_link_and_ss_information() : core::io::mmtf
• add_linker_segments() : protocols::legacy_sewing
• add_loop() : protocols::loops
• add_loop_flank_residues_bb_to_movemap() : protocols::loops
• ADD_LOOP_RES : protocols::stepwise::monte_carlo::mover
• add_loops_from_bool_vector() : protocols::antibody::design
• add_lower_terminus_type_to_conformation_residue() : core::conformation
• add_lower_terminus_type_to_pose_residue() : core::pose
• add_mm_atom_type_set_parameters_from_command_line() : core::chemical
• add_monte_carlo_viewer() : protocols::viewer
• add_motif_bb_constraints() : protocols::motifs
• add_motif_sc_constraints() : protocols::motifs
• add_movemap_from_loopres() : protocols::mpi_refinement
• add_mutant_to_vectors() : protocols::relax::membrane
• add_network_resids_to_pose() : protocols::hbnet
• ADD_NEW : protocols::enzdes
• add_new_sequence_into_global_sequence() : core::pose::full_model_info
• add_non_protein_cst() : protocols::hybridization
• add_num_neighbors() : protocols::legacy_sewing
• add_number_base_pairs() : core::pose::rna
• add_number_native_base_pairs() : core::pose::rna
• add_oop_constraint() : core::pose::ncbb
• add_overlap_to_loops() : protocols::denovo_design::movers
• add_paired_residues() : protocols::denovo_design::components
• add_per_residue_simple_metric_schema() : core::simple_metrics
• add_poseinfo_to_ss() : protocols::mpi_refinement
• ADD_PREGENERATED : protocols::enzdes
• add_relevant_restypes_to_subset() : protocols::toolbox::match_enzdes_util
• add_remark() : protocols::denovo_design
• add_residue_selectors_to_datamap() : protocols::jd3
• add_residues_to_pose() : protocols::denovo_design
• add_reslabels_to_pose() : protocols::hbnet
• add_rna_chi_rotamers() : core::pack::rotamer_set
• add_rotamers_to_pose() : core::pack::interaction_graph
• add_score_line_string() : core::pose
• add_segment() : protocols::denovo_design::components
• add_segments_for_chain() : protocols::denovo_design::components
• add_shell() : core::membrane
• add_single_cutpoint_variant() : protocols::loops
• add_single_magnesium() : protocols::magnesium
• add_strand_pairs_cst() : protocols::hybridization
• add_string_real_pair_to_current_job() : protocols::jd2
• add_string_string_pair_to_current_job() : protocols::jd2
• add_string_to_current_job() : protocols::jd2
• add_strings_to_current_job() : protocols::jd2
• add_subelement_for_constraint_combination() : protocols::toolbox::match_enzdes_util
• add_subelement_for_parse_stub_sets() : protocols::protein_interface_design::movers
• ADD_SUBMOTIF : protocols::stepwise::monte_carlo::mover
• add_syn_anti_chi_constraints() : core::pose::rna
• add_syn_chi_constraints() : core::pose::rna
• add_terminus_variants() : protocols::denovo_design::components
• add_ters_via_bonds() : core::io::mmtf
• add_these() : protocols::stepwise::modeler
• add_to_individual_sol_energies() : core::energy_methods
• add_to_list() : protocols::denovo_design
• add_to_map() : core::scoring::epr_deer
• add_to_multimodel_pdb() : core::io::pdb
• add_to_onebody() : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty
• add_to_pose() : protocols::denovo_design::components
• add_to_pose_list() : protocols::stepwise::modeler
• add_to_twobody() : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty
• add_triazole_constraint() : core::pose::ncbb
• add_upper_terminus_type_to_conformation_residue() : core::conformation
• add_upper_terminus_type_to_pose_residue() : core::pose
• add_vall_cheating_fragments() : protocols::frags
• add_vall_fragments() : protocols::frags
• add_values_from_center() : core::chemical::rna
• add_variant() : protocols::environment
• 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_O2Prime_hydrogen() : core::pose::rna
• add_virtual_res() : protocols::toolbox::sample_around
• add_virtual_residue_to_cterm() : protocols::relax
• add_virtual_sugar_res() : core::import_pose
• add_water_overcoordinated_hb_score() : protocols::hydrate
• add_whitespaces() : core::scoring::rna::chemical_shift
• add_xbond_information() : core::io::mmtf
• AddAssemblyConstraintsCOP : protocols::domain_assembly
• AddAssemblyConstraintsOP : protocols::domain_assembly
• AddBehaviorRLTCreator_registrator : core::init
• AddBehaviorRLTOP : core::pack::task::operation
• AddCDRProfileSetsOperationCOP : protocols::antibody::task_operations
• AddCDRProfileSetsOperationOP : protocols::antibody::task_operations
• AddCDRProfilesOperationCOP : protocols::antibody::task_operations
• AddCDRProfilesOperationOP : protocols::antibody::task_operations
