- a -

• a() : core::scoring::electron_density::OneGaussianScattering , core::scoring::fiber_diffraction::OneGaussianScattering
• a0() : core::scoring::FACTSRsdTypeInfo
• a1() : core::scoring::FACTSRsdTypeInfo
• a2() : core::scoring::FACTSRsdTypeInfo
• a3() : core::scoring::FACTSRsdTypeInfo
• aa() : core::chemical::ResidueType , core::conformation::Conformation , core::conformation::Residue , core::fragment::picking_old::vall::VallResidue , core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary , core::pack::rotamer_set::WaterAnchorInfo , core::pose::Pose , core::scoring::motif::Xfres , core::scoring::rna::chemical_shift::RNA_CS_residue_parameters , core::sequence::AnnotatedSequence
• aa1() : core::scoring::motif::ResPairMotif
• aa2() : core::scoring::motif::ResPairMotif
• aa_indices_from_submatrix_index() : core::pack::interaction_graph::DoubleLazyEdge
• aa_map() : core::chemical::ResidueTypeSet
• aa_penalty() : core::fragment::picking_old::vall::eval::IdentityEval
• aa_str() : core::fragment::picking_old::vall::eval::IdentityEval
• aa_submatrix_energies_retrievable() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FixedBBInteractionGraph , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::PDInteractionGraph
• aapair_to_table_index() : core::scoring::Rama2BOffset
• aas_defined_begin() : core::chemical::ResidueTypeSet
• aas_defined_end() : core::chemical::ResidueTypeSet
• aas_to_keep() : core::pack::task::operation::RestrictAbsentCanonicalAASRLT
• aatype_for_node_state() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FixedBBInteractionGraph , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::PDInteractionGraph
• aatype_for_state() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::PDNode
• abase2() : core::chemical::ResidueType , core::conformation::Residue
• ABEGO() : core::sequence::ABEGO
• abego_str() : core::fragment::picking_old::vall::eval::ABEGOEval
• ABEGOEval() : core::fragment::picking_old::vall::eval::ABEGOEval
• ABEGOManager() : core::sequence::ABEGOManager
• abort_bad_call() : core::kinematics::tree::Atom_
• abort_min() : core::optimization::Multifunc , core::pack::scmin::CartSCMinMultifunc , core::pack::scmin::SCMinMultifunc
• abs_deriv_dev() : core::optimization::SimpleDerivCheckResult
• acc_atm() : core::scoring::hbonds::HBond
• acc_atm_is_backbone() : core::scoring::hbonds::HBond
• acc_atm_is_protein_backbone() : core::scoring::hbonds::HBond
• acc_bbg_in_bb_bb_hbond() : core::scoring::hbonds::HBondSet
• acc_chem_type_from_name() : core::scoring::hbonds::HBondTypeManager
• acc_res() : core::scoring::hbonds::HBond
• acc_res_is_dna() : core::scoring::hbonds::HBond
• acc_res_is_protein() : core::scoring::hbonds::HBond
• acc_strength() : core::scoring::hbonds::HBondDatabase
• acc_type() : core::scoring::hbonds::HBEvalTuple
• acceptor_atoms() : core::chemical::ResidueType
• AcceptorAtomFilter() : core::chemical::AcceptorAtomFilter
• acceptorRes_occludingRes_geometric_sol_intra() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• acceptorRes_occludingRes_geometric_sol_one_way() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• acceptorRes_occludingRes_geometric_sol_one_way_bb_bb() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• acceptorRes_occludingRes_geometric_sol_one_way_sc() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• access_check() : core::environment::DofPassport
• accpt_pos() : core::chemical::ResidueType , core::conformation::Residue
• accpt_pos_sc() : core::chemical::ResidueType , core::conformation::Residue
• accumulate() : core::scoring::EMapVector
• accumulate_area() : core::scoring::packstat::Accumulator , core::scoring::packstat::AreaAccumulator , core::scoring::packstat::MultiProbePerSphereAccumulator , core::scoring::packstat::MultiProbePoseAccumulator , core::scoring::packstat::PerSphereAccumulator
• accumulate_dxdy() : core::scoring::packstat::Accumulator , core::scoring::packstat::AreaAccumulator , core::scoring::packstat::MultiProbePerSphereAccumulator , core::scoring::packstat::MultiProbePoseAccumulator , core::scoring::packstat::PerSphereAccumulator
• accumulate_energy() : core::scoring::constraints::CstResNeighbConstIterator , core::scoring::constraints::CstResNeighbIterator , core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::PeptideBondedNeighborConstIterator , core::scoring::PeptideBondedNeighborIterator , core::scoring::ResidueNeighborConstIterator , core::scoring::ResidueNeighborIterator
• accumulate_residue_energies() : core::scoring::Energies
• accumulate_residue_total_energies() : core::scoring::Energies
• accumulate_residue_total_energy() : core::scoring::Energies
• accumulate_single_atom_contributions() : core::scoring::methods::LK_BallEnergy
• accumulate_stack_energy() : core::scoring::methods::FreeDOF_Energy
• acknowledge_last_substititon_not_committed() : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• acknowledge_neighbors_partial_state_assignment() : core::pack::interaction_graph::FASTERNode
• acknowledge_neighbors_partial_state_substitution() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• acknowledge_neighbors_perturbed_state() : core::pack::interaction_graph::FASTERNode
• acknowledge_neighbors_state_substitution() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• acknowledge_neighbors_substitution() : core::pack::interaction_graph::HPatchNode< V, E, G >
• acknowledge_neighbors_substitution_surface() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• acknowledge_partial_state_assignment() : core::pack::interaction_graph::FASTEREdge
• acknowledge_partial_state_change() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• acknowledge_participation_in_perturbation() : core::pack::interaction_graph::FASTEREdge
• acknowledge_perturbed_state() : core::pack::interaction_graph::FASTEREdge
• acknowledge_state_change() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• acknowledge_state_zeroed() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• acknowledge_state_zeroed_surface() : core::pack::interaction_graph::SurfaceEdge< V, E, G >
• acknowledge_substitution() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• acknowledge_substitution_surface() : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G >
• actcoord() : core::conformation::Residue
• actcoord_atoms() : core::chemical::ResidueType , core::conformation::Residue
• activate_residue_dofs() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• active_1benmeths_begin() : core::scoring::MinimizationNode
• active_1benmeths_end() : core::scoring::MinimizationNode
• active_1benmeths_ext_begin() : core::scoring::MinimizationNode
