- a -

• a() : core::scoring::electron_density::OneGaussianScattering
• a0() : core::scoring::FACTSResidueInfo
• a1() : core::scoring::FACTSResidueInfo
• a2() : core::scoring::FACTSResidueInfo
• a3() : core::scoring::FACTSResidueInfo
• aa() : core::conformation::Conformation , core::sequence::AnnotatedSequence , protocols::forge::build::GrowLeft , core::conformation::Residue , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , core::fragment::picking_old::vall::VallResidue , protocols::forge::build::SegmentRebuild , protocols::frag_picker::VallResidue , core::fragment::picking_old::vall::VallResidue , protocols::frag_picker::VallResidue , protocols::noesy_assign::MethylNames , core::chemical::ResidueType , core::pack::dunbrack::SingleResidueDunbrackLibrary , protocols::noesy_assign::Resonance , protocols::optimize_weights::PNatRotOptEPositionData , core::pack::rotamer_set::WaterAnchorInfo , protocols::optimize_weights::PNatRotOptEPositionData , protocols::simple_moves::MinimalRotamer , core::chemical::ResidueType , core::pose::Pose , core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• aa_from_resid() : protocols::noesy_assign::ResonanceList
• aa_indices_from_submatrix_index() : core::pack::interaction_graph::DoubleLazyEdge
• aa_map() : core::chemical::ResidueTypeSet
• aa_name() : protocols::noesy_assign::MethylNames
• 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
• AACompositionEnergy() : protocols::fldsgn::potentials::AACompositionEnergy
• 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
• Ab_TemplateInfo() : protocols::antibody2::Ab_TemplateInfo
• abase2() : core::chemical::ResidueType , core::conformation::Residue
• abego() : protocols::jd2::parser::BluePrint
• ABEGO() : core::util::ABEGO
• abego() : protocols::jd2::parser::BluePrint
• abego_char() : protocols::frag_picker::quota::ABEGO_SS_Map
• ABEGO_SS_Config() : protocols::frag_picker::quota::ABEGO_SS_Config
• ABEGO_SS_Map() : protocols::frag_picker::quota::ABEGO_SS_Map
• ABEGO_SS_Pool() : protocols::frag_picker::quota::ABEGO_SS_Pool
• ABEGO_SS_Score() : protocols::frag_picker::scores::ABEGO_SS_Score
• abego_str() : core::fragment::picking_old::vall::eval::ABEGOEval
• ABEGOEval() : core::fragment::picking_old::vall::eval::ABEGOEval
• ABEGOManager() : core::util::ABEGOManager
• abinitio() : protocols::surface_docking::SurfaceDockingProtocol
• AbinitioBaseFilter() : protocols::simple_filters::AbinitioBaseFilter
• abort_bad_call() : core::kinematics::tree::Atom_
• abort_min() : core::optimization::Multifunc , core::pack::scmin::CartSCMinMultifunc , core::pack::scmin::SCMinMultifunc , protocols::scoring::methods::pcs2::TensorsOptimizer , protocols::scoring::methods::pcs2::TensorsOptimizerSvd
• AbrelaxApplication() : protocols::abinitio::AbrelaxApplication
• AbrelaxMover() : protocols::abinitio::AbrelaxMover
• abs_deriv_dev() : core::optimization::SimpleDerivCheckResult
• AbstractArchiveBase() : protocols::jd2::archive::AbstractArchiveBase
• 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
• accept_claims() : protocols::topology_broker::TopologyBroker
• accept_declined_claim() : protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::FragmentClaimer , protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::TopologyClaimer
• acceptable_rmsd_change() : protocols::LoopRebuild
• acceptance_rate() : protocols::moves::MoverStatistics , protocols::moves::TrialMover
• accepted() : protocols::moves::MoverStatistics , protocols::moves::TrialCounter
• acceptorRes_occludingRes_geometric_sol_one_way() : core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergy
• acceptorRes_occludingRes_geometric_sol_RNA_intra() : core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergy
• accepts() : protocols::frag_picker::quota::ABEGO_SS_Pool
• accepts_since_last_batch() : protocols::jd2::archive::ArchiveBase
• 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::PerSphereAccumulator , core::scoring::packstat::MultiProbePoseAccumulator , core::scoring::packstat::MultiProbePerSphereAccumulator , core::scoring::packstat::Accumulator , core::scoring::packstat::AreaAccumulator
• accumulate_dxdy() : core::scoring::packstat::Accumulator , core::scoring::packstat::AreaAccumulator , core::scoring::packstat::PerSphereAccumulator , core::scoring::packstat::MultiProbePoseAccumulator , core::scoring::packstat::MultiProbePerSphereAccumulator
• accumulate_energy() : core::scoring::constraints::CstResNeighbIterator , core::scoring::constraints::CstResNeighbConstIterator , core::scoring::DenseNeighborIterator , core::scoring::DenseNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::ResidueNeighborIterator , core::scoring::ResidueNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::OneToAllNeighborConstIterator , core::scoring::PeptideBondedNeighborIterator , core::scoring::PeptideBondedNeighborConstIterator
• 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
• 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 > , protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• acknowledge_neighbors_substitution_surface() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• acknowledge_partial_state_assignment() : core::pack::interaction_graph::FASTEREdge , protocols::flexpack::interaction_graph::FlexbbEdge
• 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 , protocols::flexpack::interaction_graph::MinimalistFlexbbEdge
• 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::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchEdge< V, E, G > , 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::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge , protocols::flexpack::interaction_graph::MinimalistFlexbbEdge
• acknowledge_substitution_surface() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >
• act_on_status_response() : protocols::wum2::EndPoint
• actcoord() : core::conformation::Residue
• actcoord_atoms() : core::chemical::ResidueType , core::conformation::Residue
• activate_daemon_mode() : protocols::pack_daemon::DaemonSet
• 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_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_pose_constraints() : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• active_residue() : core::pack::scmin::ResidueAtomTreeCollection , core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , 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
• active_site_grid() : protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::DownstreamBuilder
• active_site_grid_set() : protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::DownstreamBuilder
• active_variables() : protocols::pack_daemon::VariableVectorExpression , protocols::pack_daemon::IterativeVectorExpression , protocols::pack_daemon::VMax , protocols::pack_daemon::VMin , protocols::pack_daemon::VMaxBy , protocols::pack_daemon::VMinBy , protocols::pack_daemon::SurrogateVariableExpression
• active_variables_vector() : protocols::pack_daemon::VectorExpression , protocols::pack_daemon::VariableVectorExpression , protocols::pack_daemon::IterativeVectorExpression
• ActiveSiteGrid() : protocols::match::downstream::ActiveSiteGrid
• actual_bb() : protocols::match::Bool3DGrid
• actual_residue_connection() : core::conformation::Residue
• actual_twobody_memory_use() : core::pack::interaction_graph::DoubleLazyEdge
• actually_moving_res() : protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::StepWiseJobParameters
• adaptation_period() : protocols::simple_moves::GenericMonteCarloMover
• adaptive_movers() : protocols::simple_moves::GenericMonteCarloMover
• AdaptiveScoreHistogram() : protocols::frag_picker::scores::AdaptiveScoreHistogram
• add() : core::fragment::FragSet , core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , protocols::abinitio::StructureStore , protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::forge::build::BuildManager , protocols::frag_picker::BoundedCollector< StrictWeakOrdering > , protocols::frag_picker::CandidatesCollector , protocols::frag_picker::GrabAllCollector , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaCollector , protocols::frag_picker::quota::SecondaryStructurePool , protocols::moves::DataMap , protocols::noesy_assign::PeakAssignmentResidueMap , protocols::pockets::PCluster , protocols::pockets::PClusterSet , protocols::topology_broker::TopologyBroker , protocols::wum::SilentStructStore , protocols::wum::WorkUnitQueue , protocols::wum::WorkUnitQueue_Swapped
• add_() : core::fragment::ConstantLengthFragSet , core::fragment::FragSet , core::fragment::FragSetCollection , core::fragment::OrderedFragSet
• add_aa_virt_rsd_as_root() : protocols::swa::rna::StepWiseRNA_PoseSetup
• 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_additional_low_resolution_step() : protocols::docking::DockingProtocol
• add_additional_task_operaration() : protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::DockTaskFactory
• add_adduct() : core::chemical::ResidueType
• add_all_atoms() : protocols::noesy_assign::PeakAssignmentResidueMap
• add_all_evaluators() : protocols::evaluation::EvaluatorFactory
• add_all_remaining() : core::coarse::Translator
• add_aln() : protocols::comparative_modeling::AlignmentCluster
• add_angle_parameter() : core::scoring::methods::ResidueCartBondedParameters
• add_assignment() : protocols::noesy_assign::CrossPeak::Spin
• add_at_ind() : protocols::match::downstream::AtomGeometrySecMatchRPE
• add_atom() : core::chemical::ResidueType , core::coarse::Translator , 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 , core::scoring::sc::MolecularSurfaceCalculator
• add_atom_to_trie() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• add_atomgeom_evaluator() : protocols::match::downstream::GeometrySecMatchRPE
• add_background_edge() : core::pack::interaction_graph::FirstClassNode< V, E, G > , core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• add_backrub_mover() : protocols::canonical_sampling::MetropolisHastingsMover
• add_batch() : protocols::jd2::JobDistributor
• add_bb_clone() : core::conformation::symmetry::SymmetryInfo
• add_bb_csts_to_loop() : protocols::protein_interface_design::movers::PlaceOnLoop
• add_bbdep_angle_parameter() : core::scoring::methods::ResidueCartBondedParameters
• add_bbdep_length_parameter() : core::scoring::methods::ResidueCartBondedParameters
• add_behavior() : core::pack::task::ResidueLevelTask , core::pack::task::PackerTask , core::pack::task::ResidueLevelTask_ , core::pack::task::PackerTask_
• add_blacklist() : protocols::wum::WorkUnitBase
• add_bond() : core::chemical::ResidueType
• add_bond_angle_constraint() : protocols::simple_moves::ConstrainToIdealMover
• add_bond_constraint() : protocols::simple_moves::ConstrainToIdealMover
• add_bond_length() : core::chemical::IdealBondLengthSet
• add_build_set() : protocols::match::upstream::ProteinUpstreamBuilder
• add_calculator() : core::pose::metrics::PoseMetricContainer
• add_chain_ending() : core::io::silent::BinaryProteinSilentStruct , core::io::silent::ProteinSilentStruct_Template< T >
• add_chainbreak_variants() : protocols::abinitio::KinematicControl , protocols::topology_broker::TopologyBroker
• add_chainbreaks() : protocols::jumping::JumpSample
• add_chainbreaks_as_distance_constraint() : protocols::jumping::JumpSample
• add_chainbreakweights() : protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops
• add_chem_shift_info() : protocols::rna::RNA_DeNovoProtocol
• add_chi() : core::chemical::ResidueType
• add_chi_clone() : core::conformation::symmetry::SymmetryInfo
• add_chi_rotamer() : core::chemical::ResidueType
• add_choice() : protocols::genetic_algorithm::DiscreteRandomizer
• add_chunk_filter() : protocols::frag_picker::FragmentPicker
• add_chunk_set() : protocols::rna::RNA_ChunkLibrary
• add_circle() : core::scoring::packstat::Slice
• add_comment() : core::io::silent::SilentStruct
• add_complementary_sequence() : protocols::dna::DnaInterfacePacker
• add_compositeSegmentMover() : protocols::rbsegment_relax::RBSegmentRelax
• add_condition() : protocols::filters::IfThenFilter
• add_constant() : protocols::filters::CalculatorFilter
• add_constrained_atoms_from_atom_pair_constraint() : protocols::enzdes::EnzdesConstraintReporter
• add_constrained_atoms_from_multiconstraint() : protocols::enzdes::EnzdesConstraintReporter
• add_constrained_lig_atom() : protocols::enzdes::EnzdesConstraintReporter
• add_constrained_nonligand_atom() : protocols::enzdes::EnzdesConstraintReporter
• add_constraint() : core::pose::Pose , core::scoring::constraints::Constraints , core::scoring::constraints::ConstraintSet , protocols::forge::remodel::RemodelConstraintGenerator
• add_constraints() : core::pose::Pose , core::scoring::constraints::ConstraintSet , protocols::abinitio::AbrelaxApplication , protocols::forge::remodel::RemodelConstraintGenerator , protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::MetalloClaimer , protocols::topology_broker::TopologyBroker , protocols::topology_broker::TopologyClaimer
• add_constraints_to_pose() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• add_constraints_to_pose_for_block_without_clearing_and_header_processing() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• add_constraints_to_scorefunction() : protocols::docking::DockingProtocol
• add_coord_cst() : protocols::abinitio::LoopJumpFoldCst
• add_coordinate_from_string() : core::conformation::symmetry::VirtualCoordinate , core::conformation::symmetry::VirtualCoordinates
• add_core_evaluator() : protocols::abinitio::IterativeBase
• add_creator() : core::pack::task::operation::ResFilterFactory , core::pack::task::operation::ResLvlTaskOperationFactory , core::pack::task::operation::TaskOperationFactory
• add_cut_bond() : core::chemical::ResidueType
• add_cut_points() : protocols::ligand_docking::MinimizeBackbone
• add_datum() : core::scoring::rna::RNA_DataInfo
• add_decoy() : protocols::optimize_weights::PNatStructureOptEData
• add_dependency_to() : protocols::forge::build::BuildInstruction
• add_deriv_data() : core::optimization::NumericalDerivCheckResult
• add_design_task() : protocols::flxbb::FlxbbDesign
• add_dist_viol_to_assignments() : protocols::noesy_assign::NoesyModule
• add_distance() : protocols::contact_map::Contact
• add_dna_base_distance_constraints() : core::scoring::dna::DNATorsionPotential
• add_dna_states() : protocols::dna::DnaInterfaceMultiStateDesign
• add_DNA_torsion_constraint() : core::scoring::dna::DNATorsionPotential
• add_dna_torsion_tethers() : core::scoring::dna::DNATorsionPotential
• 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::Node , core::graph::Graph , 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::NodeBase , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::PDInteractionGraph