• AddChainMoverCOP : protocols::simple_moves
• AddChainMoverOP : protocols::simple_moves
• AddCompositionConstraintMoverCOP : protocols::aa_composition
• AddCompositionConstraintMoverOP : protocols::aa_composition
• AddConstraintsCOP : protocols::constraint_generator
• AddConstraintsOP : protocols::constraint_generator
• ADDED_STRUCTURE_AS_INTENDED : protocols::optimize_weights
• ADDED_STRUCTURE_OPPOSITE_AS_INTENDED : protocols::optimize_weights
• AddGood2BPairEnergyRotamersCOP : protocols::toolbox::rotamer_set_operations
• AddGood2BPairEnergyRotamersOP : protocols::toolbox::rotamer_set_operations
• AddHelixSequenceConstraintsMoverCOP : protocols::aa_composition
• AddHelixSequenceConstraintsMoverOP : protocols::aa_composition
• AddHydrogenCOP : protocols::ligand_docking
• AddHydrogenOP : protocols::ligand_docking
• AddHydrogensCOP : protocols::ligand_docking
• AddHydrogensOP : protocols::ligand_docking
• AddJobPairDataCOP : protocols::simple_moves
• AddJobPairDataOP : protocols::simple_moves
• AddLigandMotifRotamersCOP : protocols::enzdes
• AddLigandMotifRotamersOP : protocols::enzdes
• AddMembraneMoverCOP : protocols::membrane
• AddMembraneMoverOP : protocols::membrane
• AddMembraneSpanConstraintCOP : protocols::membrane
• AddMembraneSpanConstraintOP : protocols::membrane
• AddMembraneSpanTermZConstraintCOP : protocols::membrane
• AddMembraneSpanTermZConstraintOP : protocols::membrane
• AddMHCEpitopeConstraintMoverCOP : protocols::aa_composition
• AddMHCEpitopeConstraintMoverOP : protocols::aa_composition
• AddMoverCreatorCOP : protocols::stepwise::monte_carlo::mover
• AddMoverCreatorOP : protocols::stepwise::monte_carlo::mover
• AddMoverOP : protocols::stepwise::monte_carlo::mover
• AddMPLigandMoverCOP : protocols::membrane
• AddMPLigandMoverOP : protocols::membrane
• AddNetChargeConstraintMoverCOP : protocols::aa_composition
• AddNetChargeConstraintMoverOP : protocols::aa_composition
• AddOrDeleteMoverOP : protocols::stepwise::monte_carlo::mover
• AddPDBInfoMoverCOP : protocols::simple_moves
• AddPDBInfoMoverOP : protocols::simple_moves
• AddPyMOLObserver() : protocols::moves
• AddPyMOLObserver_to_conformation() : protocols::moves
• AddPyMOLObserver_to_energies() : protocols::moves
• AddResidueLabelMoverCOP : protocols::simple_moves
• AddResidueLabelMoverOP : protocols::simple_moves
• AddResidueTensorConstraintOP : protocols::simple_moves
• Address : protocols::canonical_sampling::mc_convergence_checks
• AddRigidBodyLigandConfsCOP : protocols::enzdes
• AddRigidBodyLigandConfsOP : protocols::enzdes
• AddSapConstraintMoverCOP : protocols::simple_moves
• AddSapConstraintMoverOP : protocols::simple_moves
• AddSapMathConstraintMoverCOP : protocols::simple_moves
• AddSapMathConstraintMoverOP : protocols::simple_moves
• addScoresForLoopParts() : protocols::loops
• AddSearchPatternRotSetOpCOP : protocols::hotspot_hashing
• AddSearchPatternRotSetOpOP : protocols::hotspot_hashing
• AddSegmentDataMoverCOP : protocols::denovo_design::movers
• AddSegmentDataMoverOP : protocols::denovo_design::movers
• AddStatus : protocols::optimize_weights
• ADDUCT : core::chemical
• ADDUCT_VARIANT : core::chemical
• AdductMap : core::chemical
• AdductOP : core::chemical
• AddUIObserver() : protocols::network
• AddUIObserver_to_conformation() : protocols::network
• AddUIObserver_to_energies() : protocols::network
• addVirtualResAsRoot() : core::pose
• AddZincSiteConstraintsCOP : protocols::metal_interface
• AddZincSiteConstraintsOP : protocols::metal_interface
• ADJ_LIST_MODE : protocols::cluster::calibur
• AdjacentIter : core::chemical
• AdjacentIterPair : core::chemical
• AdjacentListOP : protocols::cluster::calibur
• AdjacentRemainingNodes() : protocols::toolbox
• 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_past_virtual_residues() : protocols::denovo_design::components
• advance_to_neighbor_bin() : protocols::match
• Ag : core::chemical::element
• AHO_Scheme : protocols::antibody
• aiChain : core::io::mmtf
• AIDs : core::pose::motif
• aiGroup : core::io::mmtf
• aiModels : core::io::mmtf
• aiModels_from_sfrs() : core::io::mmtf
• aiPose : core::io::mmtf
• aiPose_from_sfr() : core::io::mmtf
• AIVD : core::io::pose_from_sfr
• Al : core::chemical::element
• alapose() : protocols::kinmatch
• ALDONIC_ACID : core::chemical
• ALDONIC_ACID_VARIANT : core::chemical
• ALDOSE : core::chemical
• AliasMap : protocols::denovo_design::components
• align_mainchain_atoms() : protocols::helical_bundle
• align_mainchain_atoms_of_residue_range() : protocols::helical_bundle