• active_1benmeths_ext_end() : core::scoring::MinimizationNode
• active_1benmeths_std_begin() : core::scoring::MinimizationNode
• active_1benmeths_std_end() : core::scoring::MinimizationNode
• active_2b_score_types() : core::scoring::EnergyGraph
• active_2benmeths_begin() : core::scoring::MinimizationEdge
• active_2benmeths_end() : core::scoring::MinimizationEdge
• active_2benmeths_ext_begin() : core::scoring::MinimizationEdge
• active_2benmeths_ext_end() : core::scoring::MinimizationEdge
• active_2benmeths_std_begin() : core::scoring::MinimizationEdge
• active_2benmeths_std_end() : core::scoring::MinimizationEdge
• active_atom_tree() : core::pack::scmin::ResidueAtomTreeCollection
• active_constraint() : core::scoring::constraints::AmbiguousConstraint
• active_constraints() : core::scoring::constraints::KofNConstraint
• active_dofs() : core::environment::DofPassport
• active_intrares2benmeths_begin() : core::scoring::MinimizationNode
• active_intrares2benmeths_end() : core::scoring::MinimizationNode
• active_intrares2benmeths_ext_begin() : core::scoring::MinimizationNode
• active_intrares2benmeths_ext_end() : core::scoring::MinimizationNode
• active_intrares2benmeths_std_begin() : core::scoring::MinimizationNode
• active_intrares2benmeths_std_end() : core::scoring::MinimizationNode
• active_jumps() : core::environment::DofPassport
• active_residue() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::ResidueAtomTreeCollection , core::pack::scmin::SCMinMinimizerMap
• active_residue_cop() : core::pack::scmin::ResidueAtomTreeCollection
• active_restype() : core::pack::scmin::ResidueAtomTreeCollection
• active_restype_index() : core::pack::scmin::ResidueAtomTreeCollection
• active_score_types() : core::scoring::EnergyGraph
• actual_residue_connection() : core::conformation::Residue
• actual_twobody_memory_use() : core::pack::interaction_graph::DoubleLazyEdge
• add() : core::fragment::FragSet , core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• add_() : core::fragment::ConstantLengthFragSet , core::fragment::FragSet , core::fragment::FragSetCollection , core::fragment::OrderedFragSet
• add_actcoord_atom() : core::chemical::ResidueType
• add_active_1benmeth_ext() : core::scoring::MinimizationNode
• add_active_1benmeth_std() : core::scoring::MinimizationNode
• add_active_2benmeth_ext() : core::scoring::MinimizationNode
• add_active_2benmeth_std() : core::scoring::MinimizationNode
• add_active_enmeth_ext() : core::scoring::MinimizationEdge
• add_active_enmeth_std() : core::scoring::MinimizationEdge
• add_adduct() : core::chemical::ResidueType
• add_angle_parameter() : core::scoring::methods::ResidueCartBondedParameters
• add_as_other_struct_if_relevant() : core::io::silent::SilentFileData
• add_atmname_using() : core::scoring::methods::GoapRsdType
• add_atom() : core::chemical::ResidueType , core::chemical::sdf::MolFileIOMolecule , core::kinematics::MinimizerMapBase , core::optimization::CartesianMinimizerMap , core::optimization::DOF_Node , core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap , core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• add_atom_alias() : core::chemical::ResidueType
• add_atom_to_trie() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• add_background_edge() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::FirstClassNode< V, E, G >
• add_bb_clone() : core::conformation::symmetry::SymmetryInfo
• add_bbdep_angle_parameter() : core::scoring::methods::ResidueCartBondedParameters
• add_bbdep_length_parameter() : core::scoring::methods::ResidueCartBondedParameters
• add_behavior() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• add_bin_transition_data() : core::scoring::bin_transitions::BinTransitionCalculator
• add_bond() : core::chemical::ResidueType , core::chemical::sdf::MolFileIOMolecule
• add_bond_length() : core::chemical::IdealBondLengthSet
• add_calculator() : core::pose::metrics::PoseMetricContainer
• add_chain_ending() : core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T >
• add_chi() : core::chemical::ResidueType
• add_chi_clone() : core::conformation::symmetry::SymmetryInfo
• add_chi_rotamer() : core::chemical::ResidueType
• add_chi_rotamer_to_last_chi() : core::chemical::ResidueType
• add_circle() : core::scoring::packstat::Slice
• add_comment() : core::io::silent::SilentStruct
• add_constraint() : core::pose::Pose , core::scoring::constraints::Constraints , core::scoring::constraints::ConstraintSet
• add_constraints() : core::pose::Pose , core::scoring::constraints::ConstraintSet
• add_coordinate_from_string() : core::conformation::symmetry::VirtualCoordinate
• add_creator() : core::pack::task::operation::ResFilterFactory , core::pack::task::operation::ResLvlTaskOperationFactory , core::pack::task::operation::TaskOperationFactory
• add_cut_bond() : core::chemical::ResidueType
• add_datum() : core::scoring::rna::data::RNA_DataInfo
• add_deriv_data() : core::optimization::NumericalDerivCheckResult
• add_dna_base_distance_constraints() : core::scoring::dna::DNATorsionPotential
• add_DNA_torsion_constraint() : core::scoring::dna::DNATorsionPotential
• add_dna_torsion_tethers() : core::scoring::dna::DNATorsionPotential
• add_dof_access() : core::environment::DofPassport
• add_dof_constraint() : core::scoring::constraints::ConstraintSet
• add_dof_deriv_1benmeth() : core::scoring::MinimizationNode
• add_dof_deriv_2benmeth() : core::scoring::MinimizationNode
• add_dof_from_string() : core::conformation::symmetry::SymDof
• add_edge() : core::graph::Graph , core::graph::Node , core::graph::UEVertex< V, E > , core::graph::UpperEdgeGraph< V, E > , core::kinematics::FoldTree , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::PDInteractionGraph
• add_edge_common() : core::graph::UEVertex< V, E >
• add_encoded_termini() : core::scoring::methods::NMerSVMEnergy
• add_energy() : core::io::silent::SilentStruct
• add_energy_edge() : core::scoring::EnergyGraph
• add_extent_eval() : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• add_extent_gen() : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• add_extra_method() : core::scoring::ScoreFunction
• add_frag_type() : core::fragment::FragFactory
• add_fragment() : core::fragment::Frame
• add_fragment_eval() : core::fragment::picking_old::vall::VallLibrarian
• add_fragment_gen() : core::fragment::picking_old::vall::VallLibrarian
• add_fragset() : core::fragment::FragSetCollection
• add_frame_type() : core::fragment::FragFactory
• add_func() : core::scoring::func::SumFunc
• add_gaussian() : core::scoring::SmoothScoreTermCoeffs
• add_hbond() : core::scoring::hbonds::HBondResPairMinData