• add_edge_common() : core::graph::UEVertex< V, E >
• add_elem_to_cache() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• add_end_variants() : protocols::swa::protein::StepWiseProteinPoseSetup
• add_energy() : core::io::silent::SilentStruct
• add_energy_edge() : core::scoring::EnergyGraph
• add_entity() : protocols::genetic_algorithm::GeneticAlgorithm
• add_entry() : protocols::abinitio::PairingStatistics
• add_enz_cst_interaction_to_pose() : protocols::enzdes::SecondaryMatchProtocol
• add_equiv_atoms() : protocols::comparative_modeling::ThreadingMover
• add_etable() : core::scoring::ScoringManager
• add_evaluated_structure() : protocols::abinitio::HedgeArchive , protocols::jd2::archive::EvaluatedArchive , protocols::jd2::archive::NormalizedEvaluatedArchive , protocols::jd2::archive::VarianceStatisticsArchive
• add_evaluation() : protocols::abinitio::AbrelaxApplication , protocols::abinitio::Protocol , protocols::evaluation::MetaPoseEvaluator , protocols::jd2::archive::EvaluatedArchive , protocols::jd2::JobOutputter
• add_evaluator() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• add_evaluator_for_target_restype() : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• add_evaluators() : protocols::simple_filters::RdcTargetEvaluatorCreator , protocols::simple_filters::RmsdEvaluatorCreator , protocols::simple_filters::RmsdTargetEvaluatorCreator , protocols::simple_filters::StructureSimilarityEvaluatorCreator , protocols::sparta::ChemicalShiftEvaluatorCreator , protocols::topology_broker::ConstraintEvaluatorWrapperCreator , protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator , protocols::constraints_additional::CombinedConstraintEvaluatorCreator , protocols::constraints_additional::ConstraintEvaluatorCreator , protocols::evaluation::EvaluatorCreator , protocols::evaluation::EvaluatorFactory , protocols::simple_filters::CamShiftEvaluatorCreator , protocols::simple_filters::ChiWellRmsdEvaluatorCreator , protocols::simple_filters::ContactMapEvaluatorCreator , protocols::simple_filters::ExtraScoreEvaluatorCreator , protocols::simple_filters::JScoreEvaluatorCreator , protocols::simple_filters::JumpNrEvaluatorCreator , protocols::simple_filters::NativeEvaluatorCreator , protocols::simple_filters::PalesEvaluatorCreator , protocols::simple_filters::PoolEvaluatorCreator , protocols::simple_filters::PredictedBurialFnEvaluatorCreator , protocols::simple_filters::RdcEvaluatorCreator , protocols::simple_filters::RdcSelectEvaluatorCreator
• add_excluded_chains() : protocols::ligand_docking::Translate
• 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_external_geom_sampler() : protocols::match::downstream::ClassicMatchAlgorithm
• add_external_geometry_samples_for_constraint() : protocols::match::Matcher
• add_extra_data() : protocols::loophash::BackboneDB
• add_extra_method() : core::scoring::ScoreFunction
• add_file_contents() : protocols::pack_daemon::DynamicAggregateFunction
• add_filter() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::filters::CalculatorFilter , protocols::filters::FilterCollection , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::match::MatcherTask , protocols::match::output::MatchProcessor , protocols::moves::FilterMover , protocols::simple_filters::Operator , protocols::simple_moves::GenericMonteCarloMover
• 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_fragments() : protocols::forge::remodel::RemodelLoopMover , protocols::loops::loop_mover::LoopMover
• add_fragset() : core::fragment::FragSetCollection
• add_frame_type() : core::fragment::FragFactory
• add_from_file() : protocols::motifs::MotifLibrary
• add_full_assignment() : protocols::noesy_assign::CrossPeak
• add_fullatom_flags() : protocols::abinitio::IterativeBase
• add_func() : core::scoring::constraints::SumFunc
• add_gap_constraints_to_pose() : protocols::hybridization::FoldTreeHybridize
• add_gaussian() : core::scoring::SmoothScoreTermCoeffs
• add_genericRBMover() : protocols::rbsegment_relax::RBSegmentRelax
• add_group() : protocols::simple_moves::symmetry::SetupNCSMover
• add_groupD() : protocols::simple_moves::symmetry::SetupNCSMover
• add_groupE() : protocols::simple_moves::symmetry::SetupNCSMover
• add_hbond() : core::scoring::hbonds::HBondResPairMinData
• add_helixMover() : protocols::rbsegment_relax::RBSegmentRelax
• add_hits() : protocols::match::HitNeighborFinder , protocols::match::MatchCounter
• add_hotspot_constraints_to_pose() : protocols::hotspot_hashing::HotspotStubSet
• add_hsstriplets() : protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::topology::HSSTripletSet
• add_improper_torsion_parameter() : core::scoring::methods::ResidueCartBondedParameters
• add_index_name_pair() : core::chemical::sdf::CtabBase
• add_individual_constraint() : core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::MultiConstraint
• add_info() : protocols::dna::PDBOutput
• add_inner_cycle_step() : protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer
• add_inputter() : protocols::inputter::InputterStream
• add_instruction() : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR
• add_interaction() : core::scoring::custom_pair_distance::AtomPairFuncList
• add_jump() : core::io::silent::BinaryProteinSilentStruct , core::io::silent::BinaryRNASilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::pack::task::operation::RestrictToInterface , protocols::docking::DockingProtocol , protocols::docking::RigidBodyInfo , protocols::docking::TemperedDocking , protocols::jumping::JumpSetup , protocols::jumping::JumpSelector , protocols::jumping::ResiduePairJumpSetup , protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::scoring::InterfaceInfo , protocols::simple_filters::InterfaceSasaFilter , protocols::toolbox::task_operations::RestrictToInterface
• add_jump_clone() : core::conformation::symmetry::SymmetryInfo
• add_leap() : protocols::loophash::LoopHashMap
• add_legacyleap() : protocols::loophash::LoopHashMap
• add_length_parameter() : core::scoring::methods::ResidueCartBondedParameters
• add_ligand_from_file() : protocols::motifs::MotifLibrary
• add_line() : core::chemical::ResidueSelector , core::util::ABEGO , protocols::frags::RMSVallData , protocols::frags::VallData
• add_list_filenames() : core::import_pose::pose_stream::PDBPoseInputStream
• add_loop() : protocols::forge::remodel::RemodelLoopMover , protocols::loops::Loops
• add_loop_size() : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
• add_lower_connect_angle_params() : core::scoring::methods::ResidueCartBondedParameters
• add_lr_gaussian() : core::scoring::CenHBPotential
• add_mainchain_segments() : protocols::backrub::BackrubMover
• add_mainchain_segments_from_options() : protocols::backrub::BackrubMover
• add_match() : protocols::match::output::BestMatchesCollection
• add_match_dspos1() : protocols::match::output::BestMatchesCollection
• add_memb_etable() : core::scoring::ScoringManager
• add_member() : protocols::cluster::Cluster
• add_member_front() : protocols::cluster::Cluster
• add_method() : core::scoring::ScoreFunction
• add_methyl() : protocols::noesy_assign::MethylNames
• add_metric_value_getter() : protocols::multistate_design::MultiStateFitnessFunction
• add_motif() : protocols::simple_filters::SymmetricMotifFilter
• add_movable_jump() : protocols::toolbox::task_operations::InterfaceTaskOperation
• add_mover() : protocols::canonical_sampling::CanonicalSamplingMover , protocols::canonical_sampling::MetropolisHastingsMover , protocols::moves::CanonicalSamplingMover , protocols::moves::CompositionMover , protocols::moves::MoverContainer , protocols::rosetta_scripts::ParsedProtocol , protocols::topology_broker::AsymFoldandDockClaimer , protocols::topology_broker::FibrilModelingClaimer , protocols::topology_broker::FoldandDockClaimer , protocols::topology_broker::MembraneTopologyClaimer , protocols::topology_broker::PcsEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::TopologyClaimer
• add_mutant() : protocols::optimize_weights::DDGMutationOptEData
• add_mutant_complex() : protocols::optimize_weights::DDGBindOptEData
• add_mutant_unbounds() : protocols::optimize_weights::DDGBindOptEData
• add_mutation() : protocols::optimize_weights::DDGBindOptEData , protocols::pmut_scan::Mutant
• add_mutation_ddG() : core::io::PositionDdGInfo::PositionDdGInfo
• add_native() : protocols::optimize_weights::PNatStructureOptEData
• add_native_fasta() : protocols::toolbox::task_operations::JointSequenceOperation
• add_native_pdb() : protocols::toolbox::task_operations::JointSequenceOperation
• add_native_pose() : protocols::toolbox::task_operations::JointSequenceOperation
• add_nbr() : core::optimization::AtomNode
• add_negative_filter() : protocols::protein_interface_design::filters::BoltzmannFilter
• add_neighbors_mass() : core::scoring::TenANeighborNode
• add_new() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• add_new_cluster() : protocols::toolbox::KClusterElement
• add_new_data() : protocols::toolbox::KClusterElement
• add_new_dof_node() : core::optimization::symmetry::SymMinimizerMap
• add_new_RNA_jump() : protocols::rna::RNA_StructureParameters
• add_npd_property_calculator_for_state() : protocols::pack_daemon::DaemonSet
• add_npdpro_calculator_creator() : protocols::pack_daemon::DaemonSet
• add_number_base_pairs() : protocols::rna::RNA_DeNovoProtocol
• add_number_native_base_pairs() : protocols::rna::RNA_DeNovoProtocol
• add_observer() : protocols::canonical_sampling::MetropolisHastingsMover
• add_observer_cache_segments_to_set() : protocols::enzdes::DetectProteinLigandInterface
• 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_overlap_loop() : protocols::loops::Loops
• add_overlapping_pair_chunks() : protocols::hybridization::HybridizeFoldtreeDynamic
• add_pack_daemon() : protocols::pack_daemon::DaemonSet
• add_pair() : protocols::fldsgn::topology::StrandPairing
• add_pairing() : core::scoring::dssp::StrandPairingSet , protocols::abinitio::PairingStatEntry , protocols::abinitio::AlternativePairings , protocols::abinitio::StrandConstraints
• add_parameters_from_file() : core::chemical::AtomTypeSet
• add_parent_entity() : protocols::genetic_algorithm::GeneticAlgorithm
• add_parent_remark() : core::io::silent::SilentStruct
• add_parents_from_current_generation() : protocols::genetic_algorithm::GeneticAlgorithm
• add_pdb() : protocols::toolbox::task_operations::JointSequenceOperation
• add_pdb_id() : protocols::frag_picker::PdbIdChunkFilter
• add_pdb_ids() : protocols::frag_picker::PdbIdChunkFilter
• add_pdb_profile_pair() : protocols::protein_interface_design::movers::SpliceSegment
• add_peak() : protocols::noesy_assign::PeakCalibrator
• add_point() : protocols::qsar::qsarMap
• add_pool() : protocols::frag_picker::quota::QuotaCollector
• add_pose() : core::pack::rotamer_set::UnboundRotamersOperation , protocols::loophash::BackboneDB , protocols::toolbox::task_operations::JointSequenceOperation
• add_pose_input_stream() : core::import_pose::pose_stream::MetaPoseInputStream
• add_pose_to_pool() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• add_position_data() : protocols::optimize_weights::OptEData
• add_position_in_pose() : protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• add_positive_filter() : protocols::protein_interface_design::filters::BoltzmannFilter
• add_precomputed_energies() : protocols::simple_moves::GreenPacker
• add_pregenerated_constraints_to_pose() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• add_pregenerated_enzdes_constraints() : protocols::enzdes::EnzdesBaseProtocol
• 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_protein() : protocols::loophash::BackboneDB
• add_proton() : protocols::noesy_assign::MethylNames
• add_protonated_H1_adenosine_variants() : protocols::swa::rna::StepWiseRNA_PoseSetup
• add_pseudobond() : core::conformation::Conformation
• add_query_ss() : protocols::frag_picker::FragmentPicker
• add_rcg() : protocols::forge::components::VarLengthBuild
• add_relax_batch() : protocols::loophash::MPI_LoopHashRefine_Master
• add_remaining_sidechain() : core::coarse::Translator
• add_remodel_constraints_to_pose() : protocols::forge::remodel::RemodelConstraintGenerator
• add_required_connection_for_residue() : protocols::simple_filters::PackerNeighborGraphFilter
• add_required_connections_between_regions() : protocols::simple_filters::PackerNeighborGraphFilter
• add_resid_to_entity_list() : protocols::pack_daemon::EntityCorrespondence
• add_residue() : core::fragment::FragData , core::pack::dunbrack::RotamerConstraint , protocols::enzdes::PoseFoundResiduesCombination , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover
• add_residue_() : protocols::simple_moves::HelicalPeptideLengthMover
• add_residue_connection() : core::chemical::ResidueType
• add_residue_constraints() : protocols::protein_interface_design::FavorNativeResidue , protocols::protein_interface_design::FavorNonNativeResidue
• add_residue_library() : core::pack::dunbrack::RotamerLibrary
• add_residue_pair() : protocols::jumping::ResiduePairJump
• add_residue_pair_constraint() : core::scoring::constraints::ConstraintSet
• add_residue_pair_jump() : protocols::jumping::ResiduePairJumpSetup
• add_residue_single() : protocols::jumping::ResiduePairJump
• add_residue_type() : core::chemical::ResidueTypeSet
• add_residue_type_by_name() : protocols::simple_filters::ResidueCountFilter
• add_residue_type_to_maps() : core::chemical::ResidueTypeSet
• add_reweighter() : core::pack::task::IGEdgeReweightContainer
• add_rigidity_jumps() : protocols::abinitio::LoopJumpFoldCst
• add_rotamer() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• add_rotamer_line_data() : protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatRotOptEPositionData
• add_rt() : core::io::silent::ProteinSilentStruct_Template< T >
• add_rv_info() : protocols::forge::remodel::ResidueVicinityRCG
• add_score() : protocols::moves::MoverStatistics , protocols::sic_dock::JointScore
• add_score_type() : protocols::simple_filters::ScoreCutoffFilter
• add_score_weights() : protocols::abinitio::KinematicControl , protocols::abinitio::CoordinateConstraintKC
• add_scored_pair() : core::sequence::PairScoringScheme
• add_scores_to_job() : protocols::ligand_docking::GrowLigand , protocols::ligand_docking::InterfaceScoreCalculator , protocols::ligand_docking::LigandDesign
• add_scoring_method() : protocols::frag_picker::FragmentPicker , protocols::frag_picker::scores::FragmentScoreManager
• add_scoring_scheme() : core::sequence::CompositeScoringScheme
• add_secondary_downstream_match_geometry_for_constraint() : protocols::match::Matcher
