- c -

• C() : core::scoring::electron_density::OneGaussianScattering , core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• c0() : core::scoring::FACTSResidueInfo
• c1() : core::scoring::FACTSResidueInfo
• c1star_atom_index() : core::chemical::rna::RNA_ResidueType
• c2() : core::scoring::FACTSResidueInfo
• c2star_atom_index() : core::chemical::rna::RNA_ResidueType
• c3() : core::scoring::FACTSResidueInfo
• c4star_atom_index() : core::chemical::rna::RNA_ResidueType
• c_alpha_index() : core::scoring::disulfides::DisulfideAtomIndices
• c_anchor() : protocols::sic_dock::Rose
• C_atom_id() : protocols::match::upstream::UpstreamResTypeGeometry
• c_beta_index() : core::scoring::disulfides::DisulfideAtomIndices
• C_pos() : protocols::match::upstream::ProteinBackboneBuildPoint
• CA() : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• CA_atom_id() : protocols::match::upstream::UpstreamResTypeGeometry
• ca_cb_orient() : protocols::fldsgn::topology::Sheet
• ca_cb_orients() : protocols::fldsgn::topology::Sheet
• ca_cprev_n_h_interres_torsion_params() : core::scoring::methods::ResidueCartBondedParameters
• ca_nnext_c_o_interres_torsion_params() : core::scoring::methods::ResidueCartBondedParameters
• CA_pos() : protocols::match::upstream::ProteinBackboneBuildPoint
• CA_rmsd() : core::io::silent::BinaryProteinSilentStruct , core::io::silent::BinaryRNASilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct
• CA_search_scores_and_tensors() : protocols::scoring::methods::pcs2::PcsEnergy
• CA_search_scores_and_tensors_with_svd() : protocols::scoring::methods::pcs2::PcsEnergy
• CaCbCb_Angle_Func() : core::scoring::disulfides::CaCbCb_Angle_Func
• CaCbCbCa_Dihedral_Func() : core::scoring::disulfides::CaCbCbCa_Dihedral_Func
• cache() : core::fragment::CacheWrapper< T, XCacheUnit > , core::fragment::Frame
• cache_fragments() : protocols::forge::components::VarLengthBuild
• cache_pose() : protocols::frag_picker::VallProvider
• cache_profile() : protocols::frag_picker::VallProvider
• cache_task() : protocols::protein_interface_design::movers::RandomMutation
• CacheableAtomID_MapVector() : core::id::CacheableAtomID_MapVector
• CacheableObserver() : core::pose::datacache::CacheableObserver
• CacheablePoseRawPtr() : core::pose::datacache::CacheablePoseRawPtr
• CacheableSequenceProfile() : core::sequence::CacheableSequenceProfile
• cached_score() : protocols::frag_picker::scores::JCoupling , protocols::frag_picker::scores::LAMBEGO_Similarity , protocols::frag_picker::scores::MidPhiOut , protocols::frag_picker::scores::MidPsiOut , protocols::frag_picker::scores::PartialSecondarySimilarity , protocols::frag_picker::scores::PCS_FragDistance , protocols::frag_picker::scores::Phi , protocols::frag_picker::scores::PhiPsiRmsd , protocols::frag_picker::scores::PhiPsiSquareWell , protocols::frag_picker::scores::ProfileScore , protocols::frag_picker::scores::ProfileScoreBlosum62 , protocols::frag_picker::scores::ProfileScoreDistWeight , protocols::frag_picker::scores::ProfileScoreL1 , protocols::frag_picker::scores::ProfileScoreStructL1 , protocols::frag_picker::scores::ProfileScoreSubMatrix , protocols::frag_picker::scores::Psi , protocols::frag_picker::scores::RamaScore , protocols::frag_picker::scores::RDCScore , protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::SolventAccessibility , protocols::frag_picker::scores::TalosSSSimilarity , protocols::frag_picker::scores::TorsionBinSimilarity , protocols::frag_picker::scores::ABEGO_SS_Score , protocols::frag_picker::scores::AmbigCSScore , protocols::frag_picker::scores::AtomPairConstraintsScore , protocols::frag_picker::scores::CachingScoringMethod , protocols::frag_picker::scores::CSScore , protocols::frag_picker::scores::DihedralConstraintsScore , protocols::frag_picker::scores::DisulfideDistance , protocols::frag_picker::scores::FragmentCrmsd , protocols::frag_picker::scores::FragmentCrmsdResDepth , protocols::frag_picker::scores::FragmentDME , protocols::frag_picker::scores::GunnCostScore , protocols::frag_picker::scores::HydrophobicityProfileSimilarity , protocols::frag_picker::scores::HydrophobicitySimilarity , protocols::frag_picker::scores::InterbondAngleScore