• add_improper_torsion_parameter() : core::scoring::methods::ResidueCartBondedParameters
• add_individual_constraint() : core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::MultiConstraint
• add_interaction() : core::scoring::custom_pair_distance::AtomPairFuncList
• add_jump() : core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RigidBodySilentStruct , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreJumpFileSilentStruct
• add_jump_clone() : core::conformation::symmetry::SymmetryInfo
• add_jump_label() : core::environment::SequenceAnnotation
• add_jump_neighbor() : core::environment::FoldTreeSketch::Node
• add_length_parameter() : core::scoring::methods::ResidueCartBondedParameters
• add_line() : core::chemical::ResidueSelector , core::sequence::ABEGO
• add_list_filenames() : core::import_pose::pose_stream::PDBPoseInputStream
• add_lower_connect_angle_params() : core::scoring::methods::ResidueCartBondedParameters
• add_lr_gaussian() : core::scoring::CenHBPotential
• add_memb_etable() : core::scoring::ScoringManager
• add_metalbinding_atom() : core::chemical::ResidueType
• add_method() : core::scoring::ScoreFunction
• add_motif() : core::scoring::motif::MotifHash
• add_motif_set_name() : core::scoring::motif::MotifHashManager
• add_mutation_ddG() : core::io::PositionDdGInfo::PositionDdGInfo
• add_neighbors_mass() : core::scoring::TenANeighborNode
• add_new_dof_node() : core::optimization::symmetry::SymMinimizerMap
• add_nu() : core::chemical::ResidueType
• add_numeric_property() : core::chemical::ResidueProperties , core::chemical::ResidueType
• add_onebody_enmeth() : core::scoring::MinimizationNode
• add_operation() : core::chemical::PatchCase
• add_orbital() : core::chemical::ResidueType
• add_orbital_bond() : core::chemical::ResidueType
• add_orbitals_to_restype() : core::chemical::orbitals::AssignOrbitals
• add_other_pose() : core::pose::full_model_info::FullModelInfo
• add_other_struct() : core::io::silent::SilentStruct
• add_pairing() : core::scoring::dssp::StrandPairingSet
• add_parameters() : core::conformation::parametric::ParametersSet
• add_parameters_from_file() : core::chemical::AtomTypeSet
• add_parameters_set() : core::conformation::Conformation
• add_parent_remark() : core::io::silent::SilentStruct
• add_peptide_neighbor() : core::environment::FoldTreeSketch::Node
• add_pose() : core::pack::rotamer_set::UnboundRotamersOperation , core::pose::xyzStripeHashPose
• add_pose_input_stream() : core::import_pose::pose_stream::MetaPoseInputStream
• add_probe_to_pose() : core::scoring::rna::data::RNA_DMS_Potential
• add_ProCorrection_values() : core::pack::interaction_graph::SymmOnTheFlyEdge
• add_ProCorrection_values_for_edge() : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• add_property() : core::chemical::AtomType , core::chemical::ResidueType
• add_property_i() : core::scoring::bin_transitions::BinTransitionData
• add_property_iplus1() : core::scoring::bin_transitions::BinTransitionData
• add_pseudobond() : core::conformation::Conformation
• add_pssm_features() : core::scoring::methods::NMerSVMEnergy
• add_reactivity() : core::scoring::rna::data::RNA_DataInfo
• add_res_identity_i() : core::scoring::bin_transitions::BinTransitionData
• add_res_identity_iplus1() : core::scoring::bin_transitions::BinTransitionData
• add_residue() : core::conformation::parametric::Parameters , core::fragment::FragData , core::pack::dunbrack::RotamerConstraint
• add_residue_connection() : core::chemical::ResidueType
• add_residue_dis() : core::scoring::TMscoreStore
• add_residue_library() : core::pack::dunbrack::RotamerLibrary
• add_residue_pair_constraint() : core::scoring::constraints::ConstraintSet
• add_residue_selector() : core::pack::task::residue_selector::AndResidueSelector , core::pack::task::residue_selector::OrResidueSelector
• add_residue_type() : core::chemical::ResidueTypeSet
• add_residue_type_to_maps() : core::chemical::ResidueTypeSet
• add_reslabel() : core::pose::PDBInfo
• add_reverse_motifs() : core::scoring::motif::ResPairMotifs
• add_reweighter() : core::pack::task::IGEdgeReweightContainer
• add_rotamer() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• add_rt() : core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RigidBodySilentStruct
• add_score() : core::scoring::motif::XformScore
• add_scored_pair() : core::sequence::PairScoringScheme
• add_scoring_scheme() : core::sequence::CompositeScoringScheme
• add_section() : core::fragment::picking_old::vall::VallLibrary
• add_segment() : core::pose::datacache::SpecialSegmentsObserver
• add_seq_label() : core::environment::SequenceAnnotation
• add_sequence() : core::sequence::CompositeSequence , core::sequence::SequenceAlignment
• add_sfd_1benmeth() : core::scoring::MinimizationNode
• add_sfd_2benmeth() : core::scoring::MinimizationNode
• add_sfd_enmeth() : core::scoring::MinimizationEdge
• add_sfs_1benmeth() : core::scoring::MinimizationNode
• add_sfs_2benmeth() : core::scoring::MinimizationNode
• add_sfs_enmeth() : core::scoring::MinimizationEdge
• add_sigmoid() : core::scoring::SmoothScoreTermCoeffs
• add_span() : core::conformation::membrane::SpanningTopology
• add_sr_gaussian() : core::scoring::CenHBPotential
• add_str_str_data() : core::chemical::sdf::MolFileIOMolecule
• add_string_property() : core::chemical::ResidueProperties , core::chemical::ResidueType
• add_string_value() : core::io::silent::SilentStruct
• add_structure() : core::io::silent::SilentFileData
• add_structure_replace_tag_if_necessary() : core::io::silent::SilentFileData
• add_sugar_ring_closure_constraints() : core::scoring::dna::DNATorsionPotential , core::scoring::rna::RNA_SugarCloseEnergy
• add_threshold_distance_allFrag() : core::indexed_structure_store::FragmentStore
• add_to_energy_map() : core::scoring::EnergyEdge
• add_to_nodes_one_body_energy() : core::pack::interaction_graph::InteractionGraphBase
• add_to_one_body_energies() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmOnTheFlyNode
• add_to_one_body_energy() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmOnTheFlyNode
• add_to_one_body_energy_for_node_state() : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• add_to_two_body_energies() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::PrecomputedPairEnergiesEdge
• add_to_two_body_energies_for_edge() : core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph
• add_to_two_body_energy() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::PrecomputedPairEnergiesEdge