• add_secondary_upstream_match_geometry_for_constraint() : protocols::match::Matcher
• add_section() : core::fragment::picking_old::vall::VallLibrary
• add_segment() : core::pose::datacache::SpecialSegmentsObserver , protocols::backrub::BackrubMover
• add_selector() : protocols::frag_picker::CompositeFragmentSelector
• add_sequence() : core::sequence::CompositeSequence , core::sequence::SequenceAlignment
• add_sequence_constraints() : protocols::protein_interface_design::movers::Splice
• add_set() : core::pack::dunbrack::CoarseSingleResidueLibrary
• add_setup_mover() : protocols::forge::components::VarLengthBuild
• 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_shear_mover() : protocols::canonical_sampling::MetropolisHastingsMover
• add_sidechain_mc_mover() : protocols::canonical_sampling::MetropolisHastingsMover
• add_sidechain_mover() : protocols::canonical_sampling::MetropolisHastingsMover
• add_sigmoid() : core::scoring::SmoothScoreTermCoeffs
• add_silent_struct() : protocols::jd2::SilentFileJobOutputter
• add_similarity() : protocols::cluster::DataPoint
• add_small_mover() : protocols::canonical_sampling::MetropolisHastingsMover
• add_spanning_region() : protocols::abinitio::MembraneAbinitio
• add_sr_gaussian() : core::scoring::CenHBPotential
• add_start_from() : protocols::ligand_docking::LigandDockProtocol
• add_state() : protocols::multistate_design::MultiStateFitnessFunction
• add_states() : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• add_strand_pairing() : protocols::hybridization::FoldTreeHybridize
• add_strand_pairings() : protocols::hybridization::FoldTreeHybridize
• add_strandMover() : protocols::rbsegment_relax::RBSegmentRelax
• add_string() : protocols::jd2::Job
• add_string_real_pair() : protocols::jd2::Job
• add_string_string_pair() : protocols::jd2::Job
• add_string_value() : core::io::silent::SilentStruct
• add_strings() : protocols::jd2::Job
• add_structure() : core::io::silent::SilentFileData , protocols::abinitio::IterativeBase , protocols::cluster::ClusterBase , protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::DebugArchive , protocols::jd2::archive::EvaluatedArchive
• add_structure_at_position() : protocols::jd2::archive::ArchiveBase
• add_structure_based_on_rms() : protocols::optimize_weights::IterativeOptEDriver
• add_structure_replace_tag_if_necessary() : core::io::silent::SilentFileData
• add_structure_to_library() : protocols::loophash::MPI_LoopHashRefine , protocols::loophash::MPI_LoopHashRefine_Master
• add_structure_to_library_add_n_replace() : protocols::loophash::MPI_LoopHashRefine
• add_structure_to_library_direct() : protocols::loophash::MPI_LoopHashRefine
• add_structure_to_library_single_replace() : protocols::loophash::MPI_LoopHashRefine
• add_structures_to_library() : protocols::loophash::MPI_LoopHashRefine , protocols::loophash::MPI_LoopHashRefine_Emperor
• add_stub_() : protocols::hotspot_hashing::HotspotStubSet
• add_stub_set() : protocols::hotspot_hashing::HotspotStubSet
• add_suckers() : protocols::simple_moves::AddCavitiesMover
• add_sugar_ring_closure_constraints() : core::scoring::dna::DNATorsionPotential , core::scoring::rna::RNA_SugarCloseEnergy
• add_sym_dof_name() : protocols::simple_filters::InterfaceSasaFilter
• add_target_constraints() : protocols::abinitio::Templates
• add_target_restype() : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• add_task_operation() : protocols::flxbb::DesignTask
• add_task_operations() : protocols::flxbb::DesignTask
• add_template() : protocols::hybridization::HybridizeProtocol
• add_terminal_res_repulsion() : protocols::swa::rna::StepWiseRNA_PoseSetup , protocols::swa::StepWisePoseSetup
• add_to_bead() : core::coarse::Rule
• add_to_energy_map() : core::scoring::EnergyEdge
• add_to_library() : protocols::motifs::MotifLibrary
• 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::NodeBase , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmOnTheFlyNode , protocols::flexpack::interaction_graph::FlexbbNode
• 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 , protocols::flexpack::interaction_graph::FlexbbNode
• add_to_one_body_energy_for_node_state() : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• add_to_swap() : protocols::wum::WorkUnitQueue_Swapped
• add_to_targets() : protocols::toolbox::match_enzdes_util::InvrotTree
• add_to_top_level() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• 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_topology() : protocols::abinitio::PairingStatistics
• 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 , protocols::canonical_sampling::MetricRecorder , protocols::rna::FragmentLibrary
• add_torsion_id() : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• add_torsion_parameter() : core::scoring::methods::ResidueCartBondedParameters
• add_trigger() : protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo
• add_twobody_enmeth() : core::scoring::MinimizationNode , core::scoring::MinimizationEdge
• add_type() : core::scoring::constraints::FuncFactory , core::sequence::ScoringSchemeFactory , protocols::comparative_modeling::features::ResidueFeatureFactory , protocols::protein_interface_design::DockDesignFilterFactory , protocols::topology_broker::TopologyClaimerFactory
• add_unfolded_energy_data() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorJobDistributor , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
• add_unrecognized_atom() : core::pose::PDBInfo
• add_upper_connect_angle_params() : core::scoring::methods::ResidueCartBondedParameters
• add_upstream_restype_for_constraint() : protocols::match::Matcher
• add_user_provided_mover() : protocols::forge::components::VarLengthBuild
• add_variant_type() : core::chemical::ResidueType
• add_vec() : protocols::evaluation::PCA
• add_vertex() : core::kinematics::FoldTree
• add_virt_res_as_root() : protocols::swa::rna::StepWiseRNA_JobParameters
• add_weights_from_file() : core::scoring::ScoreFunction
• add_whole_pose_context_enmeth() : core::scoring::MinimizationGraph
• add_wholeStructureMover() : protocols::rbsegment_relax::RBSegmentRelax
• add_wt() : protocols::optimize_weights::DDGMutationOptEData
• add_wt_complex() : protocols::optimize_weights::DDGBindOptEData
• add_wt_unbounds() : protocols::optimize_weights::DDGBindOptEData
• AddAllPositionsMPM() : protocols::match::AddAllPositionsMPM
• AddAssemblyConstraints() : protocols::domain_assembly::AddAssemblyConstraints
• AddAtom() : core::chemical::AddAtom
• AddBehaviorRLT() : core::pack::task::operation::AddBehaviorRLT
• AddBond() : core::chemical::AddBond
• AddCavitiesMover() : protocols::simple_moves::AddCavitiesMover
• AddChainBreak() : protocols::protein_interface_design::movers::AddChainBreak
• AddChi() : core::chemical::AddChi
• AddChiRotamer() : core::chemical::AddChiRotamer
• AddConnect() : core::chemical::AddConnect
• AddConstraintsToCurrentConformationMover() : protocols::simple_moves::AddConstraintsToCurrentConformationMover
• AddDot() : core::scoring::sc::MolecularSurfaceCalculator
• AddEdgeVisitor() : core::conformation::AddEdgeVisitor< Vertex, Edge >
• addEntry() : protocols::sparta::GDB
• AddHydrogen() : protocols::ligand_docking::AddHydrogen
• AddHydrogens() : protocols::ligand_docking::AddHydrogens
• AdditionalBackgroundNodesInteractionGraph() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• AddLigandMotifRotamers() : protocols::enzdes::AddLigandMotifRotamers
• addLowResStatistics() : protocols::flexpep_docking::FlexPepDockingProtocol
• AddOrRemoveMatchCsts() : protocols::enzdes::AddOrRemoveMatchCsts
• AddProperty() : core::chemical::AddProperty
• AddProtonChi() : core::chemical::AddProtonChi
• addRemark() : protocols::sparta::GDB
• AddResidue() : core::scoring::sc::MolecularSurfaceCalculator
• address() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• address_exists_in_cache() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• address_to_buf() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• address_to_string() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• AddRigidBodyLigandConfs() : protocols::enzdes::AddRigidBodyLigandConfs
• AddSearchPatternRotSetOp() : protocols::hotspot_hashing::AddSearchPatternRotSetOp
• AddSidechainConstraintsToHotspots() : protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots
• Adduct() : core::chemical::Adduct
• adduct_name() : core::chemical::Adduct
• adducts() : core::pack::task::ResidueLevelTask , core::pack::task::PackerTask , core::pack::task::ResidueLevelTask_ , core::pack::task::PackerTask_
• addVAR() : protocols::sparta::GDB
• addVirtualResAsRootMembrane() : protocols::topology_broker::MembraneTopologyClaimer
• adjust_relax_movemap() : protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::TopologyBroker , protocols::topology_broker::TopologyClaimer
• affixed_numbered_name() : protocols::jd2::JobOutputter
• aggregate_function() : protocols::multistate_design::MultiStateFitnessFunction , protocols::pack_daemon::MultistateFitnessFunction
• 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
• ala_pose_loop() : protocols::protein_interface_design::movers::PlaceOnLoop
• AlaScan() : protocols::simple_filters::AlaScan
• algorithm() : protocols::match::upstream::BuildSet
• algorithm_inputs() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• align() : core::fragment::Frame , core::fragment::NonContinuousFrame , core::sequence::Aligner , core::sequence::ExtendAlignerSW , core::sequence::MCAligner , core::sequence::NWAligner , core::sequence::SWAligner , protocols::fibril::SetupForFibrilMover
• align_all_pose() : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• align_and_output_to_silent_file() : protocols::rna::RNA_DeNovoProtocol
• align_angle() : protocols::fldsgn::topology::HelixPairing
• align_by_domain() : protocols::hybridization::HybridizeProtocol
• align_c() : protocols::sic_dock::Rose
• align_idx() : protocols::id::AlignmentID
• align_n() : protocols::sic_dock::Rose
• align_pose() : protocols::swa::StepWisePoseSetup
• align_poses() : protocols::swa::StepWisePoseSetup
• Align_RmsdEvaluator() : protocols::comparative_modeling::Align_RmsdEvaluator
• Align_RotamerEvaluator() : protocols::comparative_modeling::Align_RotamerEvaluator
• align_to_chunk() : protocols::rna::RNA_ChunkLibrary
• align_to_native() : protocols::antibody::Antibody
• align_to_quick_alignment_pose() : protocols::swa::rna::StepWiseRNA_Clusterer
• align_VDW_rep_screen_pose() : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• aligned() : protocols::star::Extender
• Aligner() : core::sequence::Aligner
• AlignEvaluator() : protocols::evaluation::AlignEvaluator
• alignment() : protocols::comparative_modeling::ExtraThreadingMover , protocols::comparative_modeling::ThreadingJob , protocols::comparative_modeling::ThreadingMover
• alignment2AtomMap() : protocols::hybridization::TMalign
• alignment2strings() : protocols::hybridization::TMalign
• alignment_id() : core::sequence::SequenceAlignment , protocols::comparative_modeling::ThreadingJob
• AlignmentCluster() : protocols::comparative_modeling::AlignmentCluster
• AlignmentClustering() : protocols::comparative_modeling::AlignmentClustering
• AlignmentID() : protocols::id::AlignmentID
• alignments() : protocols::comparative_modeling::AlignmentSet , protocols::jd2::InnerMultiThreadingJob
• AlignmentSet() : protocols::comparative_modeling::AlignmentSet
• AlignPoseToInvrotTreeMover() : protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover
• AlignRmsdTargetEvaluatorCreator() : protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator
• all_add_energy() : protocols::wum::SilentStructStore
• all_aligned() : core::id::SequenceMapping
• all_bb_atoms() : core::chemical::ResidueType , core::conformation::Residue
• all_broker_files() : protocols::jd2::archive::Batch
• all_cdr_fold_tree() : protocols::antibody::Antibody
• all_cdr_VL_VH_fold_tree() : protocols::antibody::AntibodyModeler
• all_energies() : protocols::toolbox::DecoySetEvaluation
• 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 , protocols::jd2::AtomTreeDiffJobInputter
• all_residues_begin() : core::chemical::ResidueTypeSet
• all_residues_end() : core::chemical::ResidueTypeSet
• all_sc_atoms() : core::chemical::ResidueType
• all_sort_silent_scores() : protocols::wum::SilentStructStore
• all_target_res() : protocols::toolbox::match_enzdes_util::InvrotTarget
• all_target_residues() : protocols::toolbox::match_enzdes_util::InvrotTarget , protocols::toolbox::match_enzdes_util::InvrotTreeNode , protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase
• all_torsion_info() : protocols::swa::rna::RNA_LoopCloseSampler
• all_turn_residues_are_on_the_same_chain() : protocols::features::BetaTurnDetectionFeatures
• alllevel() : core::util::ABEGOManager
• allocate_appropriate_memory() : core::scoring::Membrane_FAEmbed , core::scoring::methods::LK_hack
• allocate_buffers() : protocols::canonical_sampling::ParallelTempering
• allocated() : core::graph::NegSpaceElement< T >
• allow_aa() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• allow_all_aas() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• allow_claim() : protocols::topology_broker::FibrilModelingClaimer , protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::TopologyClaimer
• allow_design() : protocols::toolbox::task_operations::DesignAroundOperation
• allow_design_around() : protocols::toolbox::task_operations::ThreadSequenceOperation
• allow_dof() : core::conformation::symmetry::SymDof
• allow_hbond() : core::scoring::hbonds::HBondSet
• allow_insert() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::rna::RNA_ChunkLibrary , protocols::rna::RNA_StructureParameters
• allow_noncanonical_aa() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• allow_reading_cancelled_decoys() : protocols::jd2::archive::Batch
• allow_scoring() : core::scoring::MembraneTopology
• allow_tmh_scoring() : core::scoring::MembraneTopology
• allowed_closure_attempts() : protocols::forge::remodel::RemodelLoopMover
• allowed_current_slide() : protocols::simple_moves::symmetry::SymmetrySlider
• allowed_res_name3_at_position() : protocols::toolbox::match_enzdes_util::EnzConstraintIO , protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• allowed_res_name3s() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• allowed_res_types() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• 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_
• allowed_restypes() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• allowed_seqpos() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• allowed_surface_aa() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• allowed_types() : protocols::dna::DnaInterfacePacker , protocols::motifs::BuildPosition