• CacheWrapper() : core::fragment::CacheWrapper< T, XCacheUnit >
• CachingScoringMethod() : protocols::frag_picker::scores::CachingScoringMethod
• CAcstGenerator() : protocols::seeded_abinitio::CAcstGenerator
• Calc() : core::scoring::sc::MolecularSurfaceCalculator , core::scoring::sc::ShapeComplementarityCalculator
• calc_angle() : protocols::rigid::RotateJumpAxisMover , protocols::simple_moves::TorsionDOFMover
• calc_bin_and_pos() : protocols::match::VoxelSetIterator
• calc_bin_index() : protocols::match::OccupiedSpaceHash
• calc_centroid_dG() : protocols::analysis::InterfaceAnalyzerMover
• calc_crossing_angles() : protocols::features::helixAssembly::HelixBundleFeatures
• calc_deltaEpd() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode
• calc_dipscore() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
• calc_dotscore() : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• calc_ElectricField() : protocols::sparta::PDB
• calc_energy() : core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::MembraneEnvSmoothEnergy
• calc_etable_value() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• calc_fa_energy() : protocols::features::helixAssembly::HelixBundleFeatures
• calc_fit_R() : protocols::evaluation::PCA
• calc_frac_atoms_kA_to_native() : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• calc_frac_native_contacts() : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• calc_gdt() : protocols::comparative_modeling::Align_RmsdEvaluator
• calc_geometry() : protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::BetaAlphaBetaMotifSet , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::HelixPairingSet , protocols::fldsgn::topology::HSSTriplet , protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::SheetSet , protocols::fldsgn::topology::Strand , protocols::fldsgn::topology::Helix
• calc_hbond_sasaE() : protocols::analysis::InterfaceAnalyzerMover
• calc_helix_cycle() : protocols::fldsgn::topology::BetaAlphaBetaMotif
• calc_HN_S2() : protocols::sparta::PDB
• calc_inout() : protocols::fldsgn::topology::BetaAlphaBetaMotif
• calc_interaction_energy() : protocols::ub_e2c::ubi_e2c_modeler , protocols::symmetric_docking::SymDockProtocol
• calc_interface_metrics() : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• calc_jacobian_cartesians() : protocols::simple_moves::BBConRotMover
• calc_kl_divergence() : core::scoring::constraints::MixtureFunc
• calc_Lrmsd() : protocols::ub_e2c::ubi_e2c_modeler
• calc_ordermatrix() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
• calc_orderparam() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
• calc_pc_and_com() : protocols::features::helixAssembly::HelixBundleFeatures
• calc_penalty_vec() : core::scoring::constraints::FabConstraint
• calc_pep_scores() : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• calc_per_residue_energy() : protocols::analysis::InterfaceAnalyzerMover
• calc_pfront_poses_filter_ranks() : protocols::design_opt::GreedyOptMutationMover
• calc_phipsi_RMSD() : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• calc_phithetascore() : protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• calc_point_mut_filters() : protocols::design_opt::PointMutationCalculator
• calc_rms() : protocols::symmetric_docking::SymDockProtocol
• calc_rmsds() : protocols::rna::RNA_DeNovoProtocol
• calc_rot_freq() : core::pack::annealer::SimAnnealerBase
• calc_rsd_sasa() : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• calc_rsigmascore() : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• calc_sasa_bothsides() : protocols::fldsgn::topology::Sheet
• CalcAxisIntersect() : protocols::surface_docking::SurfaceParameters
• CalcDotsForAllAtoms() : core::scoring::sc::MolecularSurfaceCalculator
• CalcDotsForAtoms() : core::scoring::sc::MolecularSurfaceCalculator
• calcKineticEnergy() : protocols::cartesian::MolecularDynamics
• calcLevel1() : protocols::sparta::ANN
• calcLevel2() : protocols::sparta::ANN
• calcMetrics() : protocols::flexpep_docking::FlexPepDockingProtocol
• CalcNeighborDistance() : core::scoring::sc::ShapeComplementarityCalculator
• CalcNeighborDistanceFindClosestNeighbor() : core::scoring::sc::ShapeComplementarityCalculator