• add_torsion() : core::kinematics::MinimizerMapBase , core::optimization::CartesianMinimizerMap , core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap , core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• add_torsion_parameter() : core::scoring::methods::ResidueCartBondedParameters
• add_twobody_enmeth() : core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• add_type() : core::scoring::func::FuncFactory , core::sequence::ScoringSchemeFactory
• add_unrecognized_atom() : core::pose::PDBInfo
• add_upper_connect_angle_params() : core::scoring::methods::ResidueCartBondedParameters
• add_variant_type() : core::chemical::ResidueType
• add_vertex() : core::kinematics::FoldTree
• add_weights_from_file() : core::scoring::ScoreFunction
• add_whole_pose_context_enmeth() : core::scoring::MinimizationGraph
• AddAromaticAtomType() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• AddAtom() : core::chemical::AddAtom , core::scoring::sc::MolecularSurfaceCalculator
• AddAtomAlias() : core::chemical::AddAtomAlias
• AddAtomType() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• AddBehaviorRLT() : core::pack::task::operation::AddBehaviorRLT
• AddBond() : core::chemical::AddBond
• AddBondType() : core::chemical::AddBondType
• AddChi() : core::chemical::AddChi
• AddChiRotamer() : core::chemical::AddChiRotamer
• AddConnect() : core::chemical::AddConnect
• addcount() : core::scoring::motif::ResPairMotif
• AddDot() : core::scoring::sc::MolecularSurfaceCalculator
• AddEdgeVisitor() : core::conformation::AddEdgeVisitor< Vertex, Edge >
• AdditionalBackgroundNodesInteractionGraph() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• AddProperty() : core::chemical::AddProperty
• AddProtonChi() : core::chemical::AddProtonChi
• AddResidue() : core::scoring::sc::MolecularSurfaceCalculator
• AddResiduesRotamerSetOperation() : core::pack::rotamer_set::AddResiduesRotamerSetOperation
• Adduct() : core::chemical::Adduct
• adduct_name() : core::chemical::Adduct
• adducts() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• adjbb_elec_scale() : core::scoring::FACTSPotential
• adjbb_solv_scale() : core::scoring::FACTSPotential
• adjbs_elec_scale() : core::scoring::FACTSPotential
• adjbs_solv_scale() : core::scoring::FACTSPotential
• aggregate_add() : core::scoring::motif::XformScore
• aggregate_max() : core::scoring::motif::XformScore
• AHdist_long_fade_lookup() : core::scoring::hbonds::HBondDatabase
• AHdist_poly_lookup() : core::scoring::hbonds::HBondDatabase
• AHdist_short_fade_lookup() : core::scoring::hbonds::HBondDatabase
• Ai() : core::scoring::FACTSResidueInfo
• align() : core::fragment::Frame , core::fragment::NonContinuousFrame , core::sequence::Aligner , core::sequence::MCAligner , core::sequence::NWAligner , core::sequence::SWAligner
• align_to_residue() : core::conformation::UltraLightResidue
• Aligner() : core::sequence::Aligner
• alignment_id() : core::sequence::SequenceAlignment
• all_aligned() : core::id::SequenceMapping
• all_bb_atoms() : core::chemical::ResidueType , core::conformation::Residue
• all_energies_begin() : core::scoring::ScoreFunction
• all_energies_end() : core::scoring::ScoreFunction
• all_methods() : core::scoring::ScoreFunction
• all_pairs_shortest_paths() : core::graph::Graph
• all_ref_poses() : core::import_pose::atom_tree_diffs::AtomTreeDiff
• all_residues_begin() : core::chemical::ResidueTypeSet
• all_residues_end() : core::chemical::ResidueTypeSet
• all_sc_atoms() : core::chemical::ResidueType
• alllevel() : core::sequence::ABEGOManager
• allocate_appropriate_memory() : core::scoring::Membrane_FAEmbed , core::scoring::methods::LK_hack
• allocate_grid_of_occluded_sites() : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• allocated() : core::graph::NegSpaceElement< T >
• allow_aa() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• allow_dof() : core::conformation::symmetry::SymDof
• allow_hbond() : core::scoring::hbonds::HBondSet
• allow_noncanonical_aa() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• allow_phosphate_virtualization() : core::pack::task::rna::RNA_ResidueLevelTask
• allow_scoring() : core::scoring::MembraneTopology
• allow_tmh_scoring() : core::scoring::MembraneTopology
• allowed_residue_types() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• allowed_residue_types_begin() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• allowed_residue_types_end() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• AllResFilter() : core::pack::task::operation::AllResFilter
• alpha() : core::pose::CrystInfo , core::pose::Pose , core::scoring::CSA , core::scoring::FACTSRsdTypeInfo
• alpha_aform() : core::chemical::rna::RNA_FittedTorsionInfo
• alpha_components() : core::scoring::dna::DNATorsionPotential
• alphabet() : core::sequence::ChemicalShiftSequence , core::sequence::SequenceProfile
• alt_loc() : core::pose::PDBInfo
• alt_sc_centroid() : core::pack::interaction_graph::SimpleNode
• alt_sc_radius() : core::pack::interaction_graph::SimpleNode
• alt_state_energy() : core::pack::interaction_graph::SymmMinimalistEdge
• alt_state_exp_hphobes() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• alt_state_hphobes() : core::pack::interaction_graph::HPatchNode< V, E, G >
• alt_state_inv_dots() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• alt_state_rotamer() : core::pack::interaction_graph::HPatchNode< V, E, G >
• alter_rotamer_set() : core::pack::rotamer_set::AddResiduesRotamerSetOperation , core::pack::rotamer_set::RotamerSetOperation , core::pack::rotamer_set::UnboundRotamersOperation
• AmberPeriodicFunc() : core::scoring::func::AmberPeriodicFunc
• AmbiguousConstraint() : core::scoring::constraints::AmbiguousConstraint
• AmbiguousConstraintCreator() : core::scoring::constraints::AmbiguousConstraintCreator
• AmbiguousNMRConstraint() : core::scoring::constraints::AmbiguousNMRConstraint
• AmbiguousNMRConstraintCreator() : core::scoring::constraints::AmbiguousNMRConstraintCreator
• AmbiguousNMRDistanceConstraint() : core::scoring::constraints::AmbiguousNMRDistanceConstraint
• AmbiguousNMRDistanceConstraintCreator() : core::scoring::constraints::AmbiguousNMRDistanceConstraintCreator
• AminoAcidNeighborSparseMatrix() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• ana_deriv() : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• analytic_etable_derivatives() : core::scoring::etable::Etable
• analytic_etable_evaluation() : core::scoring::etable::Etable , core::scoring::methods::EnergyMethodOptions
• analytic_lj_generic_form() : core::scoring::etable::Etable
• analytic_ljatr_cubic_poly_ramp_to_zero() : core::scoring::etable::Etable
• analytic_ljatr_cubic_poly_ramp_to_zero_deriv() : core::scoring::etable::Etable
• analytic_ljrep_linearized() : core::scoring::etable::Etable