• align_motif_pose() : core::scoring::motif
• align_motif_pose_break() : core::scoring::motif
• align_motif_pose_by_one_frame() : core::scoring::motif
• align_motif_pose_NCAC_super() : core::scoring::motif
• align_motif_pose_super() : core::scoring::motif
• align_naive() : core::sequence
• align_pose_and_add_rmsd_constraints() : protocols::stepwise::modeler::align
• align_poses() : protocols::stepwise::modeler::rna
• align_poses_naive() : core::sequence
• ALIGN_RMSD : protocols::stepwise::screener
• Align_RmsdEvaluatorCOP : protocols::comparative_modeling
• Align_RmsdEvaluatorOP : protocols::comparative_modeling
• Align_RotamerEvaluatorCOP : protocols::comparative_modeling
• Align_RotamerEvaluatorOP : protocols::comparative_modeling
• align_to_native() : protocols::antibody
• align_virtual_atoms_in_carbohydrate_residue() : core::conformation::carbohydrates , core::pose::carbohydrates
• alignaxis() : protocols::matdes , protocols::sic_dock
• alignaxis_xform() : protocols::sic_dock
• AlignByResidueSelectorMoverCOP : protocols::fold_from_loops::movers
• AlignByResidueSelectorMoverOP : protocols::fold_from_loops::movers
• AlignChainMoverCOP : protocols::simple_moves
• AlignChainMoverOP : protocols::simple_moves
• AlignedThreadOperationCOP : protocols::task_operations
• AlignedThreadOperationOP : protocols::task_operations
• AlignEndsMoverCOP : protocols::splice
• AlignEndsMoverOP : protocols::splice
• AlignerCOP : core::sequence
• AlignerOP : core::sequence
• AlignEvaluatorCOP : protocols::evaluation
• AlignEvaluatorOP : protocols::evaluation
• alignment : core::scoring
• ALIGNMENT_ANCHOR_RES : core::pose::full_model_info
• 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
• AlignmentEnergyCOP : protocols::rna
• AlignmentEnergyOP : protocols::rna
• AlignmentFGMSettingsOP : protocols::sewing::hashing
• AlignmentFileGeneratorMoverCOP : protocols::sewing::hashing
• AlignmentFileGeneratorMoverOP : protocols::sewing::hashing
• AlignmentGeneratorCOP : protocols::sewing::hashing
• AlignmentGeneratorOP : protocols::sewing::hashing
• alignments_from_cmd_line() : protocols::comparative_modeling
• AlignmentSetCOP : protocols::comparative_modeling
• AlignmentSetOP : protocols::comparative_modeling
• AlignMove : core::sequence
• AlignOption : protocols::hybridization
• AlignPDBInfoToSequences_namer() : protocols::pdbinfo_manipulations
• AlignPDBInfoToSequencesCOP : protocols::pdbinfo_manipulations
• AlignPDBInfoToSequencesMode : protocols::pdbinfo_manipulations
• alignpdbinfotosequencesmode_to_string() : protocols::pdbinfo_manipulations
• AlignPDBInfoToSequencesOP : protocols::pdbinfo_manipulations
• AlignPoseToInvrotTreeMoverCOP : protocols::toolbox::match_enzdes_util
• AlignPoseToInvrotTreeMoverOP : protocols::toolbox::match_enzdes_util
• AlignResiduesMoverCOP : protocols::denovo_design::movers
• AlignResiduesMoverOP : protocols::denovo_design::movers
• AlignRMSD_ScreenerCOP : protocols::stepwise::screener
• AlignRMSD_ScreenerOP : protocols::stepwise::screener
• ALIPHATIC : core::chemical , core::chemical::rings
• all_atom_center() : core::conformation , core::pose
• all_atom_rmsd() : core::scoring
• all_atom_rmsd_nosuper() : core::scoring
• all_chunks : protocols::hybridization
• ALL_DNA_TYPES_ON : core::pack::palette
• all_false_selection() : core::select::residue_selector
• all_pose_residues() : protocols::rna::movers
• ALL_SASA : core::scoring::sasa
• all_scatom_rmsd_nosuper() : core::scoring
• ALL_STAGES : protocols::abinitio
• all_stats : protocols::moves
• all_true_selection() : core::select::residue_selector
• all_water_weights_iterator : core::energy_methods
• AllBB : protocols::canonical_sampling
• AllChi : protocols::canonical_sampling
• allifnone() : protocols::kinmatch
• allocate_matrix() : protocols::frag_picker::scores
• ALLOW_ALTERNATE_BACKBONE_MATCHING : core::pack::palette
• AllowedSeqposForGeomCstCOP : protocols::toolbox::match_enzdes_util
• AllowedSeqposForGeomCstOP : protocols::toolbox::match_enzdes_util
• AllowedStrandBulges : protocols::denovo_design::architects
• AllowedStrandExtended : protocols::denovo_design::architects
• AllowPdbIdFilterCOP : protocols::frag_picker
• AllowPdbIdFilterOP : protocols::frag_picker
• AllResFilterCreator_registrator : core::init
• ALPHA : core::chemical::rna , core::scoring::dna
• ALPHA6_LINKS : core::scoring::carbohydrates
• ALPHA_AA : core::chemical
• alpha_aa_rama_check : protocols::generalized_kinematic_closure::filter
• ALPHA_ATOM : core::chemical
• alpha_deriv_func() : core::scoring::fiber_diffraction