• CalcNormalVector() : protocols::surface_docking::SurfaceParameters
• calcPlane() : protocols::sparta::PDB
• CalcSc() : core::scoring::sc::ShapeComplementarityCalculator
• CalcSecondayStruct() : protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::SurfaceDockingProtocol
• CalcSecondayStruct_withSurface() : protocols::surface_docking::SurfaceDockingProtocol
• calcSurface() : protocols::sparta::PDB
• CalcTransVec() : protocols::surface_docking::SurfaceOrientMover
• calcTriangles() : protocols::sparta::PDB
• calculate() : protocols::dna::DNAParameters , protocols::pack_daemon::NPDPropCalculator , protocols::protein_interface_design::ReportSequenceDifferences , protocols::protein_interface_design::ReportPSSMDifferences , protocols::scoring::Interface , protocols::scoring::InterfaceInfo , protocols::simple_moves::ddG
• calculate_all_chainbreaks() : protocols::analysis::LoopAnalyzerMover
• calculate_alt_state_hpatch_score() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• calculate_amount_total_hydrophobic_ASA() : core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >
• calculate_atom_id_domain_map() : protocols::toolbox::AllowInsert
• calculate_atom_id_map() : protocols::toolbox::AllowInsert
• calculate_background_energies() : protocols::pack_daemon::PackDaemon
• calculate_center_xyz() : protocols::pockets::EggshellGrid
• calculate_contact_order() : core::scoring::methods::ContactOrderEnergy
• calculate_cost_only_with_svd() : protocols::scoring::methods::pcs2::PcsDataLanthanide
• calculate_derivatives_for_atoms_and_pseudo_base_atoms() : core::scoring::methods::LK_hack
• calculate_derivatives_for_residue_pair() : core::scoring::methods::LK_hack
• calculate_distance_matrix() : protocols::cluster::ClusterBase
• calculate_GBpair_apprx() : core::scoring::FACTSPotential
• calculate_GBpair_exact() : core::scoring::FACTSPotential
• calculate_highres_ref_energy() : protocols::docking::DockingEnsemble
• calculate_hpatch_deltaE() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• calculate_hydrogen_atom_reach() : core::scoring::etable::Etable
• calculate_icoor() : core::chemical::ResidueType
• calculate_index2cart() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• calculate_interface_unbound_energy() : protocols::ddg::ddGMover
• calculate_ligand_CoM() : protocols::pockets::PlaidFingerprint
• calculate_lk_ball_atom_energies() : core::scoring::methods::LK_BallEnergy
• calculate_lk_desolvation_of_single_atom_by_residue() : core::scoring::methods::LK_BallEnergy
• calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair() : core::scoring::methods::LK_BallEnergy
• calculate_lowres_ref_energy() : protocols::docking::DockingEnsemble
• calculate_map() : core::sequence::AnnotatedSequence
• calculate_nblist_distance_thresholds() : core::scoring::etable::Etable
• calculate_neighbor_table() : protocols::pmut_scan::PointMutScanDriver
• calculate_normal_disbins() : core::scoring::etable::Etable
• calculate_num_rotamers_in_subtree() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• calculate_orbital_icoor() : core::chemical::orbitals::AssignOrbitals
• calculate_orientation_vectors_and_pseudo_base_atoms() : core::scoring::methods::LK_hack
• calculate_pcs_score() : protocols::scoring::methods::pcs::PCS_Energy
• calculate_pcs_score_on_PCS_data_center_CA() : protocols::scoring::methods::pcs2::PcsEnergy
• calculate_PD_deltaE_for_substitution() : core::pack::interaction_graph::HPatchNode< V, E, G >
• calculate_per_position_scores() : core::sequence::SequenceAlignment
• calculate_protein_CoM() : protocols::pockets::NonPlaidFingerprint
• calculate_rg_score() : core::scoring::methods::RG_Energy_Fast
• calculate_rmsd() : protocols::anchored_design::AnchoredDesignMover
• calculate_rotamer_set_design_targets_partition_sum() : protocols::enzdes::EnzdesFlexibleRegion
• calculate_score_sum_of_pairs() : core::sequence::SequenceAlignment
• calculate_scores_and_tensors_from_pose_and_PCS_data() : protocols::scoring::methods::pcs::PCS_Energy
• calculate_specificity() : protocols::dna::DnaInterfacePacker