• AllowedSeqposForGeomCst() : protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst
• AllowInsert() : protocols::toolbox::AllowInsert
• AllResFilter() : core::pack::task::operation::AllResFilter
• AllResiduesChanged() : protocols::abinitio::AllResiduesChanged , protocols::hybridization::AllResiduesChanged
• allsc() : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• alpha() : core::pose::Pose , core::scoring::CSA , core::scoring::FACTSResidueInfo , protocols::dna::DNABase
• alpha_components() : core::scoring::dna::DNATorsionPotential
• alphabet() : core::sequence::ChemicalShiftSequence , core::sequence::SequenceProfile
• already_connected() : protocols::swa::StepWisePoseSetup
• already_in_queue() : protocols::match::output::UpstreamHitCacher
• also_check_fix_disulf() : protocols::frag_picker::CS2ndShift
• alt_bb() : protocols::flexpack::interaction_graph::FlexbbNode
• alt_e_up_to_date() : protocols::flexpack::interaction_graph::FlexbbEdge
• alt_energy() : protocols::flexpack::interaction_graph::FlexbbEdge
• alt_loc() : core::pose::PDBInfo
• alt_rot() : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• 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::HPatchNode< V, E, G > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• alt_state_hphobes() : core::pack::interaction_graph::HPatchNode< V, E, G >
• alt_state_inv_dots() : core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• alt_state_rotamer() : core::pack::interaction_graph::HPatchNode< V, E, G >
• alter_rotamer_set() : core::pack::rotamer_set::RotamerSetOperation , core::pack::rotamer_set::UnboundRotamersOperation , protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO , protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO , protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation
• alternate_state() : protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_info() : protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_is_being_considered() : protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_one_body_energy() : protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_total_energy() : protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_two_body_energies() : protocols::flexpack::interaction_graph::FlexbbNode
• AlterSpecDisruptionDriver() : protocols::pmut_scan::AlterSpecDisruptionDriver
• AmberPeriodicFunc() : core::scoring::constraints::AmberPeriodicFunc
• AmbigCSScore() : protocols::frag_picker::scores::AmbigCSScore
• ambiguous() : protocols::noesy_assign::CrossPeak
• AmbiguousConstraint() : core::scoring::constraints::AmbiguousConstraint
• AmbiguousConstraintCreator() : core::scoring::constraints::AmbiguousConstraintCreator
• AmbiguousMultiConstraint() : protocols::constraints_additional::AmbiguousMultiConstraint
• 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 >
• amplitude() : protocols::dna::DNABase
• 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_spline_ramp_to_zero() : core::scoring::etable::Etable
• analytic_ljatr_spline_ramp_to_zero_deriv() : core::scoring::etable::Etable
• analytic_ljrep_linearized() : core::scoring::etable::Etable
• analytic_params_for_pair() : core::scoring::etable::Etable
• AnalyticEtableEnergy() : core::scoring::etable::AnalyticEtableEnergy
• AnalyticEtableEvaluator() : core::scoring::etable::AnalyticEtableEvaluator
• Anchor() : protocols::anchored_design::Anchor
• anchor_atom() : core::pack::rotamer_set::WaterAnchorInfo
• anchor_end() : protocols::anchored_design::AnchorMoversData
• anchor_noise_constraints_setup() : protocols::anchored_design::AnchorMoversData
• anchor_offset() : protocols::multistate_design::PartitionAggregateFunction< T >
• anchor_residue() : core::pack::rotamer_set::WaterAnchorInfo
• anchor_specified() : protocols::seeded_abinitio::SeedFoldTree
• anchor_start() : protocols::anchored_design::AnchorMoversData
• anchored_loop() : protocols::anchored_design::AnchorMoversData
• AnchoredDesignMover() : protocols::anchored_design::AnchoredDesignMover
• AnchoredGraftMover() : protocols::grafting::AnchoredGraftMover
• AnchoredPerturbMover() : protocols::anchored_design::AnchoredPerturbMover
• AnchoredRefineMover() : protocols::anchored_design::AnchoredRefineMover
• AnchorMoversData() : protocols::anchored_design::AnchorMoversData
• anchors() : protocols::protein_interface_design::filters::BoltzmannFilter
• and_allow_insert() : protocols::toolbox::AllowInsert
• and_extrachi_cutoff() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• and_max_rotbump_energy() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• and_with() : protocols::match::Bool3DGrid , protocols::match::BumpGrid
• ang_U1D2() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• ang_U1D2_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• ang_U2D1() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• ang_U2D1_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• angle() : protocols::loophash::BackboneDB , protocols::simple_moves::SetTorsion , protocols::simple_moves::sidechain_moves::SetChiMover
• angle_constraint_energy() : core::scoring::constraints::ConstraintEdge
• angle_disp() : protocols::backrub::BackrubSegment
• angle_magnitude() : protocols::rigid::RigidBodyDeterministicSpinMover
• angle_max() : protocols::simple_moves::BackboneMover
• angle_parameters() : core::scoring::methods::ResidueCartBondedParameters
• AngleConstraint() : core::scoring::constraints::AngleConstraint
• AngleConstraintCreator() : core::scoring::constraints::AngleConstraintCreator
• animate() : core::conformation::ResidueKinWriter , protocols::match::output::ResidueKinemageWriter , protocols::match::output::WriteUpstreamHitKinemage
• ANN() : protocols::sparta::ANN
• annotated_sequence() : core::pose::Pose
• AnnotatedFragData() : core::fragment::AnnotatedFragData
• AnnotatedSequence() : core::sequence::AnnotatedSequence
• anomer() : core::chemical::carbohydrates::CarbohydrateInfo
• anomeric_carbon() : core::chemical::carbohydrates::CarbohydrateInfo
• Antibody() : protocols::antibody::Antibody
• antibody_modeling_insert_ter() : protocols::antibody::CDRH3Modeler
• AntibodyInfo() : protocols::antibody2::AntibodyInfo
• AntibodyModeler() : protocols::antibody::AntibodyModeler
• AntibodyModelerProtocol() : protocols::antibody2::AntibodyModelerProtocol
• antiparallel() : core::scoring::dssp::StrandPairing , protocols::abinitio::AlternativePairings
• any_active_enmeths() : core::scoring::MinimizationEdge
• any_intrares_energies() : core::scoring::ScoreFunction
• any_lr_residue_pair_energy() : core::scoring::ScoreFunction
• any_node_finished() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• any_unassigned() : core::pack::scmin::SidechainStateAssignment
• 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
• APCluster() : protocols::cluster::APCluster
• apfc_list() : core::scoring::custom_pair_distance::RespairInteractions
• append() : core::scoring::methods::LKB_ResiduesInfo
• append_atom() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• append_cached_scores() : protocols::qsar::scoring_grid::GridManager
• append_char() : core::sequence::Sequence
• append_choices() : protocols::genetic_algorithm::PositionSpecificRandomizer
• append_downstream_atom_to_active_site_required_list() : protocols::match::MatcherTask
• append_fragment() : protocols::frags::SingleResidueTorsionFragmentLibrary
• append_gap() : core::sequence::Sequence
• append_hairpin() : core::scoring::Hairpins
• append_hbond() : core::scoring::hbonds::HBondSet
• append_ligand_docking_scores() : protocols::ligand_docking::InterfaceScoreCalculator , protocols::ligand_docking::LigandDockProtocol
• append_polymer_residue_after_seqpos() : core::conformation::Conformation , core::pose::Pose
• append_res() : core::pose::PDBInfo
• append_residue() : core::conformation::Conformation , core::fragment::picking_old::vall::VallSection , core::io::pdb::FileData , core::kinematics::FoldTree , protocols::toolbox::AllowInsert
• 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_residues() : protocols::swa::protein::StepWiseProteinPoseSetup
• append_residues_cterminally() : protocols::seeded_abinitio::GrowPeptides
• append_residues_nterminally() : protocols::seeded_abinitio::GrowPeptides
• append_rotamer_operation() : core::pack::task::ResidueLevelTask , core::pack::task::PackerTask , core::pack::task::ResidueLevelTask_ , core::pack::task::PackerTask_
• append_rotamerset_operation() : core::pack::task::ResidueLevelTask , core::pack::task::PackerTask , core::pack::task::ResidueLevelTask_ , core::pack::task::PackerTask_
• append_upstream_resiue_as_defining_active_site() : protocols::match::MatcherTask
• append_virtual_anchor() : protocols::rna::RNA_StructureParameters
• AppendMainchainAtom() : core::chemical::AppendMainchainAtom
• AppendResidueRotamerSet() : core::pack::task::operation::AppendResidueRotamerSet
• AppendRotamer() : core::pack::task::operation::AppendRotamer
• AppendRotamerSet() : core::pack::task::operation::AppendRotamerSet
• applicable() : protocols::evaluation::PoseEvaluator , protocols::evaluation::SingleValuePoseEvaluator< T > , protocols::simple_filters::CamShiftEvaluator , protocols::simple_filters::ExternalEvaluator , protocols::simple_filters::PalesEvaluator , protocols::simple_filters::RPF_ScoreEvaluator , protocols::simple_filters::ScoreEvaluator , protocols::sparta::ChemicalShiftEvaluator
• applies_to() : core::chemical::PatchCase , core::chemical::Patch
• apply() : protocols::docking::stateless::SaneDockingProtocol , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::protein_interface_design::movers::SaveAndRetrieveSidechains , protocols::simple_moves::symmetry::DetectSymmetry , protocols::docking::DockMinMover , protocols::simple_moves::symmetry::SetupForSymmetryMover , protocols::docking::DockMCMCycle , protocols::simple_moves::symmetry::ExtractAsymmetricUnitMover , protocols::docking::DockingPrepackProtocol , protocols::simple_moves::symmetry::SetupNCSMover , protocols::simple_moves::symmetry::SymDockingInitialPerturbation , protocols::simple_moves::symmetry::SymDockingSlideIntoContact , protocols::docking::DockingInitialPerturbation , protocols::rna::RNA_LoopCloser , protocols::simple_moves::symmetry::SymmetrySlider , protocols::simple_moves::symmetry::SymmetricRMSMover , protocols::simple_moves::symmetry::SymMinMover , protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover , protocols::simple_moves::TailsScoreMover , protocols::simple_moves::TaskAwareMinMover , protocols::dna::SeparateDnaFromNonDna , protocols::rna::RNA_HelixAssembler , protocols::dna::DnaInterfacePacker , protocols::sparta::ChemicalShiftEvaluator , protocols::dna::DnaInterfaceMinMover , protocols::star::StarAbinitio , protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::SlideIntoSurface , protocols::ddg::ddGMover , protocols::rigid::RotateJumpAxisMover , protocols::surface_docking::SurfaceOrientMover , protocols::swa::monte_carlo::RNA_AddMover , protocols::swa::monte_carlo::RNA_AddOrDeleteMover , protocols::rna::RNA_DeNovoProtocol , protocols::rigid::RigidBodyDofRandomTransMover , protocols::swa::monte_carlo::RNA_O2StarMover , protocols::comparative_modeling::StealLigandMover , protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover , protocols::swa::monte_carlo::RNA_TorsionMover , protocols::swa::protein::StepWiseProteinCCD_Closer , protocols::comparative_modeling::LoopRelaxThreadingMover , protocols::swa::protein::StepWiseProteinPacker , protocols::rigid::RigidBodyDofRandomizeMover , protocols::swa::protein::StepWiseProteinPoseSetup , protocols::comparative_modeling::Align_RotamerEvaluator , protocols::swa::protein::StepWiseProteinScreener , protocols::swa::rna::RNA_LoopCloseSampler , protocols::rigid::RigidBodyDofTransMover , protocols::rigid::RigidBodySpinMover , protocols::swa::rna::StepWiseRNA_PoseSetup , protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::StepWisePoseSetup , protocols::canonical_sampling::TrajectoryRecorder , protocols::swa::StepWiseScreener , protocols::rigid::RigidBodyMover , protocols::symmetric_docking::SymDockProtocol , protocols::canonical_sampling::SimulatedTempering , protocols::symmetric_docking::SymFoldandDockRbTrialMover , protocols::symmetric_docking::SymRestrictTaskForDocking , protocols::rigid::MembraneNormalPerturbationMover , protocols::canonical_sampling::MetricRecorder , protocols::toolbox::task_operations::DesignAroundOperation , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::PreventChainFromRepackingOperation , protocols::toolbox::task_operations::PreventResiduesFromRepackingOperation , protocols::toolbox::task_operations::ProteinInterfaceDesignOperation , protocols::relax::FastRelax , protocols::antibody2::SnugDockProtocol , protocols::toolbox::task_operations::RestrictByCalculatorsOperation , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::antibody2::RefineBetaBarrel , protocols::rigid::MovePoseToMembraneCenterMover , protocols::rbsegment_relax::RBSegmentRelax , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation , protocols::antibody2::LHRepulsiveRamp , protocols::toolbox::task_operations::RestrictToCDRH3Loop , protocols::toolbox::task_operations::DockingNoRepack1 , protocols::toolbox::task_operations::RestrictToInterface , protocols::toolbox::task_operations::RestrictToNeighborhoodOperation , protocols::toolbox::task_operations::SelectBySASAOperation , protocols::toolbox::task_operations::RestrictConservedLowDdgOperation , protocols::rbsegment_relax::GaussianRBSegmentMover , protocols::antibody2::AntibodyModelerProtocol , protocols::rbsegment_relax::AutoRBMover , protocols::topology_broker::ConstraintEvaluatorWrapper , protocols::topology_broker::TopologyBroker , protocols::antibody::GraftOneMover , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover , protocols::qsar::qsarMover , protocols::qsar::scoring_grid::GridInitMover , protocols::anchored_design::AnchoredRefineMover , protocols::protein_interface_design::movers::SubroutineMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover , protocols::protein_interface_design::movers::SpinMover , protocols::moves::MCShowMover , protocols::protein_interface_design::movers::PrepackMover , protocols::protein_interface_design::movers::RandomMutation , protocols::protein_interface_design::movers::PlacementMinimizationMover , protocols::abinitio::MembraneAbinitio , protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::PeptideStapleDesignMover , protocols::protein_interface_design::movers::LoopLengthChange , protocols::abinitio::JumpingFoldConstraints , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::protein_interface_design::movers::InterfaceRecapitulationMover , protocols::protein_interface_design::movers::DisulfideMover , protocols::abinitio::ConstraintFragmentSampler , protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::Revert , protocols::nonlocal::SheetTranslate , core::pack::task::operation::ExtraRotamers , protocols::optimize_weights::ScaleAnnealerTemperatureOperation , protocols::moves::WhileMover , protocols::moves::RepeatMover , core::pack::task::operation::AppendResidueRotamerSet , protocols::moves::MonteCarloUtil , protocols::ligand_docking::RigidSearchMover , protocols::moves::CycleMover , core::pack::task::operation::SetRotamerCouplings , protocols::moves::PDBDumpMover , protocols::moves::Mover , protocols::moves::IfMover , protocols::moves::JumpOutMover , protocols::moves::CompositionMover , protocols::motifs::MotifDnaPacker , protocols::moves::CanonicalSamplingMover , core::pack::task::operation::DisallowIfNonnative , protocols::loops::loops_definers::LoopsFileDefiner , protocols::LoopRefine , protocols::loops::loop_mover::refine::RepackTrial , core::pack::task::operation::TaskOperation , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::loops::loop_closure::kinematic_closure::KinematicWrapper , core::pack::task::operation::AddBehaviorRLT , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::loops::FoldTreeFromLoops , protocols::loophash::LoopHashLibrary , protocols::loophash::LoopHashRelaxProtocol , protocols::ligand_docking::UnconstrainedTorsionsMover , protocols::ligand_docking::Transform , protocols::flexpack::FlexPacker , core::pack::task::operation::OptCysHG , protocols::ligand_docking::MolarMassFilter , protocols::ligand_docking::RandomConformerMover , protocols::ligand_docking::LigandDesign , core::fragment::SingleResidueFragData , protocols::ligand_docking::HighResDocker , protocols::ligand_docking::LigandDockMain , protocols::ligand_docking::GrowLigand , core::fragment::SecstructSRFD , protocols::ligand_docking::ChainExistsFilter , protocols::ligand_docking::CompoundTranslate , protocols::jd2::parser::FragmentReader , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::CartesianHybridize , protocols::hybridization::ChunkTrialMover , protocols::frag_picker::nonlocal::NonlocalFrags , core::fragment::UpJumpSRFD , protocols::forge::remodel::RemodelMover , protocols::forge::constraints::RemoveCsts , protocols::flxbb::CombinedTaskOperation , core::fragment::FragID , protocols::forge::components::VarLengthBuild , protocols::flxbb::FlxbbDesign , protocols::floppy_tail::FloppyTailMover , core::fragment::FragData , protocols::flxbb::FilterStructs_Packstat , protocols::domain_assembly::AddAssemblyConstraints , protocols::enzdes::RepackLigandSiteWithoutLigandMover , protocols::fldsgn::filters::SheetTopologyFilter , protocols::toolbox::task_operations::SetIGTypeOperation , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::FragQualFilter , core::chemical::SetNbrRadius , protocols::fldsgn::filters::HelixPairingFilter , protocols::filters::TimeFilter , protocols::filters::Filter , core::chemical::SetICoor , protocols::filters::HeavyAtomFilter , protocols::filters::IfThenFilter , protocols::filters::StochasticFilter , core::chemical::SetAtomicCharge , protocols::features::ReportToDB , protocols::evaluation::TimeEvaluator , protocols::features::ProteinSilentReport , protocols::evaluation::PoseEvaluator , protocols::evaluation::AlignEvaluator , protocols::enzdes::ApplyRandomStoredRBConf , protocols::enzdes::EnzdesScorefileFilter , core::chemical::AddProperty , protocols::enzdes::ModifyStoredRBConfs , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::AddRigidBodyLigandConfs , protocols::enzdes::LigDSasaFilter , protocols::domain_assembly::CombineChainsMover , protocols::enzdes::BackboneSampler , protocols::enzdes::EnzdesFlexBBProtocol , core::chemical::PatchCase , core::chemical::Patch , core::chemical::PatchOperation , core::chemical::DeleteAtom , core::chemical::SetBackboneHeavyatom , core::chemical::SetPolymerConnectAtom , core::chemical::AddConnect , core::chemical::DeleteProperty , core::chemical::AddChi , core::chemical::AddProtonChi , core::chemical::RedefineChi , core::chemical::AddChiRotamer , core::chemical::AddAtom , core::chemical::AddBond , core::chemical::SetAtomType , core::chemical::SetIO_String , core::chemical::SetMMAtomType , core::chemical::PrependMainchainAtom , core::chemical::AppendMainchainAtom , core::chemical::SetNbrAtom , core::chemical::SetOrientAtom , core::chemical::NCAARotLibPath , core::fragment::BBTorsionAndAnglesSRFD , core::fragment::BBTorsionSRFD , core::fragment::FragData , core::fragment::FragID , core::fragment::Frame , core::fragment::IndependentBBTorsionSRFD , core::fragment::UpJumpSRFD , core::fragment::DownJumpSRFD , core::fragment::SecstructSRFD , core::fragment::SingleResidueFragData , core::pack::task::operation::NoRepackDisulfides , core::pack::task::operation::OperateOnCertainResidues , protocols::toolbox::task_operations::ThreadSequenceOperation , core::pack::task::operation::OptH , core::pack::task::operation::ReplicateTask , core::pack::task::operation::ResLvlTaskOperation , core::pack::task::operation::RestrictToRepackingRLT , core::pack::task::operation::RestrictAbsentCanonicalAASRLT , core::pack::task::operation::DisallowIfNonnativeRLT , core::pack::task::operation::PreventRepackingRLT , core::pack::task::operation::DockingNoRepack1 , core::pack::task::operation::DockingNoRepack2 , core::pack::task::operation::RestrictToInterface , core::pack::task::operation::RestrictToRepacking , core::pack::task::operation::RestrictResidueToRepacking , core::pack::task::operation::RestrictAbsentCanonicalAAS , core::pack::task::operation::RotamerExplosion , core::pack::task::operation::InitializeFromCommandline , core::pack::task::operation::InitializeExtraRotsFromCommandline , core::pack::task::operation::IncludeCurrent , core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ReadResfile , core::pack::task::operation::ReadResfileAndObeyLengthEvents , core::pack::task::operation::SetRotamerLinks , core::pack::task::operation::AppendRotamer , core::pack::task::operation::AppendRotamerSet , core::pack::task::operation::PreserveCBeta , core::pack::task::operation::PreventRepacking , core::pack::task::operation::RestrictYSDesign , core::pack::task::operation::ExtraChiCutoff , protocols::abinitio::PcaEvaluator , protocols::abinitio::ShowViolation , protocols::abinitio::ComputeTotalDistCst , protocols::abinitio::Stage1Sampler , protocols::abinitio::AbrelaxMover , protocols::abinitio::ClassicAbinitio , protocols::abinitio::DomainAssembly , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::KinematicAbinitio , protocols::abinitio::JumpingFoldConstraintsWrapper , protocols::abinitio::KinematicTaskControl , protocols::abinitio::Protocol , protocols::abinitio::ResolutionSwitcher , protocols::analysis::InterfaceAnalyzerMover , protocols::analysis::LoopAnalyzerMover , protocols::analysis::PackStatMover , protocols::anchored_design::AnchoredDesignMover , protocols::anchored_design::AnchoredPerturbMover , protocols::antibody::AntibodyModeler , protocols::antibody::CDRH3Modeler , protocols::antibody::GraftMover , protocols::antibody::CloseOneMover , protocols::antibody::LoopRlxMover , protocols::ub_e2c::ubi_e2c_modeler , protocols::topology_broker::ConstraintEvaluatorWrapper , protocols::antibody2::CDRsMinPackMin , protocols::antibody2::CloseOneCDRLoop , protocols::antibody2::GraftCDRLoopsProtocol , protocols::antibody2::GraftOneCDRLoop , protocols::antibody2::H3CterInsert , protocols::antibody2::H3PerturbCCD , protocols::antibody2::H3RefineCCD , protocols::antibody2::LHRepulsiveRampLegacy , protocols::antibody2::LHSnugFitLegacy , protocols::antibody2::ModelCDRH3 , protocols::antibody2::RefineOneCDRLoop , protocols::antibody2::RefineOneCDRLoopCentroid , protocols::antibody2::SnugDock , protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover , protocols::canonical_sampling::CanonicalSamplingMover , protocols::canonical_sampling::PatchOperation , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::mc_convergence_checks::Pool_Evaluator , protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::canonical_sampling::TemperatureController , protocols::canonical_sampling::TemperingBase , protocols::canonical_sampling::ThermodynamicObserver , protocols::cluster::GatherPosesMover , protocols::cluster::AssignToClustersMover , protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::comparative_modeling::Align_RmsdEvaluator , protocols::comparative_modeling::Align_RotamerEvaluator , protocols::comparative_modeling::ExtraThreadingMover , protocols::comparative_modeling::LoopRelaxMover , protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::PartialThreadingMover , protocols::comparative_modeling::RecoverSideChainsMover , protocols::comparative_modeling::StealSideChainsMover , protocols::comparative_modeling::ThreadingMover , protocols::constraints_additional::CombinedConstraintEvaluator , protocols::constraints_additional::ConstraintEvaluator , protocols::contact_map::ContactMap , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::dna::DesignProteinBackboneAroundDNA , protocols::vip::VIP_Mover , protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::simple_moves::ModifyVariantTypeMover , protocols::swa::monte_carlo::RNA_DeleteMover , protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover , protocols::toolbox::task_operations::RestrictToTerminiOperation , protocols::dna::WatsonCrickRotamerCouplings , protocols::docking::ConformerSwitchMover , protocols::docking::DockingLowResFilter , protocols::docking::DockingHighResFilter , protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingHighRes , protocols::docking::DockingHighResLegacy , protocols::docking::DockingSlideIntoContact , protocols::docking::FaDockingSlideIntoContact , protocols::docking::DockingLowRes , protocols::toolbox::task_operations::SeqprofConsensusOperation , protocols::docking::DockingProtocol , protocols::docking::DockMCMProtocol , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation , protocols::docking::DockSetupMover , protocols::docking::SidechainMinMover , protocols::docking::InterfaceSidechainMinMover , protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors , protocols::docking::TemperedDocking , protocols::domain_assembly::AssembleLinkerMover , protocols::toolbox::task_operations::RestrictToInterfaceOperation , protocols::domain_assembly::PostDockAssemblyScorer , protocols::electron_density::SetupForDensityScoringMover , protocols::enzdes::AddOrRemoveMatchCsts , protocols::toolbox::task_operations::DockingNoRepack2 , protocols::enzdes::EnzdesFixBBProtocol , protocols::enzdes::PredesignPerturbMover , protocols::toolbox::task_operations::RestrictChainToRepackingOperation , protocols::toolbox::task_operations::RestrictOperationsBase , protocols::enzdes::SetCatalyticResPackBehavior , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::toolbox::task_operations::RestrictResiduesToRepackingOperation , protocols::enzdes::AddLigandMotifRotamers , protocols::enzdes::LigBurialFilter , protocols::toolbox::task_operations::RestrictNonSurfaceToRepackingOperation , protocols::enzdes::EnzScoreFilter , protocols::enzdes::DiffAtomSasaFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::toolbox::task_operations::RestrictInterGroupVectorOperation , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::GenerateStoredRBConfs , protocols::enzdes::MinimizeStoredRBConfs , protocols::enzdes::DiversifyStoredRBConfs , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::enzdes::SecondaryMatchProtocol , protocols::toolbox::task_operations::ReadResfileFromDB , protocols::evaluation::AlignEvaluator , protocols::evaluation::PoseEvaluator , protocols::evaluation::SingleValuePoseEvaluator< T > , protocols::evaluation::MetaPoseEvaluator , protocols::toolbox::task_operations::ModifyAnnealer , protocols::features::ProteinSilentReport , protocols::features::Report , protocols::swa::monte_carlo::RNA_O2StarMover , protocols::symmetric_docking::SymFoldandDockMoveRbJumpMover , protocols::symmetric_docking::SymInterfaceSidechainMinMover , protocols::fibril::SetupForFibrilMover , protocols::filters::TrueFilter , protocols::filters::FalseFilter , protocols::filters::CompoundFilter , protocols::filters::CombinedFilter , protocols::filters::MoveBeforeFilter , protocols::symmetric_docking::SymSidechainMinMover , protocols::filters::CalculatorFilter , protocols::filters::ContingentFilter , protocols::filters::Filter , protocols::symmetric_docking::SymFoldandDockSlideTrialMover , protocols::filters::FilterCollection , protocols::filters::ReplicateFilter , protocols::symmetric_docking::SymDockingHiRes , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::symmetric_docking::SymDockingLowRes , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::symmetric_docking::SymDockBaseProtocol , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::swa::StepWiseResidueSampler , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::swa::protein::StepWiseProteinResidueSampler , protocols::swa::rna::StepWiseRNA_JobParameters_Setup , protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes , protocols::flexpep_docking::FlexPepDockingProtocol , protocols::swa::rna::StepWiseRNA_Minimizer , protocols::flxbb::FilterStructs , protocols::flxbb::FilterStructs_TotalCharge , protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::flxbb::FlxbbDesignPack , protocols::flxbb::InterlockAroma , protocols::flxbb::LayerDesignOperation , protocols::swa::rna::RNA_AnalyticLoopCloser , protocols::forge::components::BDR , protocols::forge::constraints::InvrotTreeRCG , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelConstraintGenerator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelEnzdesCstModule , protocols::swa::protein::StepWiseProteinPoseMinimizer , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelRotamerLinks , protocols::swa::protein::StepWiseProteinLoopBridger , protocols::grafting::AnchoredGraftMover , protocols::hotspot_hashing::movers::PlaceProbeMover , protocols::hotspot_hashing::AddSearchPatternRotSetOp , protocols::swa::monte_carlo::RNA_TorsionMover , protocols::hybridization::CartesianSampler , protocols::hybridization::DomainAssembly , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::SwitchResidueTypeSetMover , protocols::swa::monte_carlo::RNA_AddMover , protocols::hybridization::HybridizeProtocol , protocols::hybridization::InsertChunkMover , protocols::hybridization::TMalign , protocols::hybridization::WeightedFragmentSmoothTrialMover , protocols::hybridization::WeightedFragmentTrialMover , protocols::idealize::IdealizeMover , protocols::swa::monte_carlo::RNA_DeleteMover , protocols::ligand_docking::AddHydrogen , protocols::ligand_docking::AddHydrogens , protocols::ligand_docking::AtomCountFilter , protocols::swa::monte_carlo::RNA_AddOrDeleteMover , protocols::ligand_docking::CompleteConnectionsFilter , protocols::ligand_docking::FinalMinimizer , protocols::surface_docking::FaSlideAwayFromSurface , protocols::ligand_docking::HBondAcceptorFilter , protocols::ligand_docking::HBondDonorFilter , protocols::ligand_docking::HeavyAtomFilter , protocols::surface_docking::SurfaceDockingProtocol , protocols::ligand_docking::InterfaceScoreCalculator , protocols::ligand_docking::LigandBaseProtocol , protocols::surface_docking::FaSlideIntoSurface , protocols::ligand_docking::LigandDockProtocol , protocols::ligand_docking::MinimizeBackbone , protocols::ligand_docking::MinimizeLigand , protocols::surface_docking::FullatomRelaxMover , protocols::ligand_docking::MolecularMassFilter , protocols::ligand_docking::RandomConformers , protocols::ligand_docking::Rotate , protocols::ligand_docking::Rotates , protocols::ligand_docking::SlideTogether , protocols::ligand_docking::StartFrom , protocols::simple_moves::TorsionDOFMover , protocols::ligand_docking::TetherLigand , protocols::ligand_docking::Translate , protocols::loop_build::LoopBuildMover , protocols::loophash::FastGapMover , protocols::loophash::LoopHashDiversifier , protocols::simple_moves::symmetry::SymRotamerTrialsMover , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::Mover_LoopHashRefine , protocols::loops::loop_closure::ccd::CcdLoopClosureMover , protocols::loops::loop_closure::ccd::CcdMover , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::ccd::ShortLoopClosure , protocols::simple_moves::symmetry::FaSymDockingSlideTogether , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::loop_mover::IndependentLoopMover , protocols::loops::loop_mover::LoopMover , protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub , protocols::simple_moves::symmetry::ExtractAsymmetricPoseMover , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::simple_moves::MonteCarloTest , protocols::simple_moves::sidechain_moves::SetChiMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::simple_moves::SwitchChainOrderMover , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::simple_moves::ScoreMover , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::LoopRebuild , protocols::loops::loops_definers::LoopsDatabaseDefiner , protocols::simple_moves::RepackSidechainsMover , protocols::simple_moves::ProlineFixMover , protocols::loops::loops_definers::LoopsDefiner , protocols::simple_moves::oop::OopRandomSmallMover , protocols::simple_moves::oop::OopPatcher , protocols::loops::loops_definers::LoopsExplicitDefiner , protocols::simple_moves::SuperimposeMover , protocols::match::MatcherMover , protocols::medal::MedalExchangeMover , protocols::simple_moves::MinMover , protocols::medal::MedalMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::hbs::HbsPatcher , protocols::moves::_BoolMover , protocols::moves::ChangeFoldTreeMover , protocols::simple_moves::SetReturningPackRotamersMover , protocols::simple_moves::ExtendedPoseMover , protocols::simple_moves::DME_FilterMover , protocols::moves::CyclicMover , protocols::simple_moves::ConstraintSetMover , protocols::simple_moves::ConstrainToIdealMover , protocols::moves::DsspMover , protocols::moves::FilterMover , protocols::simple_moves::SetTorsion , protocols::moves::IteratedConvergenceMover , protocols::moves::Mover , protocols::simple_moves::SequenceProfileMover , protocols::moves::MoverContainer , protocols::simple_filters::SidechainRmsdFilter , protocols::moves::SequenceMover , protocols::moves::RandomMover , protocols::simple_moves::SaneMinMover , protocols::simple_filters::RPF_ScoreEvaluator , protocols::simple_filters::LoopRmsdEvaluator , protocols::moves::NullMover , protocols::simple_filters::SelectRmsdEvaluator , protocols::simple_filters::RmsdEvaluator , protocols::moves::ProfilerMover , protocols::simple_moves::PeptideStapleMover , protocols::simple_moves::ReturnSidechainMover , protocols::simple_filters::ReportFilter , protocols::simple_filters::SelectRDC_Evaluator , protocols::moves::PyMolMover , protocols::simple_filters::PredictedBurialEvaluator , protocols::simple_filters::PoseInfoFilter , protocols::moves::PyMolMover , protocols::moves::RampingMover , protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::MinValueEvaluator< T > , protocols::simple_filters::JumpEvaluator , protocols::simple_filters::JScoreEvaluator , protocols::simple_filters::InterfaceBindingEnergyDensityFilter , protocols::simple_filters::HolesFilter , protocols::simple_moves::RotamerTrialsMinMover , protocols::moves::StructureRestrictor , protocols::simple_filters::DeltaFilter , protocols::simple_filters::ContactMapEvaluator , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::ConservedPosMutationFilter , protocols::simple_filters::ChiWellRmsdEvaluator , protocols::simple_filters::BatchNrEvaluator , protocols::simple_filters::BatchEvaluator , protocols::moves::TrialMover , protocols::seeded_abinitio::SwapSegment , protocols::seeded_abinitio::SeedSetupMover , protocols::seeded_abinitio::PlaceFragments , protocols::seeded_abinitio::GrowPeptides , protocols::seeded_abinitio::CloseFold , protocols::RotamerDump::RotamerDumpMover , protocols::rosetta_scripts::SavePoseMover , protocols::simple_moves::RepulsiveOnlyMover , protocols::rna::RNA_LoopCloser , protocols::rna::RNA_IdealCoord , protocols::rna::RNA_FragmentMover , protocols::rna::MultipleDomainMover , protocols::rigid::RollMover , protocols::noesy_assign::DistanceScoreMover , protocols::rigid::RigidBodyDofSeqTransMover , protocols::rigid::RigidBodyDofSeqRandomizeMover , protocols::rigid::UniformSphereTransMover , protocols::rigid::RigidBodyTransMover , protocols::rigid::RigidBodyRandomizeMover , protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::rigid::RigidBodyMotionMover , protocols::nonlocal::BiasedFragmentMover , protocols::rigid::MembraneCenterPerturbationMover , protocols::relax::MiniRelax , protocols::relax::ClassicRelax , protocols::nonlocal::HelixRotate , protocols::rbsegment_relax::StrandTwistingMover , protocols::rbsegment_relax::SequenceShiftMover , protocols::rbsegment_relax::HelicalGaussianMover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::rbsegment_relax::CCDMoveWrapper , protocols::qsar::RenderGridsToKinemage , protocols::protein_interface_design::movers::VLB , protocols::protein_interface_design::movers::TryRotamers , protocols::protein_interface_design::movers::Splice , protocols::protein_interface_design::movers::ShoveResidueMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::nonlocal::SingleFragmentMover , protocols::protein_interface_design::movers::RepackMinimize , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::protein_interface_design::movers::PlaceStubMover , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::NullDesignMover , protocols::protein_interface_design::movers::LoopRemodel , protocols::pb_potential::SetupPoissonBoltzmannPotential , protocols::protein_interface_design::movers::LoopFinder , protocols::protein_interface_design::movers::HotspotHasherMover , protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycle , protocols::protein_interface_design::filters::AtomicContactCountFilter , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::protein_interface_design::movers::BuildAlaPose , protocols::protein_interface_design::movers::BackrubDDMover , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::simple_moves::PackRotamersMover , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::simple_moves::oop::OopRandomPuckMover , protocols::protein_interface_design::filters::InterfaceHolesFilter , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::simple_moves::oop::OopMover , protocols::rna::RNA_LoopCloser , protocols::simple_filters::ResidueCountFilter , protocols::simple_moves::BBConRotMover , protocols::simple_moves::MembraneTopology , protocols::protein_interface_design::filters::Torsion , protocols::protein_interface_design::movers::AddChainBreak , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots , protocols::protein_interface_design::movers::BestHotspotCstMover , protocols::protein_interface_design::movers::DockAndRetrieveSidechains , protocols::protein_interface_design::movers::FavorNativeResiduePreCycle , protocols::simple_moves::MinPackMover , protocols::simple_moves::LoadPDBMover , protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopOver , protocols::simple_moves::LoadUnboundRotMover , protocols::simple_moves::HelicalPeptideLengthMover , protocols::protein_interface_design::movers::PlaceOnLoop , protocols::simple_moves::GreenPacker , protocols::simple_moves::DesignRepackMover , protocols::simple_moves::ForceDisulfidesMover , protocols::protein_interface_design::movers::SetAtomTree , protocols::protein_interface_design::movers::SetTemperatureFactor , protocols::simple_moves::FragmentMover , protocols::simple_moves::FavorSequenceProfile , protocols::protein_interface_design::movers::TaskAwareCsts , protocols::simple_moves::DumpPdb , protocols::rbsegment_relax::FragInsertAndAlignMover , protocols::rbsegment_relax::RBSegmentMover , protocols::simple_moves::CutChainMover , protocols::RBSegmentRelaxImpl , protocols::relax::CentroidRelax , protocols::simple_moves::ClearConstraintsMover , protocols::simple_filters::ResidueDistanceFilter , protocols::simple_filters::TerminusDistanceFilter , protocols::simple_moves::BackboneMover , protocols::rigid::WholeBodyTranslationMover , protocols::rigid::WholeBodyRotationMover , protocols::rigid::RigidBodyPerturbMover , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover , protocols::rigid::RigidBodyDeterministicSpinMover , protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::simple_filters::StructuralSimilarityEvaluator , protocols::rigid::RigidBodyDofPerturbMover , protocols::rigid::RigidBodyDofSeqPerturbMover , protocols::simple_filters::StructuralSimilarityEvaluator , protocols::simple_filters::Sigmoid , protocols::rna::RNA_HelixAssembler , protocols::simple_filters::SheetFilter , protocols::simple_filters::SymmetricRmsdEvaluator , protocols::simple_filters::ScoreCutoffFilter , protocols::rna::RNA_Relaxer , protocols::rosetta_scripts::ParsedProtocol , protocols::simple_filters::ScoreEvaluator , protocols::simple_filters::SAXSScoreFilter , protocols::seeded_abinitio::DefineMovableLoops , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::AlaScan , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::SelectGdtEvaluator , protocols::simple_filters::RmsdEvaluator , protocols::simple_filters::COFilter , protocols::simple_filters::RGFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::RDC_Evaluator , protocols::simple_filters::EvaluatedTrialMover , protocols::simple_filters::ExpiryFilter , protocols::simple_filters::ExternalEvaluator , protocols::simple_filters::FileExistFilter , protocols::simple_filters::FileRemoveFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::JScoreEvaluator , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::Operator , protocols::simple_filters::PackerNeighborGraphFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::PredictedBurialEvaluator , protocols::simple_filters::PoseMetricEvaluator< T > , protocols::simple_filters::RangeFilter , protocols::simple_filters::PDDFScoreFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_filters::ResiduesInInterfaceFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::NeighborTypeFilter , protocols::simple_filters::SelectMaxsubEvaluator , protocols::simple_filters::JumpNrEvaluator , protocols::simple_filters::TruncatedScoreEvaluator , protocols::simple_filters::ScoreTypeFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::SymmetricMotifFilter , protocols::simple_moves::AddCavitiesMover , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover , protocols::rna::RNA_Minimizer , protocols::simple_moves::BBG8T3AMover , protocols::simple_moves::carbohydrates::RingConformationMover , protocols::simple_moves::chiral::ChiralMover , protocols::simple_moves::ConsensusDesignMover , protocols::simple_filters::DdgFilter , protocols::simple_moves::ddG , protocols::simple_filters::ContactMapEvaluator , protocols::simple_moves::FragmentMover , protocols::simple_moves::ClassicFragmentMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_filters::PoseMetricEvaluator< T > , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_moves::MakePolyXMover , protocols::simple_moves::MissingDensityToJumpMover , protocols::simple_moves::MutateResidue , protocols::simple_moves::O2M_MutateMover , protocols::simple_filters::AbinitioBaseFilter , protocols::seeded_abinitio::SegmentHybridizer , protocols::simple_moves::PDBReloadMover , protocols::seeded_abinitio::SeedFoldTree , protocols::simple_moves::EnergyCutRotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::EnergyCutRotamerTrialsMover , protocols::seeded_abinitio::CoordinateCst , protocols::seeded_abinitio::CAcstGenerator , protocols::simple_moves::ShakeStructureMover , protocols::rotamer_recovery::RotamerRecoveryMover
• apply_after_jump_change() : protocols::coarse_rna::CoarseRNA_LoopCloser
• apply_and_return_jump() : protocols::rna::MultipleDomainMover
• apply_at_all_positions() : protocols::simple_moves::FragmentMover
• apply_at_domain() : protocols::rna::MultipleDomainMover
• apply_body() : protocols::docking::DockingInitialPerturbation
• apply_bulge_variant() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• apply_bulge_variants() : protocols::swa::StepWisePoseSetup , protocols::swa::rna::StepWiseRNA_PoseSetup
• apply_check() : protocols::motifs::Motif
• apply_chem_shift_data() : protocols::rna::RNA_DeNovoProtocol
• apply_cutpoint_variants() : protocols::swa::StepWisePoseSetup , protocols::swa::rna::StepWiseRNA_PoseSetup
• apply_disulfides() : protocols::relax::RelaxProtocolBase
• apply_dof_conformer() : protocols::jumping::ResiduePairJump
• apply_dof_tasks_to_movemap() : protocols::simple_moves::MinMover
• apply_filter() : protocols::rosetta_scripts::ParsedProtocol , protocols::topology_broker::TopologyBroker
• apply_frag() : protocols::hybridization::CartesianHybridize
• apply_fragment() : protocols::simple_moves::LoggedFragmentMover , protocols::simple_moves::SymmetricFragmentMover , protocols::simple_moves::WobbleMover , protocols::simple_moves::ClassicFragmentMover