• alpha_func() : core::scoring::fiber_diffraction
• ALPHA_LINKS : core::scoring::carbohydrates
• ALPHA_SUGAR : core::chemical
• ALREADY_SYMMETRIZED : core::pack::task
• AltCodeMap : core::io
• ALTERNATIVE_PROTONATION : core::chemical
• ALWAYS_CLEAR : protocols::forge::components::VLB_VallMemoryUsage
• Am : core::chemical::element
• AmberPeriodicFuncCOP : core::scoring::func
• AmberPeriodicFuncOP : core::scoring::func
• ambiguous_constraint_wrap() : protocols::constraint_generator
• AmbiguousConstraintCOP : core::scoring::constraints
• AmbiguousConstraintCreator_registrator : core::init
• AmbiguousConstraintOP : core::scoring::constraints
• AmbiguousMultiConstraintCOP : protocols::constraints_additional
• AmbiguousMultiConstraintOP : protocols::constraints_additional
• AmbiguousNMRConstraintCOP : core::scoring::constraints
• AmbiguousNMRConstraintCreator_registrator : core::init
• AmbiguousNMRConstraintOP : core::scoring::constraints
• AmbiguousNMRDistanceConstraintCOP : core::scoring::constraints
• AmbiguousNMRDistanceConstraintCreator_registrator : core::init
• AmbiguousNMRDistanceConstraintOP : core::scoring::constraints
• AMINO_SUGAR : core::chemical
• AnalyticEtableEvaluatorOP : core::scoring::etable
• analyze_base_bin_map() : protocols::stepwise::modeler::rna::rigid_body
• analyze_for_homology() : core::fragment::rna
• AnalyzeLoopModelingCOP : protocols::pose_length_moves
• AnalyzeLoopModelingOP : protocols::pose_length_moves
• anc_grandparent : core::chemical
• anc_greatgrandparent : core::chemical
• anc_parent : core::chemical
• Ancestor : core::chemical
• anchor_num : protocols::protein_interface_design::movers
• ANCHOR_SUGAR : protocols::stepwise::screener
• 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
• AnchorSugarScreenerCOP : protocols::stepwise::screener
• AnchorSugarScreenerOP : protocols::stepwise::screener
• AND : protocols::filters , protocols::task_operations
• AND_combine() : core::select::residue_selector
• and_logic : core::select::residue_selector
• AndJumpSelectorCOP : core::select::jump_selector
• AndJumpSelectorOP : core::select::jump_selector
• ANDNOT : protocols::filters , protocols::task_operations
• AndResidueSelectorCOP : core::select::residue_selector
• AndResidueSelectorOP : core::select::residue_selector
• ang_delta() : protocols::environment , protocols::loops::loop_mover
• Angle : core
• angle_between() : protocols::rigid
• angle_constraint : core::scoring
• angle_cpy() : protocols::abinitio::abscript
• angle_diff() : protocols::abinitio::abscript
• angle_distance() : core::scoring::motif
• angleA : protocols::jumping
• angleB : protocols::jumping
• AngleConstraintCOP : core::scoring::constraints
• AngleConstraintCreator_registrator : core::init
• AngleConstraintOP : core::scoring::constraints
• angles() : core::scoring , core::scoring::packstat::old , core::scoring::sasa
• AngleToVectorCOP : protocols::simple_filters
• AngleToVectorOP : protocols::simple_filters
• AngleVector : core::pack::dunbrack
• ANISOU : core::io::pdb
• AnnealableGraphBaseCOP : core::pack::interaction_graph
• AnnealableGraphBaseOP : core::pack::interaction_graph
• AnnealerObserverCOP : core::pack::annealer
• AnnealerObserverOP : core::pack::annealer
• annotate_backbone() : core::chemical
• annotated_atom_graph_from_conformation() : core::conformation
• annotated_to_oneletter_sequence() : core::pose
• AnnotatedFragDataCOP : core::fragment
• AnnotatedFragDataOP : core::fragment
• Annotation : core::io::rna
• ANTI : core::chemical::rna , core::fragment::rna , core::scoring::carbohydrates
• antibody_grafting_usable() : protocols::antibody::grafting
• AntibodyCDRGraftDesignOptions : protocols::antibody::design
• AntibodyCDRGrafterCOP : protocols::antibody
• AntibodyCDRGrafterOP : protocols::antibody
• AntibodyCDRSeqDesignOptions : protocols::antibody::design
• AntibodyCDRSetOptions : protocols::antibody
• AntibodyDatabaseManagerCOP : protocols::antibody
• AntibodyDatabaseManagerOP : protocols::antibody
• AntibodyDesignEnumManagerCOP : protocols::antibody::design
• AntibodyDesignEnumManagerOP : protocols::antibody::design
• AntibodyDesignMoverCOP : protocols::antibody::design
• AntibodyDesignMoverOP : protocols::antibody::design
• AntibodyDesignProtocolEnum : protocols::antibody::design
• AntibodyEnumManagerCOP : protocols::antibody
• AntibodyEnumManagerOP : protocols::antibody
• AntibodyFeaturesCOP : protocols::antibody
• AntibodyFeaturesOP : protocols::antibody
• AntibodyInfoAP : protocols::antibody
