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

- a -

• a() : core::pose::motif
• AA : 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_b3a : core::chemical
• aa_b3c : core::chemical
• aa_b3cisACHC : core::chemical
• aa_b3cisACPC : core::chemical
• aa_b3cisACPrC : 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_b3v : core::chemical
• aa_b3w : core::chemical
• aa_b3y : core::chemical
• aa_cmp : 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_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_phe : core::chemical
• aa_pro : core::chemical
• 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_vrt : core::chemical
• abego : core::scoring
• 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
• above : core::sequence
• AbstractRotamerTrieCOP : core::conformation
• AbstractRotamerTrieOP : core::conformation
• Ac : core::chemical::element
• AcceptorAtomEIter : core::chemical
• AcceptorAtomGraph : core::chemical
• AcceptorAtomVIter : core::chemical
• AcceptorAtomVIterPair : core::chemical
• AccumulatorOP : core::scoring::packstat
• add_atom() : core::kinematics
• add_atom_type_set_parameters_from_command_line() : core::chemical
• add_comment() : core::pose
• 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_coordinate_constraints() : core::scoring::constraints
• add_covalent_linkage() : core::util
• add_covalent_linkage_helper() : core::util
• add_covalent_linkages_to_metal() : core::util
• add_dens_scores_from_cmdline_to_scorefxn() : core::scoring::electron_density
• 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_hbs_constraint() : core::pose::ncbb
• add_lower_terminus_type_to_conformation_residue() : core::conformation
• add_lower_terminus_type_to_pose_residue() : core::pose
• add_oop_constraint() : core::pose::ncbb
• add_rna_chi_rotamers() : core::pack::rotamer_set
• add_score_line_string() : core::pose
• 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_values_from_center() : core::chemical::rna
• add_variant_type_to_conformation_residue() : core::conformation
• add_variant_type_to_pose_residue() : core::pose
• add_variant_type_to_residue() : core::pose
• add_whitespaces() : core::scoring::rna::chemical_shift
• AddBehaviorRLTCreator_registrator : core::init
• AddBehaviorRLTOP : core::pack::task::operation
• AdductMap : core::chemical
• AdductOP : core::chemical
• addVirtualResAsRoot() : core::pose
• AdjacentIter : core::chemical
• AdjacentIterPair : core::chemical
• Ag : core::chemical::element
• AIDs : core::pose::motif
• AIVD : core::io::pdb
• Al : core::chemical::element
• 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_poses_naive() : core::sequence
• align_virtual_atoms_in_carbohydrate_residue() : core::pose::carbohydrates
• AlignerCOP : core::sequence
• AlignerOP : core::sequence
• alignment_from_pose() : core::sequence
• alignment_into_pose() : core::sequence
• AlignMove : core::sequence
• all_atom_rmsd() : core::scoring
• all_atom_rmsd_nosuper() : core::scoring
• all_scatom_rmsd_nosuper() : core::scoring
• all_visited() : core::graph
• all_water_weights_iterator : core::scoring::geometric_solvation
• AllResFilterCreator_registrator : core::init
• ALPHA : core::chemical::rna , core::scoring::dna
• ALREADY_SYMMETRIZED : core::pack::task
• Am : core::chemical::element
• AmberPeriodicFuncCOP : core::scoring::func
• AmberPeriodicFuncOP : core::scoring::func
• AmbiguousConstraintCOP : core::scoring::constraints
• AmbiguousConstraintCreator_registrator : core::init
• AmbiguousConstraintOP : core::scoring::constraints
• AmbiguousNMRConstraintCOP : core::scoring::constraints
• AmbiguousNMRConstraintCreator_registrator : core::init
• AmbiguousNMRConstraintOP : core::scoring::constraints
• AmbiguousNMRDistanceConstraintCOP : core::scoring::constraints
• AmbiguousNMRDistanceConstraintCreator_registrator : core::init
• AmbiguousNMRDistanceConstraintOP : core::scoring::constraints
• AnalyticEtableEvaluatorOP : core::scoring::etable
• AndResidueSelectorCOP : core::pack::task::residue_selector
• AndResidueSelectorOP : core::pack::task::residue_selector
• Angle : core
• angle_constraint : core::scoring
• angle_distance() : core::scoring::motif
