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

- a -

• AA : protocols::optimize_weights
• AAProbabilities : protocols::antibody::design
• Ab_TemplateInfoCOP : protocols::antibody
• Ab_TemplateInfoOP : protocols::antibody
• 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
• AbinitioMoverWeightAP : protocols::topology_broker::weights
• AbinitioMoverWeightCAP : protocols::topology_broker::weights
• AbinitioMoverWeightCOP : protocols::topology_broker::weights
• AbinitioMoverWeightOP : protocols::topology_broker::weights
• AbrelaxMoverCOP : protocols::abinitio
• AbrelaxMoverOP : protocols::abinitio
• ABS : protocols::simple_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
• AbstractArchiveBaseCOP : protocols::jd2::archive
• AbstractArchiveBaseOP : protocols::jd2::archive
• accept : protocols::hotspot_hashing
• accept_reject : protocols::moves
• AcceptanceCheckCOP : protocols::loop_modeling::utilities
• AcceptanceCheckOP : protocols::loop_modeling::utilities
• access_ptr_bool : protocols::jd2::utility::pointer
• access_ptr_char : protocols::jd2::utility::pointer
• access_ptr_double : protocols::jd2::utility::pointer
• access_ptr_float : protocols::jd2::utility::pointer
• access_ptr_int : protocols::jd2::utility::pointer
• access_ptr_long : protocols::jd2::utility::pointer
• access_ptr_longdouble : protocols::jd2::utility::pointer
• access_ptr_schar : protocols::jd2::utility::pointer
• access_ptr_short : protocols::jd2::utility::pointer
• access_ptr_size_t : protocols::jd2::utility::pointer
• access_ptr_uchar : protocols::jd2::utility::pointer
• access_ptr_uint : protocols::jd2::utility::pointer
• access_ptr_ulong : protocols::jd2::utility::pointer
• access_ptr_ushort : protocols::jd2::utility::pointer
• ActiveSiteGridCOP : protocols::match::downstream
• ActiveSiteGridOP : protocols::match::downstream
• AdaptiveScoreHistogramCOP : protocols::frag_picker::scores
• AdaptiveScoreHistogramOP : protocols::frag_picker::scores
• ADD : protocols::stepwise::monte_carlo
• 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_conformation_viewer() : protocols::viewer
• add_constraints_from_file() : protocols::dna
• add_coordinate_constraints() : protocols::protein_interface_design::movers , protocols::seeded_abinitio
• add_coordinate_constraints_to_pose() : protocols::loops , protocols::relax
• add_cutpoint_variants() : protocols::forge::methods , protocols::loops
• add_daemon : protocols::pack_daemon
• add_dist_constraints() : protocols::seeded_abinitio
• add_edges() : protocols::forge::methods
• add_fade_chain_break_constraint_across_gap() : protocols::stepwise::sampling::rna
• add_harmonic_chain_break_constraint() : protocols::stepwise::sampling::rna
• add_harmonic_cluster_constraint() : protocols::antibody
• add_harmonic_cluster_constraints() : protocols::antibody
• 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_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_PREGENERATED : protocols::enzdes
• add_relevant_restypes_to_subset() : protocols::toolbox::match_enzdes_util
• add_single_cutpoint_variant() : protocols::loops
• add_strand_pairs_cst() : protocols::hybridization
• add_vall_cheating_fragments() : protocols::frags
• add_vall_fragments() : protocols::frags
• add_vec() : protocols::toolbox
• add_vertex() : protocols::forge::methods
• add_virtual_O2Prime_hydrogen() : protocols::stepwise::sampling::rna
• add_virtual_residue_to_cterm() : protocols::relax
• AddAssemblyConstraintsCOP : protocols::domain_assembly
• AddAssemblyConstraintsOP : protocols::domain_assembly
• AddChainMoverCOP : protocols::simple_moves
• AddChainMoverOP : protocols::simple_moves
• 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
• AddJobPairDataCOP : protocols::simple_moves