• analytic_lk_derivatives() : core::scoring::etable::Etable
• analytic_lk_energy() : core::scoring::etable::Etable
• analytic_lk_evaluation() : core::scoring::etable::Etable
• analytic_lk_evaluation_individual() : core::scoring::etable::Etable
• analytic_params_for_pair() : core::scoring::etable::Etable
• AnalyticEtableEnergy() : core::scoring::etable::AnalyticEtableEnergy
• AnalyticEtableEvaluator() : core::scoring::etable::AnalyticEtableEvaluator
• anchor_atom() : core::pack::rotamer_set::WaterAnchorInfo
• anchor_residue() : core::pack::rotamer_set::WaterAnchorInfo
• and_extrachi_cutoff() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• and_max_rotbump_energy() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• AndResidueSelector() : core::pack::task::residue_selector::AndResidueSelector
• angle() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• angle_constraint_energy() : core::scoring::constraints::ConstraintEdge
• angle_parameters() : core::scoring::methods::ResidueCartBondedParameters
• AngleConstraint() : core::scoring::constraints::AngleConstraint
• AngleConstraintCreator() : core::scoring::constraints::AngleConstraintCreator
• AngularMomentumQuantumNumber_strings() : core::chemical::ElectronConfiguration
• animate() : core::conformation::ResidueKinWriter
• annealer_file() : core::pack::annealer::DebuggingAnnealer
• annotated_sequence() : core::pose::Pose
• AnnotatedFragData() : core::fragment::AnnotatedFragData
• AnnotatedSequence() : core::sequence::AnnotatedSequence
• annotations() : core::io::rna::RDAT
• anomer() : core::chemical::carbohydrates::CarbohydrateInfo
• anomeric_carbon() : core::chemical::carbohydrates::CarbohydrateInfo
• anomeric_carbon_index() : core::chemical::carbohydrates::CarbohydrateInfo
• anomeric_carbon_name() : core::chemical::carbohydrates::CarbohydrateInfo
• antiparallel() : core::scoring::dssp::StrandPairing
• any_active_enmeths() : core::scoring::MinimizationEdge
• any_intrares_energies() : core::scoring::ScoreFunction
• any_lr_residue_pair_energy() : core::scoring::ScoreFunction
• any_neighbors_for_residue() : core::scoring::constraints::CstEnergyContainer , core::scoring::DenseEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::LREnergyContainer , core::scoring::OneToAllEnergyContainer , core::scoring::PeptideBondedEnergyContainer
• any_unassigned() : core::pack::scmin::SidechainStateAssignment
• any_upper_neighbors_for_residue() : core::scoring::constraints::CstEnergyContainer , core::scoring::DenseEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::LREnergyContainer , core::scoring::OneToAllEnergyContainer , core::scoring::PeptideBondedEnergyContainer
• any_vertex_state_unassigned() : core::pack::interaction_graph::InteractionGraphBase
• AnyResFilter() : core::pack::task::operation::AnyResFilter
• APBSConfig() : core::scoring::APBSConfig
• APBSResult() : core::scoring::APBSResult
• APBSWrapper() : core::scoring::APBSWrapper
• apfc_list() : core::scoring::custom_pair_distance::RespairInteractions
• apolar_hydrogens() : core::chemical::ResidueType
• APolarHydrogenFilter() : core::chemical::APolarHydrogenFilter
• append() : core::scoring::methods::LKB_ResiduesInfo
• append_atom() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• append_char() : core::sequence::Sequence
• append_gap() : core::sequence::Sequence
• append_hairpin() : core::scoring::Hairpins
• append_hbond() : core::scoring::hbonds::HBondSet
• append_peptide() : core::environment::FoldTreeSketch
• append_polymer_residue_after_seqpos() : core::conformation::Conformation , core::pose::Pose
• append_pose_by_jump() : core::pose::Pose
• append_res() : core::pose::PDBInfo
• append_residue() : core::conformation::Conformation , core::environment::FoldTreeSketch , core::fragment::picking_old::vall::VallSection , core::io::pdb::FileData , core::kinematics::FoldTree
• append_residue_by_bond() : core::conformation::Conformation , core::pose::Pose
• append_residue_by_chemical_bond() : core::kinematics::FoldTree
• append_residue_by_jump() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::pose::Pose
• append_rotamer_operation() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• append_rotamerset_operation() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• append_seq() : core::environment::SequenceAnnotation
• AppendInterchangeabilityGroup_String() : core::chemical::AppendInterchangeabilityGroup_String
• AppendMainchainAtom() : core::chemical::AppendMainchainAtom
• AppendResidueRotamerSet() : core::pack::task::operation::AppendResidueRotamerSet
• AppendRotamer() : core::pack::task::operation::AppendRotamer
• AppendRotamerSet() : core::pack::task::operation::AppendRotamerSet
• applies_to() : core::chemical::Patch , core::chemical::PatchCase
• apply() : core::chemical::AddAtom , core::chemical::AddAtomAlias , core::chemical::AddBond , core::chemical::AddBondType , core::chemical::AddChi , core::chemical::AddChiRotamer , core::chemical::AddConnect , core::chemical::AddProperty , core::chemical::AddProtonChi , core::chemical::AppendInterchangeabilityGroup_String , core::chemical::AppendMainchainAtom , core::chemical::DeleteAtom , core::chemical::DeleteMetalbindingAtom , core::chemical::DeleteProperty , core::chemical::DeleteTerminalChi , core::chemical::NCAARotLibPath , core::chemical::Patch , core::chemical::PatchCase , core::chemical::PatchOperation , core::chemical::PrependMainchainAtom , core::chemical::RedefineChi , core::chemical::SetAtomicCharge , core::chemical::SetAtomType , core::chemical::SetBackboneHeavyatom , core::chemical::SetFormalCharge , core::chemical::SetICoor , core::chemical::SetInterchangeabilityGroup_String , core::chemical::SetIO_String , core::chemical::SetMMAtomType , core::chemical::SetNbrAtom , core::chemical::SetNbrRadius , core::chemical::SetOrientAtom , core::chemical::SetPolymerConnectAtom , core::fragment::BBTorsionAndAnglesSRFD , core::fragment::BBTorsionSRFD , core::fragment::DownJumpSRFD , core::fragment::FragData , core::fragment::FragID , core::fragment::Frame , core::fragment::IndependentBBTorsionSRFD , core::fragment::SecstructSRFD , core::fragment::SingleResidueFragData , core::fragment::UpJumpSRFD , core::pack::task::operation::AddBehaviorRLT , core::pack::task::operation::AppendResidueRotamerSet , core::pack::task::operation::AppendRotamer , core::pack::task::operation::AppendRotamerSet , core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::DisallowIfNonnativeRLT , core::pack::task::operation::ExtraChiCutoff , core::pack::task::operation::ExtraRotamers , core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::IncludeCurrent , core::pack::task::operation::InitializeExtraRotsFromCommandline , core::pack::task::operation::InitializeFromCommandline , core::pack::task::operation::NoRepackDisulfides , core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::OperateOnResidueSubset , core::pack::task::operation::OptCysHG , core::pack::task::operation::OptH , core::pack::task::operation::PreserveCBeta , core::pack::task::operation::PreventRepacking , core::pack::task::operation::PreventRepackingRLT , core::pack::task::operation::ReadResfile , core::pack::task::operation::ReadResfileAndObeyLengthEvents , core::pack::task::operation::ReplicateTask , core::pack::task::operation::ResLvlTaskOperation , core::pack::task::operation::RestrictAbsentCanonicalAAS , core::pack::task::operation::RestrictAbsentCanonicalAASRLT , core::pack::task::operation::RestrictResidueToRepacking , core::pack::task::operation::RestrictToRepacking , core::pack::task::operation::RestrictToRepackingRLT , core::pack::task::operation::RestrictYSDesign , core::pack::task::operation::RotamerExplosion , core::pack::task::operation::SetRotamerCouplings , core::pack::task::operation::SetRotamerLinks , core::pack::task::operation::TaskOperation , core::pack::task::residue_selector::AndResidueSelector , core::pack::task::residue_selector::ChainSelector , core::pack::task::residue_selector::ClashBasedRepackShellSelector , core::pack::task::residue_selector::InterGroupInterfaceByVectorSelector , core::pack::task::residue_selector::JumpDownstreamSelector , core::pack::task::residue_selector::JumpUpstreamSelector , core::pack::task::residue_selector::NeighborhoodResidueSelector , core::pack::task::residue_selector::NotResidueSelector , core::pack::task::residue_selector::NumNeighborsSelector , core::pack::task::residue_selector::OrResidueSelector , core::pack::task::residue_selector::ResidueIndexSelector , core::pack::task::residue_selector::ResidueNameSelector , core::pack::task::residue_selector::ResidueSelector , core::pack::task::residue_selector::TrueResidueSelector , core::pose::copydofs::CopyDofs , core::pose::rna::RNA_IdealCoord , core::scoring::TMscore , core::scoring::TMscoreStore
• apply_and_to_subset() : core::pack::task::residue_selector::AndResidueSelector
• apply_coords() : core::pose::rna::RNA_IdealCoord
• apply_or_to_subset() : core::pack::task::residue_selector::OrResidueSelector
• apply_patch_from_file() : core::scoring::ScoreFunction
• apply_patches() : core::chemical::ResidueTypeSet
• apply_pucker() : core::pose::rna::RNA_IdealCoord
• apply_sequence_mapping() : core::kinematics::FoldTree
• apply_ss() : core::fragment::DownJumpSRFD , core::fragment::FragData , core::fragment::FragID , core::fragment::Frame , core::fragment::SecstructSRFD , core::fragment::SingleResidueFragData , core::fragment::UpJumpSRFD
• apply_transform_downstream() : core::conformation::Residue
• apply_transform_Rx_plus_v() : core::conformation::Residue , core::pose::Pose
• apply_transformation() : core::conformation::symmetry::SymmetricConformation
• apply_transformation_norecompute() : core::conformation::symmetry::SymmetricConformation
• apply_user_defined_reweighting_() : core::scoring::ScoreFunctionFactory
• approximate_vdw_radius() : core::scoring::AtomVDW
• are_normally_bonded() : core::scoring::bin_transitions::BinTransitionCalculator
• are_they_neighbors() : core::scoring::ScoreFunction
• AreaAccumulator() : core::scoring::packstat::AreaAccumulator
• Armijo() : core::optimization::ArmijoLineMinimization
• ArmijoLineMinimization() : core::optimization::ArmijoLineMinimization
• aromatic_atoms() : core::chemical::ResidueType
• AromaticAtomFilter() : core::chemical::AromaticAtomFilter
• aromaticity() : core::chemical::Bond
• array() : core::graph::NegSpaceElement< T >
• Array0() : core::graph::Array0< T >
• Array2D() : core::scoring::packstat::Array2D
• array_pool() : core::scoring::EnergyGraph
• array_size() : core::graph::ArrayPool< T >
• ArrayPool() : core::graph::ArrayPool< T >
• ArrayPoolElement() : core::graph::ArrayPoolElement< T >
• assemble_datamatrix() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
• assert_is_calc_chem_shift_atom() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• assign() : core::pose::rna::RNA_SuiteName , core::scoring::DockingScoreFunction , core::scoring::MinScoreScoreFunction , core::scoring::ScoreFunction , core::scoring::symmetry::SymmetricScoreFunction
• assign_best_rotamer() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• assign_BMEC() : core::pack::interaction_graph::FASTERInteractionGraph
• assign_chi_for_interpolated_rotamer() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N >
• assign_dofs_to_mobile_residues() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• assign_energy() : core::pack::scmin::SidechainStateAssignment
• assign_haro_derivs_one_way() : core::scoring::orbitals::OrbitalsScore
• assign_hpol_derivs_one_way() : core::scoring::orbitals::OrbitalsScore
• assign_internal_coordinates() : core::chemical::ResidueType
• assign_neighbor_atom() : core::chemical::ResidueType
• assign_only_pi_orbitals_to_atom() : core::chemical::orbitals::AssignOrbitals
• assign_orb_H_derivs() : core::scoring::orbitals::OrbitalsScore
• assign_orb_orb_derivs() : core::scoring::orbitals::OrbitalsScore
• assign_orbitals() : core::chemical::orbitals::AssignOrbitals
• assign_parameters_to_full_etables() : core::scoring::etable::Etable
• assign_random_chi() : core::pack::dunbrack::DunbrackRotamerSampleData
• assign_random_rotamer() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N >
• assign_random_rotamer_with_bias() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleLigandRotamerLibrary , core::pack::dunbrack::SingleResidueRotamerLibrary
• assign_random_rotamer_with_bias_bbdep() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• assign_random_rotamer_with_bias_bbind() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• assign_rosetta_torsions() : core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap
• assign_rosetta_torsions_and_trim() : core::optimization::CartesianMinimizerMap
• assign_sp2_orbitals_to_one_bonded_atom() : core::chemical::orbitals::AssignOrbitals
• assign_sp2_sp_orbitals_to_one_bonded_atom() : core::chemical::orbitals::AssignOrbitals
• assign_state() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , core::pack::scmin::SidechainStateAssignment
• assign_state_surface() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• assign_zero_state() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• AssignAtomRadius() : core::scoring::sc::MolecularSurfaceCalculator