• AngleConstraintCOP : core::scoring::constraints
• AngleConstraintCreator_registrator : core::init
• AngleConstraintOP : core::scoring::constraints
• angles() : core::scoring , core::scoring::packstat::old , core::scoring::sasa
• AngleVector : core::pack::dunbrack
• 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
• any_atoms_within_cutoff() : core::pack::task::operation::util
• ANY_BASE_EDGE : core::chemical::rna
• ANY_CHI : 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
• APolarHydrogenEIter : core::chemical
• APolarHydrogenGraph : core::chemical
• APolarHydrogenVIter : core::chemical
• APolarHydrogenVIterPair : core::chemical
• append_pose_to_pose() : core::pose
• append_subpose_to_pose() : core::pose
• 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_dofs() : core::pose::copydofs
• apply_ideal_c2endo_sugar_coords() : core::pose::rna
• apply_lk_ball_fraction_weight_for_hbonds() : core::scoring::methods
• apply_non_main_chain_sugar_coords() : core::pose::rna
• apply_pucker() : core::pose::rna
• apply_virtual_rna_residue_variant_type() : core::pose::rna
• Ar : core::chemical::element
• Arc : core::scoring::packstat
• ArcIter : core::scoring::packstat
• Arcs : core::scoring::packstat
• AreaAccumulatorOP : core::scoring::packstat
• AromaticAtomEIter : core::chemical
• AromaticAtomGraph : core::chemical
• AromaticAtomVIter : core::chemical
• AromaticAtomVIterPair : core::chemical
• AromaticBond : core::chemical
• As : core::chemical::element
• assign_abase_derivs() : core::scoring::hbonds
• assign_gasteiger_atom_types() : core::chemical::gasteiger
• assign_pucker() : core::pose::rna
• assign_random_continuous_rotamer() : core::pack
• assign_random_rotamers() : core::pack
• assign_rna_atom_type() : core::scoring::elec
• asymmetrize_scorefunction() : core::scoring::symmetry
• At : core::chemical::element
• at() : core::io::serialization
• atom_graph_from_conformation() : core::conformation
• atom_id_from_icoor_line() : core::chemical
• atom_id_to_named_atom_id() : core::conformation , core::pose
• atom_is_acceptor() : core::pose::rna
• atom_is_aro() : core::scoring::elec
• atom_is_aro2() : core::scoring::elec
• atom_is_polar() : core::pose::rna
• atom_next_to_connect_atom() : core::pose::carbohydrates
• atom_pair_constraint : core::scoring
• ATOM_RADIUS : core::scoring::sc
• atom_tree_dfunc() : core::optimization , core::optimization::symmetry
• atom_tree_get_atompairE_deriv() : core::optimization , core::optimization::symmetry
• AtomAP : core::chemical , core::kinematics::tree
• AtomAPs : core::chemical
• AtomCAP : core::kinematics::tree
• AtomChain : core::io::pdb
• AtomCOP : core::chemical , core::kinematics::tree
• AtomCOPs : core::chemical
• AtomDOFChangeSet : core::kinematics
• AtomGraph : core::conformation
• AtomGraphOP : core::conformation
• AtomID_Mask : core::id
• AtomIndex : core::chemical::sdf
• AtomIndices : core::chemical
• AtomInfoGraph : core::io::pdb
• atomitem : core::scoring::rna::chemical_shift
• AtomMemo : core::chemical
• AtomMemoOP : core::chemical
• AtomNeighbors : core::scoring
• AtomOP : core::chemical , core::kinematics::tree
• AtomOPs : core::chemical
• AtomPairConstraintCOP : core::scoring::constraints
• AtomPairConstraintCreator_registrator : core::init
• AtomPairConstraintOP : core::scoring::constraints
• 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
• atoms_involved_in_phosphate_torsion : core::chemical::rna
• AtomTreeAP : core::kinematics
• AtomTreeCAP : core::kinematics
• AtomTreeCollectionCOP : core::pack::scmin
• AtomTreeCollectionOP : core::pack::scmin
• AtomTreeCOP : core::kinematics
• AtomTreeDiffCOP : core::import_pose::atom_tree_diffs
• 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
• AtomVDWCOP : core::scoring
• AtomVDWOP : core::scoring
• ATTEN_2 : core::scoring::sc
• ATTEN_6 : core::scoring::sc
• ATTEN_BLOCKER : core::scoring::sc
• ATTEN_BURIED_FLAGGED : core::scoring::sc
• Au : core::chemical::element
• 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_setup_metal_bonds() : core::util
• AUTOMATIC : core::conformation
• automorphic_rmsd() : core::scoring
• AutomorphismIteratorCOP : core::chemical
• AutomorphismIteratorOP : core::chemical