• AddJobPairDataOP : protocols::simple_moves
• AddLigandMotifRotamersCOP : protocols::enzdes
• AddLigandMotifRotamersOP : protocols::enzdes
• AddMoverOP : protocols::stepwise::monte_carlo::rna
• AddOrDeleteMoverOP : protocols::stepwise::monte_carlo::rna
• 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
• AddZincSiteConstraintsCOP : protocols::metal_interface
• AddZincSiteConstraintsOP : protocols::metal_interface
• 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_to_neighbor_bin() : protocols::match
• AHO_Scheme : protocols::antibody
• alapose() : protocols::kinmatch
• align_motif_pose_break() : protocols::motif_hash
• align_motif_pose_super() : protocols::motif_hash
• align_poses() : protocols::stepwise::sampling::rna
• 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
• alignaxis() : protocols::sic_dock
• alignaxis_xform() : protocols::sic_dock
• AlignChainMoverCOP : protocols::simple_moves
• AlignChainMoverOP : protocols::simple_moves
• AlignEvaluatorCOP : protocols::evaluation
• AlignEvaluatorOP : protocols::evaluation
• alignment_from_cmd_line() : protocols::comparative_modeling
• 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
• AlignOption : protocols::hybridization
• AlignPoseToInvrotTreeMoverCOP : protocols::toolbox::match_enzdes_util
• AlignPoseToInvrotTreeMoverOP : protocols::toolbox::match_enzdes_util
• ALL : protocols::sic_dock
• all_chunks : protocols::hybridization
• ALL_STAGES : protocols::abinitio
• all_stats : protocols::moves
• 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
• ALWAYS_CLEAR : protocols::forge::components::VLB_VallMemoryUsage
• AmbiguousMultiConstraintCOP : protocols::constraints_additional
• AmbiguousMultiConstraintOP : protocols::constraints_additional
• analyze_base_bin_map() : protocols::stepwise::sampling::rna::rigid_body
• 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
• ANDNOT : protocols::filters
• angle_between() : protocols::rigid
• angle_diff() : protocols::MakeRotLib
• angleA : protocols::jumping
• angleB : protocols::jumping
• AntibodyCDRDesignerCOP : protocols::antibody::design
• AntibodyCDRDesignerOP : protocols::antibody::design
• AntibodyDatabaseManagerCOP : protocols::antibody::design
• AntibodyDatabaseManagerOP : protocols::antibody::design
• AntibodyDesignModelerCOP : protocols::antibody::design
• AntibodyDesignModelerOP : protocols::antibody::design
• AntibodyDesignMoverCOP : protocols::antibody::design
• AntibodyDesignMoverOP : protocols::antibody::design
• AntibodyEnumManagerCOP : protocols::antibody
• AntibodyEnumManagerOP : protocols::antibody
• AntibodyGraftDesignerCOP : protocols::antibody::design
• AntibodyGraftDesignerOP : protocols::antibody::design
• AntibodyInfoAP : protocols::antibody
• AntibodyInfoCAP : protocols::antibody
• AntibodyInfoCOP : protocols::antibody
• AntibodyInfoOP : protocols::antibody
• AntibodyModelerCOP : protocols
• AntibodyModelerOP : protocols
• AntibodyModelerProtocolCOP : protocols::antibody
• AntibodyModelerProtocolOP : protocols::antibody
• AntibodyNumberingParserCOP : protocols::antibody
• AntibodyNumberingParserOP : protocols::antibody
• AntibodyNumberingSchemeEnum : protocols::antibody
• AntibodyNumberingSchemeEnum_start : protocols::antibody
• AntibodyNumberingSchemeEnum_total : protocols::antibody
• ANY : protocols::rotamer_sampler
• 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
• apply_chi_cst() : protocols::stepwise::sampling::rna::legacy
• apply_full_to_sub_mapping() : protocols::stepwise::sampling::rna
• apply_ideal_coordinates_for_alternative_pucker() : protocols::simple_moves
• apply_numbering() : protocols::stepwise
• apply_protonated_H1_adenosine_variant_type() : protocols::stepwise::sampling::rna
• apply_rotamer() : protocols::stepwise::sampling::rna