• AntibodyInfoCAP : protocols::antibody
• AntibodyInfoCOP : protocols::antibody
• AntibodyInfoOP : protocols::antibody
• AntibodyModelerCOP : protocols
• AntibodyModelerOP : protocols
• AntibodyModelerProtocolCOP : protocols::antibody
• AntibodyModelerProtocolOP : protocols::antibody
• AntibodyNumberingConverterMoverCOP : protocols::antibody
• AntibodyNumberingConverterMoverOP : protocols::antibody
• AntibodyNumberingParserCOP : protocols::antibody
• AntibodyNumberingParserOP : protocols::antibody
• AntibodyNumberingSchemeEnum : protocols::antibody
• AntibodyNumberingSchemeEnum_start : protocols::antibody
• AntibodyNumberingSchemeEnum_total : protocols::antibody
• AntibodyRegionEnum : protocols::antibody
• AntibodyRegionEnum_start : protocols::antibody
• AntibodyRegionEnum_total : protocols::antibody
• AntibodyRegionSelectorCOP : protocols::antibody::residue_selector
• AntibodyRegionSelectorOP : protocols::antibody::residue_selector
• AntibodySeqDesignTFCreatorCOP : protocols::antibody::design
• AntibodySeqDesignTFCreatorOP : protocols::antibody::design
• antigen_region : protocols::antibody
• ANTIPARALLEL : core::chemical::rna
• ANY : core::fragment::rna , protocols::toolbox
• any_atoms_within_cutoff() : core::select::util
• ANY_BASE_DOUBLET_ORIENTATION : core::chemical::rna
• ANY_BASE_EDGE : core::chemical::rna
• ANY_BASE_STACK_SIDE : core::chemical::rna
• ANY_CHI : core::chemical::rna
• ANY_LW_BASE_DOUBLET_ORIENTATION : core::chemical::rna
• ANY_PUCKER : core::chemical::rna
• ANY_TORSION : core::chemical::rna
• AnyResFilterCreator_registrator : core::init
• 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
• APolarHydrogenEIter : core::chemical
• APolarHydrogenGraph : core::chemical
• APolarHydrogenVIter : core::chemical
• APolarHydrogenVIterPair : core::chemical
• append_fold_tree_to_file() : protocols::backrub
• append_mg_bound_water() : protocols::magnesium
• append_new_chain_from_template_segment() : protocols::denovo_design::components
• append_new_residues() : protocols::denovo_design::components
• append_pose_by_bond() : protocols::indexed_structure_store
• append_pose_to_pose() : core::pose
• append_pose_to_pose_keep_fold_tree() : protocols::fold_from_loops::utils
• append_pose_with_glycan_residues() : core::pose
• append_pose_with_overlap() : protocols::indexed_structure_store
• append_residue_selector_subelements() : protocols::jd3
• append_residues_from_template_segment() : protocols::denovo_design::components
• append_rsd_by_jump_near_atom() : protocols::pose_metric_calculators
• append_single_far_away_water() : protocols::hydrate
• append_single_scorefxn_subelement() : protocols::jd3
• append_subelement_and_attributes_for_parse_loops_from_tag() : protocols::loop_modeling::utilities
• append_subelement_for_parse_movemap_factory_legacy() : protocols::rosetta_scripts
• append_subpose_to_pose() : core::pose
• append_to_map() : core::scoring::epr_deer
• append_virtual_residue_to_full_model_info() : core::pose::full_model_info
• AppendAssemblyMoverCOP : protocols::sewing::movers
• AppendAssemblyMoverOP : protocols::sewing::movers
• AppendResidueRotamerSetOP : core::pack::task::operation
• AppendRotamerCreator_registrator : core::init
• AppendRotamerOP : core::pack::task::operation
• AppendRotamerSetCreator_registrator : core::init
• AppendRotamerSetOP : core::pack::task::operation
• apply_adducts_to_residue() : core::chemical
• apply_Aform_torsions() : core::pose::rna
• apply_best_scoring_fragdata() : core::fragment
• apply_charge_transforms() : core::chemical::rdkit
• apply_chi_cst() : protocols::stepwise::legacy::modeler::rna
• apply_dofs() : core::pose::copydofs
• apply_full_to_sub_mapping() : protocols::stepwise::modeler::rna
• apply_ideal_c2endo_sugar_coords() : core::pose::rna
• apply_ideal_coordinates_for_alternative_pucker() : protocols::simple_moves
• apply_non_main_chain_sugar_coords() : core::pose::rna
• apply_numbering() : protocols::stepwise::modeler
• apply_protonated_H1_adenosine_variant_type() : protocols::stepwise::modeler::rna
• apply_pucker() : core::pose::rna
• apply_residue_entries_to_pose() : protocols::indexed_structure_store
• apply_rotamer() : protocols::stepwise::legacy::modeler::rna
• apply_rotate() : protocols::ligand_docking
• apply_sequence_mapping() : protocols::loops
• apply_set_weights() : core::scoring
• apply_sub_to_full_mapping() : protocols::stepwise::modeler::rna
• apply_suite_torsion_info() : core::pose::rna
• apply_superposition_transform() : protocols::toolbox