• apply_frame() : protocols::hybridization::CartesianSampler , protocols::hybridization::CartesianHybridize , protocols::seeded_abinitio::PlaceFragments , protocols::seeded_abinitio::SegmentHybridizer
• apply_frames() : protocols::simple_moves::ClassicFragmentMover , protocols::simple_moves::FragmentMover
• apply_full_to_sub_mapping() : protocols::swa::StepWiseJobParameters , protocols::swa::StepWisePoseSetup
• apply_holes() : protocols::vip::VIP_Mover
• apply_input_samples() : protocols::swa::RigidBodySampler
• apply_mover_filter_pair() : protocols::rosetta_scripts::ParsedProtocol
• apply_nucleoside_torsion() : protocols::swa::monte_carlo::RNA_TorsionMover
• apply_nucleoside_torsion_Aform() : protocols::swa::monte_carlo::RNA_TorsionMover
• apply_patch_from_file() : core::scoring::ScoreFunction
• apply_patches() : core::chemical::ResidueTypeSet
• apply_peptide_plane_variants() : protocols::swa::StepWisePoseSetup
• apply_peptide_plane_variants_OLD() : protocols::swa::StepWisePoseSetup
• apply_probability() : protocols::rosetta_scripts::ParsedProtocol
• apply_random() : protocols::loophash::LoopHashLibrary
• apply_random_fragment() : protocols::rna::FullAtomRNA_Fragments , protocols::rna::RNA_Fragments , protocols::coarse_rna::CoarseRNA_Fragments
• apply_random_nucleoside_torsion() : protocols::swa::monte_carlo::RNA_TorsionMover
• apply_random_suite_torsion() : protocols::swa::monte_carlo::RNA_TorsionMover
• apply_ranked_fragment() : protocols::enzdes::EnzdesFlexibleRegion
• apply_regular_packer() : protocols::swa::protein::StepWiseProteinResidueSampler , protocols::swa::protein::StepWiseProteinPacker
• apply_residue() : protocols::ligand_docking::RandomConformers
• apply_rigid_body_moves() : protocols::ligand_docking::HighResDocker
• apply_rigid_body_settings() : protocols::swa::RigidBodySampler
• apply_rotation_offset_to_pose_() : protocols::pockets::PlaidFingerprint
• apply_sequence_mapping() : core::kinematics::FoldTree
• apply_solutions() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::swa::rna::RNA_AnalyticLoopCloser
• apply_ss() : core::fragment::Frame , core::fragment::UpJumpSRFD , core::fragment::DownJumpSRFD , core::fragment::SingleResidueFragData , core::fragment::FragData , core::fragment::FragID , core::fragment::SecstructSRFD , core::fragment::SingleResidueFragData
• apply_suite_torsion() : protocols::swa::monte_carlo::RNA_TorsionMover
• apply_suite_torsion_Aform() : protocols::swa::monte_carlo::RNA_TorsionMover
• apply_terminus_variants_at_protein_rna_boundaries() : protocols::swa::StepWisePoseSetup
• apply_to() : protocols::jumping::JumpSample
• apply_to_pose() : protocols::loophash::BackboneSegment
• apply_to_rotpack() : protocols::simple_moves::PackRotamersMoverLazy
• apply_transform_downstream() : core::conformation::Residue
• apply_transform_Rx_plus_v() : core::pose::Pose , core::conformation::Residue
• apply_transformation() : core::conformation::symmetry::SymmetricConformation
• apply_user_defined_reweighting_() : core::scoring::ScoreFunctionFactory
• apply_virtual_phosphate_variants() : protocols::swa::StepWisePoseSetup , protocols::swa::rna::StepWiseRNA_PoseSetup
• apply_virtual_res_variant() : protocols::swa::StepWisePoseSetup , protocols::swa::rna::StepWiseRNA_PoseSetup
• applyANNTransformation() : protocols::sparta::ANN
• applyForces_BeeMan() : protocols::cartesian::MolecularDynamics
• applyForces_ConjugateGradient() : protocols::cartesian::MolecularDynamics
• applyForces_LangevinIntegration() : protocols::cartesian::MolecularDynamics
• ApplyRandomStoredRBConf() : protocols::enzdes::ApplyRandomStoredRBConf
• applyRotation() : protocols::rbsegment_relax::RBSegmentMover
• applySpin() : protocols::rbsegment_relax::RBSegmentMover
• applyTransformation() : protocols::rbsegment_relax::RBSegmentMover
• applyTranslation() : protocols::rbsegment_relax::RBSegmentMover
• applyVecAverage() : protocols::sparta::ANN
• applyVecNormalization() : protocols::sparta::ANN
• approved() : protocols::topology_broker::DofClaim
• approximate_vdw_radius() : core::scoring::AtomVDW
• aquireNextQueue() : protocols::viewer::triangleIterator
• arccos_() : protocols::sparta::PDB
• archive_rank() : protocols::jd2::archive::MPIArchiveJobDistributor
• ArchiveBase() : protocols::jd2::archive::ArchiveBase
• ArchiveManager() : protocols::jd2::archive::ArchiveManager
• are_colliding() : protocols::match::downstream::DownstreamAlgorithm
• are_they_neighbors() : core::scoring::ScoreFunction
• AreaAccumulator() : core::scoring::packstat::AreaAccumulator
• Armijo() : core::optimization::ArmijoLineMinimization
• ArmijoLineMinimization() : core::optimization::ArmijoLineMinimization
• aromatic_motifs() : protocols::motifs::MotifDnaPacker
• aromatic_ring_center() : core::scoring::orbitals::OrbitalsAssigned
• array() : core::graph::NegSpaceElement< T >
• Array0() : core::graph::Array0< T >
• array_pool() : core::scoring::EnergyGraph
• array_size() : core::graph::ArrayPool< T >
• array_to_farray() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::DataBuffer , protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• ArrayPool() : core::graph::ArrayPool< T >
• ArrayPoolElement() : core::graph::ArrayPoolElement< T >
• assemble_datamatrix() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
• assemble_enzdes_fragdata() : protocols::enzdes::EnzdesFlexibleRegion
• assemble_next_best_loop_combination() : protocols::enzdes::EnzdesFlexBBProtocol
• assemble_outtag() : protocols::match::output::PDBWriter
• assemble_remark_lines() : protocols::match::output::PDBWriter
• AssembleLinkerMover() : protocols::domain_assembly::AssembleLinkerMover
• assert_calculators() : protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• assert_is_calc_chem_shift_atom() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• assign() : protocols::noesy_assign::NoesyModule , protocols::toolbox::KCluster , protocols::toolbox::GreedyKCenter , protocols::noesy_assign::NoesyModule , protocols::toolbox::KMedoid , protocols::noesy_assign::NoesyModule
• assign_BMEC() : core::pack::interaction_graph::FASTERInteractionGraph
• assign_chi_for_interpolated_rotamer() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
• assign_CSPs() : protocols::ub_e2c::ubi_e2c_modeler
• assign_dofs_to_mobile_residues() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap
• assign_downstream_position_group_for_match() : protocols::match::output::SameSequenceAndDSPositionGrouper
• assign_energy() : core::pack::scmin::SidechainStateAssignment
• assign_entity_sequence_to_variables() : protocols::pack_daemon::EntityFunc
• assign_exemplars() : protocols::cluster::APCluster
• assign_group_for_match() : protocols::match::output::MatchGrouper , protocols::match::output::SameChiBinComboGrouper , protocols::match::output::SameSequenceGrouper , protocols::match::output::SameSequenceAndDSPositionGrouper , protocols::match::output::SameRotamerComboGrouper , protocols::match::output::MatchGrouper , protocols::match::output::SameRotamerComboGrouper , protocols::match::output::SameChiBinComboGrouper
• 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_jobs_to_local_daemon_set() : protocols::pack_daemon::DynamicAggregateFunction
• assign_jobs_to_remote_daemon_sets() : protocols::pack_daemon::DynamicAggregateFunction
• assign_labelled_spin() : protocols::noesy_assign::CrossPeak3D
• assign_last_rotamers_to_pose() : protocols::pack_daemon::PackDaemon
• assign_neighbor_atom() : core::chemical::ResidueType
• assign_non_CSPs() : protocols::ub_e2c::ubi_e2c_modeler
• 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::RotamericSingleResidueDunbrackLibrary< T >
• assign_random_rotamer_with_bias() : core::pack::dunbrack::SingleResidueRotamerLibrary , core::pack::dunbrack::SingleLigandRotamerLibrary , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
• assign_random_rotamer_with_bias_bbdep() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• assign_random_rotamer_with_bias_bbind() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• assign_rosetta_torsions() : core::optimization::symmetry::SymMinimizerMap , core::optimization::MinimizerMap
• 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_spin() : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::CrossPeak3D , protocols::noesy_assign::CrossPeak4D , protocols::noesy_assign::CrossPeak3D , protocols::noesy_assign::CrossPeak4D , protocols::noesy_assign::CrossPeak
• assign_state() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , core::pack::interaction_graph::PDNode , core::pack::scmin::SidechainStateAssignment , core::pack::interaction_graph::LinearMemNode , protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• assign_state_energies_to_variables_and_subexpressions() : protocols::pack_daemon::DynamicAggregateFunction
• assign_state_surface() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• assign_tag() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• assign_type_data() : protocols::toolbox::KClusterElement
• assign_WC_edges_to_base_pair12() : protocols::swa::RigidBodySampler
• assign_zero_state() : core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::SymmLinearMemNode , protocols::flexpack::interaction_graph::MinimalistFlexbbNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::SymmMinimalistNode , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode
• AssignAtomRadius() : core::scoring::sc::MolecularSurfaceCalculator
• AssignAttentionNumbers() : core::scoring::sc::ShapeComplementarityCalculator , core::scoring::sc::MolecularSurfaceCalculator
• assigned() : protocols::noesy_assign::CrossPeak
• assignment() : protocols::noesy_assign::CrossPeak::Spin
• assignment_index() : protocols::noesy_assign::CrossPeak::Spin
• assignments() : protocols::noesy_assign::PeakAssignmentResidueMap , protocols::noesy_assign::CrossPeakList , protocols::noesy_assign::CrossPeak
• AssignOrbitals() : core::chemical::orbitals::AssignOrbitals
• AssignToClustersMover() : protocols::cluster::AssignToClustersMover
• AsymFoldandDockClaimer() : protocols::topology_broker::AsymFoldandDockClaimer
• AsymFoldandDockMoveRbJumpMover() : protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover
• AsymFoldandDockRbTrialMover() : protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover
• asymmetric_dof() : core::optimization::symmetry::SymMinimizerMap
• at() : protocols::frag_picker::scores::FragmentScoreMap , protocols::frag_picker::scores::AdaptiveScoreHistogram , protocols::frag_picker::VallChunk , protocols::frag_picker::VallProvider , protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering > , core::sequence::Sequence , protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering >
• at_end() : protocols::match::VoxelSetIterator
• at_inds() : protocols::match::downstream::AtomGeometrySecMatchRPE
• atom() : core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::SequenceProfileConstraint , core::id::StubID , core::conformation::Residue , core::scoring::constraints::AngleConstraint , core::scoring::trie::RotamerDescriptorAtom< AT, CPDAT > , core::scoring::trie::RotamerDescriptor< AT, CPDAT > , core::chemical::ResidueType , protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::SequenceCouplingConstraint , core::scoring::constraints::ResidueTypeConstraint , core::scoring::packstat::SimplePDB , core::scoring::trie::RotamerDescriptor< AT, CPDAT >
• Atom() : core::chemical::Atom
• atom() : core::scoring::constraints::MultiConstraint , core::scoring::constraints::Constraint
• Atom() : core::kinematics::tree::Atom
• atom() : core::conformation::Residue , core::kinematics::AtomTree , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BigBinConstraint , core::scoring::constraints::DistancePairConstraint , protocols::noesy_assign::EXCN_UnknownResonance , core::id::EXCN_AtomNotFound , core::chemical::ResidueType
• Atom() : core::kinematics::tree::Atom , core::conformation::Atom , core::chemical::Atom
• atom() : core::scoring::constraints::NonResidueTypeConstraint , core::scoring::packstat::SimplePDB
• Atom() : core::conformation::Atom
• atom() : protocols::pockets::PocketConstraint , protocols::noesy_assign::Resonance , protocols::noesy_assign::PeakAssignment , core::chemical::ResidueType
• Atom() : core::scoring::sc::Atom
• atom() : core::id::NamedAtomID , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::ConstantConstraint , core::id::NamedAtomID , core::conformation::Residue , core::pack::dunbrack::RotamerConstraint , core::scoring::constraints::CoordinateConstraint , core::pack::dunbrack::DunbrackConstraint , core::scoring::constraints::BackboneStubConstraint , core::pack::scmin::SCMinMinimizerMap , core::scoring::constraints::ResidueTypeLinkingConstraint
• Atom() : core::chemical::Atom
• atom() : core::scoring::trie::RotamerDescriptorAtom< AT, CPDAT > , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::trie::TrieNode< AT, CPDATA > , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::AtomTreeSCMinMinimizerMap , core::id::NamedStubID
• atom1() : core::scoring::constraints::Obsolet_NamedAtomPairConstraint , core::scoring::RDC , core::scoring::DC , core::scoring::CSA
• atom1_atom2_atom3_angle() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::toolbox::match_enzdes_util::LigandConformer , protocols::match::downstream::LigandConformerBuilder
• atom1_atom2_distance() : protocols::match::downstream::RigidLigandBuilder , protocols::match::downstream::DownstreamBuilder , protocols::toolbox::match_enzdes_util::LigandConformer , protocols::match::downstream::LigandConformerBuilder
• atom1_belongs_in_active_site() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::match::downstream::LigandConformerBuilder
• atom1_radius() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• atom2() : core::scoring::DC , core::scoring::constraints::Obsolet_NamedAtomPairConstraint , core::scoring::RDC , core::scoring::CSA
• atom2_atom3_distance() : protocols::toolbox::match_enzdes_util::LigandConformer , protocols::match::downstream::RigidLigandBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::DownstreamBuilder
• atom2_belongs_in_active_site() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::match::downstream::LigandConformerBuilder
• atom2_radius() : protocols::match::downstream::RigidLigandBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::DownstreamBuilder
• atom3() : core::scoring::CSA
• atom3_belongs_in_active_site() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::match::downstream::LigandConformerBuilder
• atom3_radius() : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::RigidLigandBuilder
• Atom_() : core::kinematics::tree::Atom_
• atom_base() : core::conformation::Residue , core::chemical::ResidueType