• AssignAttentionNumbers() : core::scoring::sc::MolecularSurfaceCalculator , core::scoring::sc::ShapeComplementarityCalculator
• AssignOrbitals() : core::chemical::orbitals::AssignOrbitals
• asymmetric_dof() : core::optimization::symmetry::SymMinimizerMap
• at() : core::sequence::Sequence
• atmid() : core::scoring::methods::GoapRsdType
• atmname_using() : core::scoring::methods::GoapRsdType
• Atom() : core::chemical::Atom
• atom() : core::chemical::ResidueType
• Atom() : core::conformation::Atom
• atom() : core::conformation::Residue , core::id::EXCN_AtomNotFound , core::id::NamedAtomID , core::id::NamedStubID , core::id::StubID , core::kinematics::AtomTree
• Atom() : core::kinematics::tree::Atom
• atom() : core::pack::dunbrack::DunbrackConstraint , core::pack::dunbrack::RotamerConstraint , core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint , core::scoring::constraints::BigBinConstraint , core::scoring::constraints::ConstantConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::ResidueTypeLinkingConstraint , core::scoring::constraints::SequenceProfileConstraint , core::scoring::packstat::SimplePDB
• Atom() : core::scoring::sc::Atom
• atom() : core::scoring::trie::RotamerDescriptor< AT, CPDAT > , core::scoring::trie::RotamerDescriptorAtom< AT, CPDAT > , core::scoring::trie::TrieNode< AT, CPDATA >
• atom1() : core::chemical::sdf::MolFileIOBond , core::scoring::constraints::Obsolet_NamedAtomPairConstraint , core::scoring::CSA , core::scoring::DC , core::scoring::methods::WaterBuilder , core::scoring::RDC
• atom13() : core::scoring::methods::ProQ_Energy
• atom13_0() : core::scoring::methods::ProQ_Energy
• atom2() : core::chemical::sdf::MolFileIOBond , core::scoring::constraints::Obsolet_NamedAtomPairConstraint , core::scoring::CSA , core::scoring::DC , core::scoring::methods::WaterBuilder , core::scoring::RDC
• atom3() : core::scoring::CSA , core::scoring::methods::WaterBuilder
• Atom_() : core::kinematics::tree::Atom_
• atom_atom_context_derivative() : core::scoring::FACTSPotential
• atom_base() : core::chemical::ResidueType , core::conformation::Residue
• atom_begin() : core::conformation::Residue
• atom_being_shadowed() : core::chemical::ResidueType
• atom_charge() : core::chemical::Adduct
• atom_data() : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• atom_derivatives() : core::optimization::CartesianMinimizerMap , core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• atom_dont_do_update() : core::kinematics::AtomTree
• atom_end() : core::conformation::Residue
• atom_feature() : core::scoring::methods::ProQ_Energy
• atom_forms_residue_connection() : core::chemical::ResidueType
• atom_gets_derivatives() : core::scoring::disulfides::DisulfideAtomIndices
• atom_gradient() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• atom_has_exp_chemical_shift_data() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• atom_has_orbital() : core::chemical::AtomType
• atom_hbonds() : core::scoring::hbonds::HBondSet
• atom_id() : core::chemical::ICoorAtomID , core::id::DOF_ID , core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::optimization::DOF_Node
• atom_index() : core::chemical::ResidueType , core::chemical::sdf::MolFileIOMolecule , core::conformation::Residue , core::scoring::methods::dfire::DFIRE_Potential
• atom_is_acceptor() : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::hbonds::HBond
• atom_is_apolar_h() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• atom_is_backbone() : core::chemical::ResidueType , core::conformation::Residue
• atom_is_backbone_norefold() : core::conformation::Conformation
• atom_is_donor_h() : core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody
• atom_is_donorH() : core::scoring::hbonds::HBond
• atom_is_heavy() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• atom_is_hydrogen() : core::chemical::ResidueType , core::conformation::Residue
• atom_is_independent() : core::conformation::symmetry::SymmetryInfo
• atom_is_on_path_from_root() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• atom_is_phosphate() : core::chemical::rna::RNA_ResidueType
• atom_is_polar_hydrogen() : core::chemical::ResidueType , core::conformation::Residue
• atom_is_valid_base() : core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody
• atom_is_virtual() : core::chemical::rna::RNA_ResidueType
• atom_iterators() : core::chemical::ResidueType
• atom_name() : core::chemical::Adduct , core::chemical::ResidueType , core::conformation::AtomGraphVertexData , core::conformation::Residue , core::pose::MiniPose , core::pose::UnrecognizedAtomRecord , core::scoring::packing::PoseBalls
• atom_names_list() : core::pose::MiniPose
• atom_neighbors() : core::scoring::NeighborList , core::scoring::ResidueNblistData , core::scoring::ResiduePairNeighborList
• atom_num() : core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• atom_numbers_for_mg_calculation() : core::scoring::rna::RNA_ScoringInfo
• atom_numbers_for_vdw_calculation() : core::scoring::rna::RNA_ScoringInfo
• atom_overlap_is_exposed() : core::pack::interaction_graph::InvRotamerDots
• atom_pair_constraint_energy() : core::scoring::constraints::ConstraintEdge
• atom_pair_cutoff() : core::scoring::NeighborList
• atom_pair_energy() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::TableLookupEvaluator , core::scoring::vdwaals::VDW_Energy
• atom_pair_energy_v() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::EtableEvaluator , core::scoring::etable::TableLookupEvaluator
• atom_pair_lk_energy_and_deriv_v() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::EtableEvaluator , core::scoring::etable::TableLookupEvaluator
• atom_pair_lk_energy_and_deriv_v_efficient() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::EtableEvaluator , core::scoring::etable::TableLookupEvaluator
• atom_pointer() : core::kinematics::AtomTree
• atom_radius_squared() : core::conformation::AtomGraphVertexData
• atom_set() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• atom_tree() : core::conformation::Conformation , core::pose::Pose
• atom_tree_torsion() : core::conformation::Conformation
• atom_type() : core::chemical::gasteiger::GasteigerAtomTypeSet , core::chemical::ResidueType , core::conformation::Residue , core::scoring::elec::ElecAtom , core::scoring::etable::Etable , core::scoring::etable::etrie::EtableAtom , core::scoring::etable::MembEtable , core::scoring::packing::PoseBalls , core::scoring::vdwaals::VDWAtom
• atom_type_index() : core::chemical::Atom , core::chemical::AtomTypeSet , core::chemical::gasteiger::GasteigerAtomTypeSet , core::chemical::MMAtomTypeSet , core::conformation::Residue