• calculate_subtree_containing_radii() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• calculate_tensor_and_cost_with_svd() : protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcs2::PcsDataLanthanide
• calculate_tensor_only_with_svd() : protocols::scoring::methods::pcs2::PcsDataLanthanide
• calculate_total_cst_score() : core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::KofNConstraint
• calculated() : core::scoring::CenListInfo , core::scoring::Membrane_FAEmbed , core::scoring::MembraneEmbed , core::scoring::rna::RNA_CentroidInfo , core::scoring::rna::RNA_FilteredBaseBaseInfo , core::scoring::rna::RNA_RawBaseBaseInfo , core::scoring::rna::RNA_ScoringInfo , core::scoring::SigmoidWeightedCenList< T > , protocols::scoring::InterfaceInfo
• calculated_atom_id_domain_map() : protocols::toolbox::AllowInsert
• calculator() : protocols::toolbox::pose_metric_calculators::MetricValueGetter
• calculator_name() : protocols::pack_daemon::NPDPropCalculatorCreator
• CalculatorFactory() : core::pose::metrics::CalculatorFactory
• CalculatorFilter() : protocols::filters::CalculatorFilter
• calibrate() : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::CrossPeakList
• calibration_atom_type() : protocols::noesy_assign::PeakAssignment , protocols::noesy_assign::Resonance
• calibration_constant() : protocols::noesy_assign::PeakCalibrator
• call_order() : protocols::rosetta_scripts::ParsedProtocol
• call_setup() : protocols::simple_moves::PackRotamersMoverLazy
• came_from() : core::sequence::Cell
• CamShiftEvaluator() : protocols::simple_filters::CamShiftEvaluator
• CamShiftEvaluatorCreator() : protocols::simple_filters::CamShiftEvaluatorCreator
• can_pair() : core::chemical::AutomorphismIterator
• cancel_batch() : protocols::jd2::archive::ArchiveManager
• cancel_batches_previous_to() : protocols::jd2::archive::ArchiveManager
• Candidate() : protocols::nonlocal::SmoothPolicy::Candidate
• candidate_res_atoms_reqd_near_target_atom() : protocols::match::downstream::AtomDistanceSecMatchRPE , protocols::match::downstream::GeometrySecMatchRPE , protocols::match::downstream::SecMatchResiduePairEvaluator
• CanonicalSamplingMover() : protocols::canonical_sampling::CanonicalSamplingMover , protocols::moves::CanonicalSamplingMover
• carbohydrate_info() : core::chemical::ResidueType , core::conformation::Residue
• CarbohydrateInfo() : core::chemical::carbohydrates::CarbohydrateInfo
• CarbonHBondEnergy() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• CarbonHBondPotential() : core::scoring::carbon_hbonds::CarbonHBondPotential
• carry_out_filtering() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• cart2frac() : core::scoring::electron_density::ElectronDensity
• cart2idx() : core::scoring::electron_density::ElectronDensity , core::scoring::PoissonBoltzmannPotential
• cart_product() : protocols::fldsgn::MatchResidues
• cartesian() : protocols::relax::RelaxProtocolBase , protocols::simple_moves::MinMover , protocols::simple_moves::SaneMinMover
• CartesianBondedEnergy() : core::scoring::methods::CartesianBondedEnergy
• CartesianHybridize() : protocols::hybridization::CartesianHybridize
• CartesianMinimizer() : core::optimization::CartesianMinimizer
• CartesianMinimizerMap() : core::optimization::CartesianMinimizerMap
• CartesianMultifunc() : core::optimization::CartesianMultifunc
• CartesianSampler() : protocols::hybridization::CartesianSampler
• CartesianSearchPattern() : protocols::hotspot_hashing::CartesianSearchPattern
• CartGrid() : core::grid::CartGrid< T >
• CartSCMinMinimizerMap() : core::pack::scmin::CartSCMinMinimizerMap
• CartSCMinMultifunc() : core::pack::scmin::CartSCMinMultifunc
• cast_flexbb_edge() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• cast_minimalist_flexbb_edge() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• cast_otfflexbb_edge() : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• catalog() : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::vall::VallLibrarian
• catalytic_res() : protocols::enzdes::EnzdesBaseProtocol
• catch_fragment() : protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::ccd::ShortLoopClosure
• CatPiCalculator() : protocols::toolbox::pose_metric_calculators::CatPiCalculator
• CavityBall() : core::scoring::packstat::CavityBall