• atom_begin() : core::conformation::Residue
• atom_charge() : core::chemical::Adduct
• atom_controlled_by_any_chi() : protocols::match::upstream::UpstreamResTypeGeometry
• atom_coordinate_unacceptable() : protocols::match::upstream::ProteinUpstreamBuilder
• atom_data() : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• atom_derivatives() : core::optimization::symmetry::SymMinimizerMap , core::pack::scmin::SCMinMinimizerMap , core::optimization::MinimizerMap , core::optimization::CartesianMinimizerMap
• atom_dont_do_update() : core::kinematics::AtomTree
• atom_end() : core::conformation::Residue
• atom_forms_residue_connection() : core::chemical::ResidueType
• atom_geom_rpes() : protocols::match::downstream::GeometrySecMatchRPE
• 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_nonchi_coordinate() : protocols::match::upstream::UpstreamResTypeGeometry
• atom_has_orbital() : core::chemical::AtomType
• atom_hbonds() : core::scoring::hbonds::HBondSet
• atom_id() : core::kinematics::tree::Atom_ , core::id::DOF_ID , core::kinematics::tree::Atom , core::optimization::DOF_Node , core::chemical::ICoorAtomID
• atom_index() : core::scoring::methods::dfire::DFIRE_Potential , core::chemical::ResidueType , core::conformation::Residue
• atom_inds_for_restype() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• atom_inds_for_restype_begin() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• atom_inds_for_restype_end() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• atom_is_acceptor() : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::hbonds::HBond , core::scoring::geometric_solvation::GeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody
• 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_chitip() : protocols::match::upstream::UpstreamResTypeGeometry
• atom_is_donor() : core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergy
• atom_is_donor_h() : core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy
• atom_is_donorH() : core::scoring::hbonds::HBond
• atom_is_heavy() : core::scoring::geometric_solvation::GeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy
• atom_is_hydrogen() : core::conformation::Residue , core::chemical::ResidueType
• atom_is_ideal() : protocols::simple_moves::MinimalRotamer
• 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::conformation::Residue , core::chemical::ResidueType
• atom_is_valid_base() : core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody
• atom_is_virtual() : core::chemical::rna::RNA_ResidueType
• atom_name() : core::conformation::AtomGraphVertexData , core::conformation::Residue , core::chemical::ResidueType , core::pose::UnrecognizedAtomRecord , core::scoring::packing::PoseBalls , protocols::scoring::methods::pcs::PCS_line_data , core::pose::MiniPose , core::chemical::Adduct , core::conformation::AtomGraphVertexData
• atom_name1() : protocols::rna::RNA_PairingTemplate
• atom_name2() : protocols::rna::RNA_PairingTemplate
• atom_name_from_index() : core::chemical::sdf::CtabBase
• atom_names_list() : core::pose::MiniPose
• atom_neighbors() : core::scoring::ResiduePairNeighborList , core::scoring::NeighborList , core::scoring::ResidueNblistData
• 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_constraint_weight() : protocols::idealize::IdealizeMover
• atom_pair_cutoff() : core::scoring::NeighborList
• atom_pair_energy() : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::TableLookupEvaluator , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::AnalyticEtableEvaluator , core::coarse::CoarseEtable , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::TableLookupEvaluator
• atom_pair_energy_() : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::CoarseEtableEnergy
• atom_pair_energy_v() : core::scoring::etable::TableLookupEvaluator , core::scoring::etable::AnalyticEtableEvaluator
• atom_pointer() : core::kinematics::AtomTree
• atom_radius() : protocols::match::upstream::BuildSet
• atom_radius_squared() : core::conformation::AtomGraphVertexData
• atom_score() : protocols::qsar::scoring_grid::GridManager , protocols::qsar::scoring_grid::HbdGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::ChargeGrid , protocols::qsar::scoring_grid::HbaGrid , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::VdwGrid
• atom_set() : core::scoring::etable::MembEtable , core::coarse::CoarseEtable , core::scoring::etable::Etable , core::scoring::etable::MembEtable
• atom_tree() : core::pose::Pose , core::conformation::Conformation
• atom_tree_torsion() : core::conformation::Conformation
• atom_type() : core::scoring::etable::Etable , core::scoring::etable::etrie::EtableAtom , core::scoring::packing::PoseBalls , core::conformation::Residue , core::chemical::ResidueType , protocols::noesy_assign::PeakCalibrator , core::scoring::hackelec::ElecAtom , core::scoring::etable::MembEtable , core::scoring::etable::etrie::EtableAtom , core::scoring::hackelec::ElecAtom , core::scoring::etable::MembEtable
• atom_type_index() : core::chemical::Atom , core::chemical::MMAtomTypeSet , core::conformation::Residue , core::chemical::CSDAtomTypeSet , core::chemical::AtomTypeSet
• atom_type_name() : core::chemical::Adduct , core::chemical::AtomType , core::chemical::orbitals::OrbitalType
• atom_type_set() : core::chemical::ChemicalManager , core::conformation::Residue , core::chemical::ResidueType
• atom_type_set_ptr() : core::chemical::ResidueType
• atom_type_set_tag() : core::chemical::ResidueLoaderOptions
• atom_vdw_atom_type_set_name() : core::scoring::methods::EnergyMethodOptions
• AtomAngleSecMatchRPE() : protocols::match::downstream::AtomAngleSecMatchRPE
• AtomAtomPairFeatures() : protocols::features::AtomAtomPairFeatures
• AtomAtomPairFeaturesCreator() : protocols::features::AtomAtomPairFeaturesCreator
• AtomBasedConstraintsScore() : protocols::frag_picker::scores::AtomBasedConstraintsScore
• AtomCountFilter() : protocols::ligand_docking::AtomCountFilter
• AtomDihedralSecMatchRPE() : protocols::match::downstream::AtomDihedralSecMatchRPE
• AtomDistanceSecMatchRPE() : protocols::match::downstream::AtomDistanceSecMatchRPE
• AtomGeometrySecMatchRPE() : protocols::match::downstream::AtomGeometrySecMatchRPE
• AtomGraphEdgeData() : core::conformation::AtomGraphEdgeData
• AtomGraphVertexData() : core::conformation::AtomGraphVertexData
• atomic_charge() : core::conformation::Residue
• atomic_interaction_cutoff() : core::scoring::methods::MMTorsionEnergy , core::scoring::methods::CenPairEnergy , core::scoring::orbitals::OrbitalsScore , core::scoring::methods::PairEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::HybridVDW_Energy , core::scoring::methods::MembraneEnvSmoothEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::methods::CSD_TorsionEnergy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::rna::RNA_Mg_Energy , core::scoring::hackelec::HackElecEnergy , core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::ShortRangeTwoBodyEnergy , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::rna::RNA_VDW_Energy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::PeptideBondEnergy , core::scoring::methods::DNA_BaseEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::methods::SecondaryStructureEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hackaro::HackAroEnergy , core::scoring::methods::RamachandranEnergy2B , core::scoring::rna::RNA_LJ_BaseEnergy , core::scoring::methods::SuckerEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , protocols::scoring::methods::InterchainPairEnergy , core::scoring::rna::RNA_BaseBaseEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MMBondAngleEnergy , core::scoring::geometric_solvation::DatabaseOccSolEne , core::scoring::rna::RNA_TorsionEnergy , core::scoring::methods::VDW_Energy , core::scoring::methods::WholeStructureEnergy , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::methods::LK_CosThetaEnergy , core::scoring::methods::LK_BallEnergy , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::rna::RNA_FA_Stack , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_DataBackboneEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::methods::LK_hack , core::scoring::interface::DDPscore , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::EnvSmoothEnergy
• atomic_radius() : core::scoring::GenBornResidueInfo
• AtomicContactCountFilter() : protocols::protein_interface_design::filters::AtomicContactCountFilter
• AtomicContactFilter() : protocols::simple_filters::AtomicContactFilter
• AtomicDistanceFilter() : protocols::simple_filters::AtomicDistanceFilter
• AtomICoor() : core::chemical::AtomICoor
• AtomID() : core::id::AtomID
• AtomID_Map() : core::id::AtomID_Map< T >
• atomids() : core::scoring::packing::PoseBalls
• AtomInformation() : core::io::pdb::AtomInformation
• AtomInResidueAtomInResiduePairFeatures() : protocols::features::AtomInResidueAtomInResiduePairFeatures
• AtomInResidueAtomInResiduePairFeaturesCreator() : protocols::features::AtomInResidueAtomInResiduePairFeaturesCreator
• atomname() : protocols::contact_map::ContactPartner
• AtomNeighbor() : core::scoring::AtomNeighbor
• atomno() : core::chemical::ResidueConnection , core::scoring::AtomNeighbor , core::optimization::DOF_Node , core::chemical::ICoorAtomID , core::optimization::AtomNode , core::id::AtomID , core::id::DOF_ID , core::chemical::ResidueConnection , core::id::AtomID
• atomno1() : core::scoring::SmallAtNb
• atomno2() : core::scoring::SmallAtNb
• AtomNode() : core::optimization::AtomNode
• AtomPairConstraint() : core::scoring::constraints::AtomPairConstraint
• AtomPairConstraintCreator() : core::scoring::constraints::AtomPairConstraintCreator
• AtomPairConstraintsData() : protocols::frag_picker::scores::AtomPairConstraintsData
• AtomPairConstraintsScore() : protocols::frag_picker::scores::AtomPairConstraintsScore
• AtomPairFuncList() : core::scoring::custom_pair_distance::AtomPairFuncList
• AtomRadiusMap() : core::scoring::packstat::AtomRadiusMap
• AtomRecord() : core::pose::PDBInfo::AtomRecord
• atoms() : core::conformation::Residue , protocols::features::LoopAnchorFeatures , core::conformation::Residue , core::scoring::packstat::SimplePDB , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::optimization::DOF_Node
• atoms_are_equiv() : protocols::comparative_modeling::ThreadingMover
• atoms_begin() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• atoms_end() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::kinematics::tree::Atom
• atoms_last_controlled_by_chi() : core::chemical::ResidueType
• atoms_with_orb_index() : core::conformation::Residue , core::chemical::ResidueType
• 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
• AtomTreeDiffJobDistributor() : protocols::jobdist::AtomTreeDiffJobDistributor
• AtomTreeDiffJobInputter() : protocols::jd2::AtomTreeDiffJobInputter
• AtomTreeDiffJobOutputter() : protocols::jd2::AtomTreeDiffJobOutputter
• AtomTreeMinimizer() : core::optimization::AtomTreeMinimizer
• AtomTreeMultifunc() : core::optimization::AtomTreeMultifunc
• AtomTreeSCMinMinimizerMap() : core::pack::scmin::AtomTreeSCMinMinimizerMap
• AtomType() : core::chemical::AtomType
• AtomTypeDatabaseIO() : core::chemical::AtomTypeDatabaseIO
• atomTyper() : core::chemical::sdf::atomTyper
• AtomTypeSet() : core::chemical::AtomTypeSet
• AtomTypesFeatures() : protocols::features::AtomTypesFeatures
• AtomTypesFeaturesCreator() : protocols::features::AtomTypesFeaturesCreator
• AtomVDW() : core::scoring::AtomVDW
• AtomWithDOFChange() : core::kinematics::AtomWithDOFChange
• atr_weight() : core::scoring::etable::EtableEvaluator
• AtrGrid() : protocols::qsar::scoring_grid::AtrGrid
• ats_n_func_list() : core::scoring::custom_pair_distance::AtomPairFuncList
• attach() : protocols::moves::PyMolObserver , 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::pose::Pose , core::conformation::Conformation
• attach_identity_obs() : core::conformation::Conformation
• attach_impl() : core::pose::datacache::CacheableObserver , core::pose::datacache::LengthEventCollector , core::pose::datacache::SpecialSegmentsObserver , protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• attach_length_obs() : core::conformation::Conformation
• attach_observer_to_last_accepted_conformation() : protocols::moves::MonteCarlo
• attach_observer_to_last_accepted_pose() : protocols::moves::MonteCarlo
• attach_observer_to_lowest_score_conformation() : protocols::moves::MonteCarlo
• attach_observer_to_lowest_score_pose() : protocols::moves::MonteCarlo
• attach_secondary_structure_pools() : protocols::frag_picker::quota::QuotaCollector
• attach_to() : protocols::viewer::SilentObserver , core::pose::PDBInfo , protocols::boinc::BoincCurrentPoseObserver , protocols::viewer::ConformationViewer , core::pose::datacache::CacheableObserver , core::pose::metrics::PoseMetricContainer , protocols::forge::build::BuildInstruction
• 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 , core::chemical::ResidueType , core::conformation::Residue
• attached_H_end() : core::conformation::Residue , core::chemical::ResidueType , core::conformation::Residue
• attaches_to_residue_type() : core::pack::rotamer_set::WaterAnchorInfo
• auction_results() : protocols::protein_interface_design::movers::PlacementAuctionMover
• auto_choose_cutpoint() : protocols::loops::Loop
• auto_choose_cutpoints() : protocols::loops::Loops
• auto_frag_insertion_weight() : protocols::hybridization::FoldTreeHybridize
• autoexpanding_pocket_eval() : protocols::pockets::PocketGrid
• autofill() : protocols::hotspot_hashing::HotspotStubSet
• autogenerate_constseq_frags() : protocols::anchored_design::AnchorMoversData
• autogenerate_design_frags() : protocols::anchored_design::AnchorMoversData
• autogenerate_frags() : protocols::anchored_design::AnchorMoversData
• automatic_distance_cutoff() : protocols::protein_interface_design::movers::AddChainBreak
• AutomorphismIterator() : core::chemical::AutomorphismIterator
• AutoRBMover() : protocols::rbsegment_relax::AutoRBMover
• autotemp_accept() : protocols::moves::MonteCarlo
• autotemp_reject() : protocols::moves::MonteCarlo
• average() : protocols::ddg::ddGMover
• average_dist() : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• average_dist6() : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• average_residue_hASA() : core::pack::interaction_graph::SurfacePotential , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• average_score_components() : protocols::ddg::ddGMover
• AverageDegreeFilter() : protocols::protein_interface_design::filters::AverageDegreeFilter
• avoid_sc_hbonds() : core::scoring::hbonds::hbtrie::HBCPData
• ax_init() : core::optimization::MinimizerOptions