• apply_superposition_transform_to_jump() : protocols::toolbox
• apply_symm_gly_corrections() : core::chemical
• apply_tensor_transformation() : core::scoring::nmr
• apply_transformation() : protocols::forge::methods , protocols::hybridization
• apply_vector_rotation() : core::scoring::nmr
• apply_vector_transformation() : core::scoring::nmr
• apply_virtual_rna_residue_variant_type() : core::pose::rna
• ApplyRandomStoredRBConfCOP : protocols::enzdes
• ApplyRandomStoredRBConfOP : protocols::enzdes
• approximate_buried_unsat_penalty : core::scoring
• ApproximateBuriedUnsatPenaltyCOP : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty
• ApproximateBuriedUnsatPenaltyCreator_registrator : core::init
• ApproximateBuriedUnsatPenaltyOP : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty
• AqueousPoreFinderCOP : protocols::membrane
• AqueousPoreFinderOP : protocols::membrane
• AqueousPoreParametersCOP : core::conformation::membrane
• AqueousPoreParametersOP : core::conformation::membrane
• Ar : core::chemical::element
• ARAMID : core::chemical
• Arc : core::scoring::packstat
• archive_size_for_pose() : protocols::multistage_rosetta_scripts
• 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_selections_equal() : core::select::residue_selector
• are_seqs_different() : protocols::vip
• AreaAccumulatorOP : core::scoring::packstat
• AreConnectablePredicateCOP : protocols::denovo_design::connection
• AreConnectablePredicateOP : protocols::denovo_design::connection
• arg_cation_pi : core::scoring
• arg_max() : protocols::mean_field
• arg_min() : protocols::mean_field
• ArgCationPiEnergyCOP : core::energy_methods
• ArgCationPiEnergyCreator_registrator : core::init
• ArgCationPiEnergyOP : core::energy_methods
• argrot_dna_dis2() : protocols::dna
• AROMATIC : core::chemical , core::chemical::rings
• AROMATIC_CARBON_WITH_FREE_VALENCE : core::chemical
• AROMATIC_HYDROGEN : core::chemical
• aromatic_restraint : core::scoring
• AromaticAtomEIter : core::chemical
• AromaticAtomGraph : core::chemical
• AromaticAtomVIter : core::chemical
• AromaticAtomVIterPair : core::chemical
• AromaticBackboneRestraintEnergyCOP : core::energy_methods
• AromaticBackboneRestraintEnergyCreator_registrator : core::init
• AromaticBackboneRestraintEnergyOP : core::energy_methods
• AromaticBond : core::chemical
• Aroop : protocols::antibody
• As : core::chemical::element
• as_set() : protocols::medal
• aspartimide_penalty : core::scoring
• aspartimide_penalty_lr : core::scoring::methods
• AspartimidePenaltyEnergyAP : core::energy_methods
• AspartimidePenaltyEnergyCAP : core::energy_methods
• AspartimidePenaltyEnergyCOP : core::energy_methods
• AspartimidePenaltyEnergyCreator_registrator : core::init
• AspartimidePenaltyEnergyOP : core::energy_methods
• assemble_remark_line() : protocols::toolbox::match_enzdes_util
• AssembleLinkerMoverCOP : protocols::domain_assembly
• AssembleLinkerMoverOP : protocols::domain_assembly
• AssemblyCOP : protocols::legacy_sewing
• AssemblyMoverCOP : protocols::sewing::movers
• AssemblyMoverOP : protocols::sewing::movers
• AssemblyOP : protocols::legacy_sewing
• AssemblyRequirementCOP : protocols::sewing::requirements
• AssemblyRequirementCreatorCOP : protocols::sewing::requirements
• AssemblyRequirementCreatorOP : protocols::sewing::requirements
• AssemblyRequirementOP : protocols::sewing::requirements
• AssemblyScorerCOP : protocols::sewing::scoring
• AssemblyScorerCreatorCOP : protocols::sewing::scoring
• AssemblyScorerCreatorOP : protocols::sewing::scoring
• AssemblyScorerOP : protocols::sewing::scoring
• assert_phosphate_nomenclature_matches_mini() : core::pose::rna
• assert_that_all_atoms_are_moved_by_chi_angle() : protocols::constraint_movers
• assign_abase_derivs() : core::scoring::hbonds
• assign_gasteiger_atom_types() : core::chemical::gasteiger
• assign_initial_medoids() : protocols::multistage_rosetta_scripts::cluster
• assign_initial_medoids_on_the_fly() : protocols::multistage_rosetta_scripts::cluster
• assign_medoids() : protocols::multistage_rosetta_scripts::cluster
• assign_medoids_on_the_fly() : protocols::multistage_rosetta_scripts::cluster
• assign_non_medoids_to_clusters() : protocols::multistage_rosetta_scripts::cluster
• assign_non_medoids_to_clusters_on_the_fly() : protocols::multistage_rosetta_scripts::cluster
• assign_pucker() : core::pose::rna
• assign_random_continuous_rotamer() : core::pack
• assign_random_rotamers() : core::pack
• assign_rna_atom_type() : core::energy_methods
• 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