• CB() : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• CB_Angle_Func() : core::scoring::disulfides::CB_Angle_Func
• CB_atom_id() : protocols::match::upstream::UpstreamResTypeGeometry
• CB_dist_cutoff() : protocols::toolbox::task_operations::RestrictInterGroupVectorOperation , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• Cb_Distance_Func() : core::scoring::disulfides::Cb_Distance_Func
• cb_force() : protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlacementMinimizationMover
• CBScore() : protocols::sic_dock::CBScore
• CBScoreVisitor() : protocols::sic_dock::CBScoreVisitor
• CBSG_Dihedral_Func() : core::scoring::disulfides::CBSG_Dihedral_Func
• cbx() : protocols::frag_picker::VallResidue
• cby() : protocols::frag_picker::VallResidue
• cbz() : protocols::frag_picker::VallResidue
• ccd() : protocols::dna::DesignProteinBackboneAroundDNA , protocols::protein_interface_design::movers::Splice
• ccd_closure() : protocols::simple_moves::WobbleMover
• CCD_loop_close() : protocols::swa::protein::StepWiseProteinCCD_Closer
• CCD_loop_close_sample_omega_recursively() : protocols::swa::protein::StepWiseProteinCCD_Closer
• CcdLoopClosureMover() : protocols::loops::loop_closure::ccd::CcdLoopClosureMover
• CcdMover() : protocols::loops::loop_closure::ccd::CcdMover
• CCDMoveWrapper() : protocols::rbsegment_relax::CCDMoveWrapper
• cd_1b_types() : core::scoring::ScoreFunction
• cd_2b_begin() : core::scoring::ScoreFunction
• cd_2b_end() : core::scoring::ScoreFunction
• cd_2b_intrares_begin() : core::scoring::ScoreFunction
• cd_2b_intrares_end() : core::scoring::ScoreFunction
• cd_2b_types() : core::scoring::ScoreFunction
• cd_lr_2b_methods_begin() : core::scoring::ScoreFunction
• cd_lr_2b_methods_end() : core::scoring::ScoreFunction
• cd_lr_2b_types() : core::scoring::ScoreFunction
• CDR_H3_filter() : protocols::antibody::CDRH3Modeler
• CDRH3Modeler() : protocols::antibody::CDRH3Modeler
• CDRsMinPackMin() : protocols::antibody2::CDRsMinPackMin
• Cell() : core::sequence::Cell
• Cen_Distance_Func() : core::scoring::disulfides::Cen_Distance_Func
• cen_score() : protocols::abinitio::IterativeBase
• cen_score_patch() : protocols::abinitio::IterativeBase
• cen_scorefxn() : protocols::comparative_modeling::LoopRelaxMover
• Cend_orient() : protocols::fldsgn::topology::SS_Base
• Cend_pos() : protocols::fldsgn::topology::SS_Base
• cenfilter() : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
• CenHBEnergy() : core::scoring::methods::CenHBEnergy
• CenHBPotential() : core::scoring::CenHBPotential
• cenlist_from_pose() : core::scoring::EnvPairPotential , core::scoring::SmoothEnvPairPotential
• CenListInfo() : core::scoring::CenListInfo
• CenPairEnergy() : core::scoring::methods::CenPairEnergy
• center() : core::id::StubID , core::id::NamedStubID , core::pose::Pose , core::scoring::MembraneEmbed , core::scoring::packstat::PackingScore , protocols::scoring::Interface
• center_all() : protocols::toolbox::DecoySetEvaluation
• center_of_mass() : protocols::hybridization::FoldTreeHybridize , protocols::loops::Loops
• center_structure() : protocols::toolbox::DecoySetEvaluation
• central_atoms_to_score() : core::scoring::mm::MMBondAngleResidueTypeParamSet
• central_residue() : protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator
• central_residues() : protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator
• centroid() : core::import_pose::ImportPoseOptions
• centroid_build() : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelMover
• centroid_filter() : protocols::ub_e2c::ubi_e2c_modeler
• centroid_loop_mover_str() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• centroid_mode_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
• centroid_scorefunction() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• centroid_scorefxn() : protocols::abinitio::Protocol
• CentroidDisulfideEnergy() : core::scoring::disulfides::CentroidDisulfideEnergy
• CentroidDisulfideEnergyComponents() : core::scoring::disulfides::CentroidDisulfideEnergyComponents
• CentroidDisulfideEnergyContainer() : core::scoring::disulfides::CentroidDisulfideEnergyContainer