• atom_type_name() : core::chemical::Adduct , core::chemical::AtomType , core::chemical::orbitals::OrbitalType
• atom_type_set() : core::chemical::ChemicalManager , core::chemical::ResidueType , core::chemical::ResidueTypeSet , core::conformation::Residue
• atom_type_set_name() : core::scoring::AtomVDW
• atom_type_set_ptr() : core::chemical::ResidueType
• atom_type_set_tag() : core::chemical::ResidueLoaderOptions
• atom_vdw_atom_type_set_name() : core::scoring::methods::EnergyMethodOptions
• atom_vertex() : core::chemical::ResidueType
• atom_weights() : core::scoring::methods::LKB_ResidueInfo
• atom_z_position() : core::conformation::membrane::MembraneInfo
• AtomGraphEdgeData() : core::conformation::AtomGraphEdgeData
• AtomGraphVertexData() : core::conformation::AtomGraphVertexData
• atomic_charge() : core::conformation::Residue
• atomic_interaction_cutoff() : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_GrpElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::DatabaseOccSolEne , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergyEvaluator , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::hackaro::HackAroEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::interface_::DDPscore , core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::membrane::FaMPSolvEnergy , core::scoring::membrane::MPPairEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::CenRotPairEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::GoapEnergy , core::scoring::methods::HybridVDW_Energy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::LK_hack , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MembraneEnvSmoothEnergy , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::PeptideBondEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::ProQ_Energy , core::scoring::methods::Rama2BOffsetEnergy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::SecondaryStructureEnergy , core::scoring::methods::ShortRangeTwoBodyEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::SuckerEnergy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::methods::WholeStructureEnergy , core::scoring::orbitals::OrbitalsScore , core::scoring::rna::data::RNA_ChemicalMappingEnergy , core::scoring::rna::data::RNA_DataBackboneEnergy , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_JR_SuiteEnergy , core::scoring::rna::RNA_LJ_BaseEnergy , core::scoring::rna::RNA_Mg_Energy , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::RNA_SuiteEnergy , core::scoring::rna::RNA_TorsionEnergy , core::scoring::rna::RNA_VDW_Energy , core::scoring::rna::StackElecEnergy , core::scoring::vdwaals::VDW_Energy , core::scoring::vdwaals::VDWTrieEvaluator
• atomic_radius() : core::scoring::GenBornResidueInfo
• AtomICoor() : core::chemical::AtomICoor
• AtomicOrbitalTypes_strings() : core::chemical::gasteiger::GasteigerAtomTypeData
• AtomID() : core::id::AtomID
• AtomID_Map() : core::id::AtomID_Map< T >
• atomids() : core::scoring::packing::PoseBalls
• AtomInformation() : core::io::pdb::AtomInformation
• AtomNeighbor() : core::scoring::AtomNeighbor
• atomno() : core::chemical::ICoorAtomID , core::chemical::ResidueConnection , core::id::AtomID , core::id::DOF_ID , core::optimization::DOF_Node , core::scoring::AtomNeighbor
• atomno1() : core::scoring::SmallAtNb
• atomno2() : core::scoring::SmallAtNb
• atompair_scale() : core::scoring::FACTSPotential
• AtomPairConstraint() : core::scoring::constraints::AtomPairConstraint
• AtomPairConstraintCreator() : core::scoring::constraints::AtomPairConstraintCreator
• AtomPairFuncList() : core::scoring::custom_pair_distance::AtomPairFuncList
• AtomRadiusMap() : core::scoring::packstat::AtomRadiusMap
• AtomRecord() : core::pose::PDBInfo::AtomRecord
• atoms() : core::conformation::Residue , core::optimization::DOF_Node , core::scoring::packstat::SimplePDB , core::scoring::trie::RotamerTrie< AT, CPDATA >
• atoms_are_bonded() : core::chemical::ResidueType , core::conformation::Conformation
• atoms_begin() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• atoms_end() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• atoms_last_controlled_by_chi() : core::chemical::ResidueType
• atoms_with_orb_index() : core::chemical::ResidueType , core::conformation::Residue
• atoms_within_one_bond_of_a_residue_connection() : core::chemical::ResidueType
• atoms_within_two_bonds_of_a_residue_connection() : core::chemical::ResidueType
• AtomTree() : core::kinematics::AtomTree
• AtomTreeCollection() : core::pack::scmin::AtomTreeCollection
• AtomTreeDiff() : core::import_pose::atom_tree_diffs::AtomTreeDiff
• AtomTreeMinimizer() : core::optimization::AtomTreeMinimizer
• AtomTreeMultifunc() : core::optimization::AtomTreeMultifunc
• AtomTreeSCMinMinimizerMap() : core::pack::scmin::AtomTreeSCMinMinimizerMap
• AtomType() : core::chemical::AtomType
• AtomTypeDatabaseIO() : core::chemical::AtomTypeDatabaseIO
• AtomTypeSet() : core::chemical::AtomTypeSet
• AtomVDW() : core::scoring::AtomVDW
• AtomWithDOFChange() : core::kinematics::AtomWithDOFChange
• atr_weight() : core::scoring::etable::EtableEvaluator
• ats_n_func_list() : core::scoring::custom_pair_distance::AtomPairFuncList
• attach() : core::pose::datacache::ObserverCache
• attach_conformation_obs() : core::pose::Pose
• attach_connection_obs() : core::conformation::Conformation
• attach_destruction_obs() : core::pose::Pose
• attach_energy_obs() : core::pose::Pose
• attach_general_obs() : core::conformation::Conformation , core::pose::Pose
• attach_identity_obs() : core::conformation::Conformation
• attach_impl() : core::pose::datacache::CacheableObserver , core::pose::datacache::LengthEventCollector , core::pose::datacache::SpecialSegmentsObserver
• attach_length_obs() : core::conformation::Conformation
• attach_to() : core::pose::datacache::CacheableObserver , core::pose::metrics::PoseMetricContainer , core::pose::PDBInfo
• attach_to_conformation() : core::scoring::constraints::ConstraintSet
• attach_topological_observer() : core::kinematics::AtomTree
• attach_xyz_obs() : core::conformation::Conformation
• attached_H_begin() : core::chemical::ResidueType , core::conformation::Residue
• attached_H_end() : core::chemical::ResidueType , core::conformation::Residue
• attaches_to_residue_type() : core::pack::rotamer_set::WaterAnchorInfo
• auto_clash() : core::scoring::motif::ResPairMotifQuery
• autodetermine_chi_bonds() : core::chemical::ResidueType
• AutomorphismIterator() : core::chemical::AutomorphismIterator
• average_residue_hASA() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfacePotential
• avoid_sc_hbonds() : core::scoring::hbonds::hbtrie::HBCPData
• ax_init() : core::optimization::MinimizerOptions