• apply_rotate() : protocols::ligand_docking
• apply_sequence_mapping() : protocols::loops
• apply_sub_to_full_mapping() : protocols::stepwise::sampling::rna
• apply_superposition_transform() : protocols::toolbox
• apply_superposition_transform_to_jump() : protocols::toolbox
• apply_transformation() : protocols::forge::methods , protocols::hybridization
• apply_virtual_rna_residue_variant_type() : protocols::stepwise::sampling::rna
• ApplyRandomStoredRBConfCOP : protocols::enzdes
• ApplyRandomStoredRBConfOP : protocols::enzdes
• ArchiveBaseCOP : protocols::jd2::archive
• ArchiveBaseOP : protocols::jd2::archive
• ArchiveManagerAP : protocols::jd2::archive
• ArchiveManagerCAP : protocols::jd2::archive
• ArchiveManagerCOP : protocols::jd2::archive
• ArchiveManagerOP : protocols::jd2::archive
• are_seqs_different() : protocols::vip
• argrot_dna_dis2() : protocols::dna
• Aroop : protocols::antibody
• 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_phosphate_nomenclature_matches_mini() : protocols::farna
• 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
• atom_is_acceptor() : protocols::farna
• atom_is_polar() : protocols::farna
• atom_map_valid_size() : protocols::hybridization
• atom_specific_rms() : protocols::motifs
• atom_square_deviation() : protocols::stepwise::sampling::rna
• atom_tracer : protocols::ligand_docking
• ATOM_TREE_FILE : protocols::jd2::JobInputterInputSource
• AtomAngleSecMatchRPECOP : protocols::match::downstream
• AtomAngleSecMatchRPEOP : protocols::match::downstream
• AtomAtomPairFeaturesCOP : protocols::features
• AtomAtomPairFeaturesOP : protocols::features
• AtomBasedConstraintsScoreCOP : protocols::frag_picker::scores
• AtomBasedConstraintsScoreOP : protocols::frag_picker::scores
• AtomCoordinateCstMoverCOP : protocols::relax
• AtomCoordinateCstMoverOP : protocols::relax
• AtomDihedralSecMatchRPECOP : protocols::match::downstream
• AtomDihedralSecMatchRPEOP : protocols::match::downstream
• AtomDistanceSecMatchRPECOP : protocols::match::downstream
• AtomDistanceSecMatchRPEOP : protocols::match::downstream
• AtomGeometrySecMatchRPECOP : protocols::match::downstream
• AtomGeometrySecMatchRPEOP : protocols::match::downstream
• AtomGrps : protocols::noesy_assign
• AtomInResidueAtomInResiduePairFeaturesCOP : protocols::features
• AtomInResidueAtomInResiduePairFeaturesOP : protocols::features
• AtomPairConstraintsDataCOP : protocols::frag_picker::scores
• AtomPairConstraintsDataOP : protocols::frag_picker::scores
• AtomPairConstraintsScoreCOP : protocols::frag_picker::scores
• AtomPairConstraintsScoreOP : protocols::frag_picker::scores
• AtomTreeDiffJobInputterOP : protocols::jd2
• AtomTreeDiffJobOutputterCOP : protocols::jd2
• AtomTreeDiffJobOutputterOP : protocols::jd2
• AtomTypesFeaturesCOP : protocols::features
• AtomTypesFeaturesOP : protocols::features
• ATR_REP : protocols::stepwise::screener
• AtrRepCheckerCOP : protocols::stepwise::sampling::rna::checker
• AtrRepCheckerOP : protocols::stepwise::sampling::rna::checker
• AtrRepScreenerCOP : protocols::stepwise::screener
• AtrRepScreenerOP : protocols::stepwise::screener
• attach_debugger() : protocols::optimize_weights
• attachment_type_from_string() : protocols::stepwise::monte_carlo
• attachment_type_name : protocols::stepwise::monte_carlo
• AttachmentCOP : protocols::stepwise::monte_carlo
• AttachmentOP : protocols::stepwise::monte_carlo
• Attachments : protocols::stepwise::monte_carlo
• AttachmentType : protocols::stepwise::monte_carlo
• auto_trim_floppy_termini() : protocols::sic_dock
• AutoCutDataCOP : protocols::environment
• AutoCutDataOP : protocols::environment
• 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
• avg_cluster_cen_dist() : protocols::MakeRotLib