• CentroidDisulfideNeighborConstIterator() : core::scoring::disulfides::CentroidDisulfideNeighborConstIterator
• CentroidDisulfideNeighborIterator() : core::scoring::disulfides::CentroidDisulfideNeighborIterator
• CentroidDisulfidePotential() : core::scoring::disulfides::CentroidDisulfidePotential
• CentroidRelax() : protocols::relax::CentroidRelax
• CentroidRelaxMover() : protocols::surface_docking::CentroidRelaxMover
• cenx() : protocols::frag_picker::VallResidue
• ceny() : protocols::frag_picker::VallResidue
• cenz() : protocols::frag_picker::VallResidue
• chain() : core::conformation::Residue , core::fragment::FragData , core::fragment::AnnotatedFragData , core::pack::task::operation::ChainIs , core::pose::PDBInfo , core::pose::Pose , protocols::ligand_docking::StartFrom , protocols::loops::ResidueIndexDescription , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::toolbox::task_operations::PreventChainFromRepackingOperation , protocols::toolbox::task_operations::RestrictChainToRepackingOperation , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation
• chain1() : protocols::simple_filters::AlaScan
• chain2() : protocols::simple_filters::AlaScan
• chain_begin() : core::conformation::Conformation
• chain_boundaries() : protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::StepWiseJobParameters
• Chain_break_screening() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• Chain_break_screening_general() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• chain_cut() : protocols::simple_moves::CutChainMover
• chain_end() : core::conformation::Conformation
• chain_endings() : core::conformation::Conformation , core::io::silent::BinaryProteinSilentStruct , core::io::silent::ProteinSilentStruct_Template< T >
• chain_endings_str() : core::io::silent::BinaryProteinSilentStruct , core::io::silent::ProteinSilentStruct_Template< T >
• chain_id() : protocols::simple_moves::CutChainMover
• chain_letter_to_number() : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• chain_letters() : protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator
• chain_numbers() : protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator
• chain_order() : protocols::simple_moves::SwitchChainOrderMover
• chain_sequence() : core::pose::Pose
• chainbreak_bias() : protocols::rigid::RigidBodyMotionMover
• ChainbreakDistFunc() : core::scoring::constraints::ChainbreakDistFunc
• ChainbreakEnergy() : core::scoring::methods::ChainbreakEnergy
• chainbreaks() : protocols::idealize::IdealizeMover
• chainbreakweights() : protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops
• ChainExistsFilter() : protocols::ligand_docking::ChainExistsFilter
• ChainIs() : core::pack::task::operation::ChainIs
• ChainIsnt() : core::pack::task::operation::ChainIsnt
• ChainPos() : core::pack::task::operation::ResiduePDBIndexIs::ChainPos
• chains() : protocols::ligand_docking::InterfaceScoreCalculator
• chains_from_termini() : core::conformation::Conformation
• chains_whose_residues_are_separate_chemical_entities() : core::io::pdb::FileDataOptions
• change_chi_without_replacing_residue() : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• change_conformer() : protocols::ligand_docking::Transform
• change_foldtree() : protocols::protein_interface_design::movers::AddChainBreak
• ChangeFoldTreeMover() : protocols::moves::ChangeFoldTreeMover
• char2ss_type() : protocols::comparative_modeling::features::SSFeature
• char_type() : protocols::rbsegment_relax::RBResidueRange
• charge() : core::chemical::Atom , core::scoring::hackelec::ElecAtom
• charge_charge_electrostatic() : protocols::qsar::scoring_grid::ChargeGrid
• ChargeAtom() : protocols::qsar::scoring_grid::ChargeAtom
• ChargeCalculator() : protocols::toolbox::pose_metric_calculators::ChargeCalculator
• ChargeChargeFeatures() : protocols::features::ChargeChargeFeatures
• ChargeChargeFeaturesCreator() : protocols::features::ChargeChargeFeaturesCreator
• ChargeGrid() : protocols::qsar::scoring_grid::ChargeGrid
• CharmmPeriodicFunc() : core::scoring::constraints::CharmmPeriodicFunc
• CHEAT_CoM() : protocols::pockets::FingerprintBase
• check() : protocols::toolbox::KClusterElement
• check2bsc() : protocols::match::downstream::ScoringSecMatchRPE