• AsymmetricUnitSelectorCOP : core::select::residue_selector
• AsymmetricUnitSelectorOP : core::select::residue_selector
• At : core::chemical::element
• at_interface() : protocols::constel
• ATOM : core::io::pdb
• atom_dist_with_zero() : protocols::splice
• atom_distance() : protocols::protein_interface_design::filters , protocols::simple_filters
• atom_graph_from_conformation() : core::conformation
• atom_id_to_named_atom_id() : core::conformation , core::pose
• atom_is_acceptor() : core::pose::rna
• atom_is_aro() : core::energy_methods
• atom_is_aro2() : core::energy_methods
• atom_is_hydratable() : protocols::hydrate
• atom_is_polar() : core::pose::rna
• atom_map_valid_size() : protocols::hybridization
• atom_pair_constraint : core::scoring
• atom_pair_distance : protocols::generalized_kinematic_closure::filter
• ATOM_RADIUS : core::scoring::sc
• atom_specific_rms() : protocols::motifs
• atom_square_deviation() : protocols::stepwise::modeler::rna
• atom_tracer() : protocols::ligand_docking
• atom_tree_dfunc() : core::optimization , core::optimization::symmetry
• ATOM_TREE_FILE : protocols::jd2::JobInputterInputSource
• atom_tree_get_atompairE_deriv() : core::optimization , core::optimization::symmetry
• atom_vdw_ : core::scoring::epr_deer
• AtomAngleSecMatchRPECOP : protocols::match::downstream
• AtomAngleSecMatchRPEOP : protocols::match::downstream
• AtomAP : core::chemical , core::kinematics::tree
• AtomAPs : core::chemical
• AtomAtomPairFeaturesCOP : protocols::features
• AtomAtomPairFeaturesOP : protocols::features
• AtomBasedConstraintsScoreCOP : protocols::frag_picker::scores
• AtomBasedConstraintsScoreOP : protocols::frag_picker::scores
• AtomCAP : core::kinematics::tree
• AtomCoordinateCstMoverCOP : protocols::relax
• AtomCoordinateCstMoverOP : protocols::relax
• AtomCOP : core::chemical , core::kinematics::tree
• 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
• atomic_depth() : core::scoring::atomic_depth
• AtomicDepthCOP : core::scoring::atomic_depth
• AtomicDepthOP : core::scoring::atomic_depth
• AtomID_MapperCOP : core::pose::toolbox
• AtomID_MapperOP : core::pose::toolbox
• AtomID_Mask : core::id
• AtomIndex : core::chemical::sdf
• AtomIndices : core::chemical
• AtomInfoGraph : core::io::pose_from_sfr
• AtomInResidueAtomInResiduePairFeaturesCOP : protocols::features
• AtomInResidueAtomInResiduePairFeaturesOP : protocols::features
• atomitem : core::scoring::rna::chemical_shift
• AtomLevelDomainMapCOP : core::pose::toolbox
• AtomLevelDomainMapOP : core::pose::toolbox
• AtomMap : protocols::legacy_sewing , protocols::sewing::hashing
• AtomMemo : core::chemical
• AtomMemoOP : core::chemical
• AtomNamePosMap : core::scoring::nmr
• AtomNeighbors : core::scoring
• AtomOP : core::chemical , core::kinematics::tree
• AtomOPs : core::chemical
• AtomPairConstraintCOP : core::scoring::constraints
• AtomPairConstraintCreator_registrator : core::init
• AtomPairConstraintGeneratorCOP : protocols::constraint_generator
• AtomPairConstraintGeneratorOP : protocols::constraint_generator
• 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
• AtomPairKey : core::scoring::nmr
• AtomPointer1D : core::kinematics
• AtomPointer2D : core::kinematics
• AtomPropertiesCOP : core::chemical
• AtomPropertiesOP : core::chemical
• AtomProperty : core::chemical
• Atoms : core::conformation
• atoms_deeper_than() : core::scoring::atomic_depth
• atoms_have_bond_to_bonded_atoms() : protocols::rna::movers
• atoms_have_mutual_bond_to_atom() : protocols::rna::movers
• atoms_interact() : core::scoring::methods
• atoms_involved_in_phosphate_torsion : core::chemical::rna
• AtomSelectionAP : core::io::nmr
• AtomSelectionCAP : core::io::nmr
• AtomSelectionCOP : core::io::nmr
• AtomSelectionOP : core::io::nmr
• AtomToAxisConstraintCOP : core::scoring::constraints
• AtomToAxisConstraintOP : core::scoring::constraints
• 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
• AtomTypeSetCOP : core::chemical
• AtomTypeSetOP : core::chemical
• AtomTypesFeaturesCOP : protocols::features
• AtomTypesFeaturesOP : protocols::features
• AtomVDWCOP : core::scoring
• AtomVDWOP : core::scoring
• AtomWeights : core::scoring::lkball
• ATR_REP : protocols::stepwise::screener
• attach_debugger() : protocols::optimize_weights
• attach_n_and_c_unfolded_poses_to_pose() : protocols::fold_from_loops::utils
• attach_unfolded_pose_to_pose_c_term() : protocols::fold_from_loops::utils
• attach_unfolded_pose_to_pose_n_term() : protocols::fold_from_loops::utils