• check_and_act_clearcommand() : protocols::wum2::EndPoint
• check_and_act_status_request() : protocols::wum2::EndPoint
• check_and_create_fragments() : protocols::hybridization::HybridizeProtocol , protocols::seeded_abinitio::SegmentHybridizer
• check_and_initialize() : protocols::hotspot_hashing::movers::PlaceProbeMover
• check_atom_bin_in_range() : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• check_atom_numbers_for_backbone_oxygens() : core::scoring::rna::RNA_LowResolutionPotential
• check_atomset_compatibility() : core::coarse::CoarseEtable
• check_base_base_OK() : core::scoring::rna::RNA_FullAtomStackingEnergy
• check_base_pairing() : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• check_base_pairs() : protocols::rna::RNA_StructureParameters
• check_batch() : protocols::jd2::BatchJobInputter
• check_bounds() : core::scoring::constraints::SOGFunc , core::scoring::constraints::SOGFunc_Impl
• check_calculator_exists() : core::pose::metrics::CalculatorFactory
• check_cap_distances() : protocols::features::helixAssembly::HelixBundleFeatures
• Check_centroid_interaction() : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• check_chainbreak_variants() : protocols::topology_broker::TopologyBroker
• check_clash() : protocols::swa::rna::RNA_LoopCloseSampler
• check_clear_for_stacking() : core::scoring::rna::RNA_LowResolutionPotential
• check_close_chain_break() : protocols::swa::StepWisePoseSetup
• check_closure() : protocols::rna::RNA_LoopCloser
• check_closure_criteria() : protocols::forge::remodel::RemodelLoopMover
• check_compatibility() : protocols::swa::rna::FloatingBaseChainClosureJobParameter
• check_connections() : protocols::rna::RNA_ChunkLibrary
• check_contact() : protocols::swa::RigidBodySampler
• check_data_consistency() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• check_default_full_repacker() : protocols::relax::ClassicRelax
• check_default_mc() : protocols::relax::ClassicRelax
• check_default_rottrial() : protocols::relax::ClassicRelax
• check_domain_map() : core::scoring::NeighborList
• check_downstream_hit_incompatibility() : protocols::match::Matcher
• check_each_job_has_startstruct() : protocols::jd2::JD2ResourceManagerJobInputter
• check_edges_for_atom_info() : core::kinematics::FoldTree
• check_fa_dun() : protocols::match::upstream::BuildSet
• check_fa_rep() : protocols::swa::RigidBodySampler
• check_features_reporter_dependencies() : protocols::features::ReportToDB
• check_filters() : protocols::abinitio::AbrelaxApplication , protocols::flexpep_docking::FlexPepDockingProtocol
• check_fold_tree() : core::kinematics::FoldTree
• check_fold_tree_OK() : protocols::rna::ChunkSet , protocols::rna::RNA_ChunkLibrary
• check_for_aromatic() : core::chemical::sdf::CtabBase
• check_for_base_neighbor() : core::scoring::rna::RNA_LowResolutionPotential
• check_for_closeness() : protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::StepWiseClusterer
• check_for_closeness_without_job_parameters() : protocols::swa::rna::StepWiseRNA_Clusterer
• check_for_symmetric_peaks() : protocols::noesy_assign::PeakAssignmentResidueMap
• check_forming_base_pair() : core::scoring::rna::RNA_LowResolutionPotential
• check_forward_backward() : protocols::rna::RNA_JumpLibrary , protocols::rna::RNA_StructureParameters
• check_frequency() : protocols::moves::MonteCarlo
• check_hairpin() : core::scoring::SS_Killhairpins_Info
• check_high_res_protocol() : protocols::docking::DockingProtocol
• check_if_connected_residues_belong_to_regions() : protocols::simple_filters::RegionalConnections
• check_if_really_connected() : protocols::simple_moves::ConstrainToIdealMover
• check_if_residues_are_Ctermini() : core::io::pdb::FileDataOptions
• check_if_residues_are_Ntermini() : core::io::pdb::FileDataOptions
• check_if_rna_from_sequence_line() : core::io::silent::SilentFileData
• check_in_bond_angle_list() : protocols::simple_moves::ConstrainToIdealMover
• check_in_bonded_list() : protocols::simple_moves::ConstrainToIdealMover
• check_in_chain_connections() : protocols::rna::RNA_StructureParameters
• check_internals() : protocols::comparative_modeling::MultiThreadingMover