• attachment_type_from_string() : protocols::stepwise::monte_carlo::mover
• attachment_type_name : protocols::stepwise::monte_carlo::mover
• AttachmentCOP : protocols::stepwise::monte_carlo::mover
• AttachmentOP : protocols::stepwise::monte_carlo::mover
• Attachments : protocols::stepwise::monte_carlo::mover
• AttachmentType : protocols::stepwise::monte_carlo::mover
• ATTEN_2 : core::scoring::sc
• ATTEN_6 : core::scoring::sc
• ATTEN_BLOCKER : core::scoring::sc
• ATTEN_BURIED_FLAGGED : core::scoring::sc
• attributes_for_get_ab_design_global_scorefxn() : protocols::antibody::design
• attributes_for_get_ab_design_min_scorefxn() : protocols::antibody::design
• attributes_for_get_cdr_bool_from_tag() : protocols::antibody
• attributes_for_get_resnum_selector() : core::pose
• attributes_for_get_resnum_string() : core::pose
• attributes_for_get_score_function_name() : core::scoring
• attributes_for_get_score_function_name_w_description() : core::scoring
• attributes_for_load_loop_definitions() : protocols::loops::loops_definers
• attributes_for_parse_constraint_generators() : protocols::constraint_generator
• attributes_for_parse_database_session() : protocols::rosetta_scripts
• attributes_for_parse_grid_set_from_tag() : protocols::qsar::scoring_grid
• attributes_for_parse_jump_selector() : core::select::jump_selector
• attributes_for_parse_jump_selector_default_option_name() : core::select::jump_selector
• attributes_for_parse_jump_selector_when_required() : core::select::jump_selector
• attributes_for_parse_movemap_factory() : core::select::movemap
• attributes_for_parse_movemap_factory_default_attr_name() : core::select::movemap
• attributes_for_parse_movemap_factory_when_required() : core::select::movemap
• attributes_for_parse_movemap_factory_when_required_default_name() : core::select::movemap
• attributes_for_parse_optional_grid_set_from_tag() : protocols::qsar::scoring_grid
• attributes_for_parse_residue_level_operations() : core::pack::task::operation
• attributes_for_parse_residue_selector() : core::select::residue_selector , protocols::rosetta_scripts
• attributes_for_parse_residue_selector_default_option_name() : core::select::residue_selector
• attributes_for_parse_residue_selector_logic_string() : core::select::residue_selector
• attributes_for_parse_residue_selector_when_required() : core::select::residue_selector
• attributes_for_parse_resnum() : core::pose
• attributes_for_parse_score_function() : core::scoring
• attributes_for_parse_score_function_w_description() : core::scoring
• attributes_for_parse_score_function_w_description_when_required() : core::scoring
• attributes_for_parse_task_operations() : core::pack::task
• attributes_for_parse_task_operations_w_factory() : core::pack::task
• attributes_for_parse_xyz_vector() : protocols::rosetta_scripts
• attributes_for_saved_reference_pose() : core::pose , protocols::rosetta_scripts
• attributes_for_saved_reference_pose_w_description() : core::pose , protocols::rosetta_scripts
• attributes_for_set_scorefxn_from_tag() : protocols::loop_modeling::utilities
• attributes_for_set_task_factory_from_tag() : protocols::loop_modeling::utilities
• Au : core::chemical::element
• AUTHOR : core::io::pdb
• AUTHOR_AND_NOTE : update_ResidueType_enum_files
• auto_detect_atoms() : core::scoring::constraints
• auto_setup_all_metal_bonds() : core::util
• auto_setup_all_metal_constraints() : core::util
• auto_trim_floppy_termini() : protocols::sic_dock
• auto_use_linmem_ig() : core::pack::interaction_graph
• AutoCutDataCOP : protocols::environment
• AutoCutDataOP : protocols::environment
• AUTOMATIC : core::conformation
• AutomaticSheetConstraintGeneratorCOP : protocols::fold_from_loops::constraint_generator
• AutomaticSheetConstraintGeneratorOP : protocols::fold_from_loops::constraint_generator
• automorphic_rmsd() : core::scoring
• AutomorphismIteratorCOP : core::chemical
• AutomorphismIteratorOP : core::chemical
• average_antiparallel_embeddings() : protocols::membrane
• average_embeddings() : protocols::membrane
• AverageDegreeCountFilterCOP : protocols::protein_interface_design::filters
• AverageDegreeCountFilterOP : protocols::protein_interface_design::filters
• AverageDegreeFilterCOP : protocols::protein_interface_design::filters
• AverageDegreeFilterOP : protocols::protein_interface_design::filters
• AveragePathLengthFilterCOP : protocols::simple_filters
• AveragePathLengthFilterOP : protocols::simple_filters
• avg_ca_position() : protocols::nonlocal
• AxEqDesignation : core::chemical::rings
• AXIAL : core::chemical::rings