• check_internals_() : core::sequence::ChemicalShiftSequence , core::sequence::SequenceProfile
• check_intra_residue() : core::scoring::rna::RNA_TorsionPotential
• check_jump_match() : protocols::rna::RNA_ChunkLibrary
• check_library_expiry_dates() : protocols::loophash::MPI_LoopHashRefine_Master
• check_methods() : core::scoring::ScoreFunction
• check_mmt() : protocols::simple_moves::TorsionDOFMover
• check_moving_res_in_chain() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup , protocols::swa::StepWisePoseSetup
• check_new_pairing_dists() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• check_next_pairing() : protocols::jumping::SheetBuilder
• check_non_upstream_only_hit_incompatibility() : protocols::match::Matcher
• check_num_hbonds() : protocols::swa::RigidBodySampler
• check_o2star_needs_optimization() : protocols::swa::RigidBodySampler
• check_order() : core::kinematics::FoldTree
• check_overlap() : protocols::hybridization::InsertChunkMover
• check_pairing_intersect() : protocols::jumping::SheetBuilder
• check_pleat() : core::scoring::dssp::StrandPairing , core::scoring::dssp::StrandPairingSet
• check_pose_tree_compatibility() : protocols::toolbox::match_enzdes_util::InvrotTree , protocols::toolbox::match_enzdes_util::TheozymeInvrotTree
• check_rama() : core::util::ABEGO , core::util::ABEGOManager , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::simple_moves::BackboneMover
• check_rama2() : core::util::ABEGO
• check_res_map() : protocols::rna::RNA_ChunkLibrary
• check_res_map_recursively() : protocols::rna::RNA_ChunkLibrary
• check_residue_records_size() : core::pose::PDBInfo
• check_resource_loader_type() : protocols::jd2::JD2ResourceManager
• check_score_filter() : protocols::rna::RNA_DeNovoProtocol
• check_sequence() : protocols::noesy_assign::FragsToAtomDist , protocols::swa::InputStreamWithResidueInfo
• check_sheet_dis_antiparallel() : protocols::features::strand_assembly::StrandBundleFeatures
• check_sheet_dis_parallel() : protocols::features::strand_assembly::StrandBundleFeatures
• check_sheet_pairings() : protocols::jumping::SheetBuilder
• check_spanning() : core::scoring::MembranePotential
• check_ss() : protocols::simple_moves::ClassicFragmentMover
• check_stack_base() : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• check_state() : protocols::forge::remodel::RemodelDesignMover
• check_status() : protocols::frag_picker::quota::ABEGO_SS_Map
• check_steric_overlap() : protocols::swa::RigidBodySampler
• check_sugar_atom() : core::scoring::rna::RNA_DataBackboneEnergy
• check_superimpose_res() : protocols::swa::StepWisePoseSetup
• check_tag() : protocols::cluster::GatherPosesMover
• check_temp_consistency() : protocols::canonical_sampling::TemperingBase
• Check_that_terminal_res_are_unstacked() : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• check_topology() : core::kinematics::FoldTree
• check_two_pairings() : protocols::jumping::SheetBuilder
• check_value() : protocols::match::downstream::AtomGeometrySecMatchRPE
• check_VDW_screen_bin_is_setup() : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• CheckAtomCollision2() : core::scoring::sc::MolecularSurfaceCalculator
• checkFormat() : protocols::sparta::GDB
• checkpoint() : protocols::abinitio::MembraneAbinitio , protocols::checkpoint::CheckPointer
• checkpoint_clear() : protocols::jd2::BOINCJobDistributor , protocols::jobdist::BaseJobDistributor
• checkpoint_completed() : protocols::boinc::Boinc
• checkpoint_read() : protocols::jd2::BOINCJobDistributor , protocols::jobdist::BaseJobDistributor
• checkpoint_write() : protocols::jd2::BOINCJobDistributor , protocols::jobdist::BaseJobDistributor
• CheckPointCollision() : core::scoring::sc::MolecularSurfaceCalculator
• checkpointed_cycle_block() : protocols::abinitio::FragmentSampler
• CheckPointer() : protocols::checkpoint::CheckPointer
• checkpointing_file() : protocols::protein_interface_design::movers::Splice
• CheckProbeCollision() : core::scoring::sc::MolecularSurfaceCalculator
• ChemicalManager() : core::chemical::ChemicalManager
• ChemicalShiftAnisotropy() : core::scoring::ChemicalShiftAnisotropy
• ChemicalShiftAnisotropyEnergy() : core::scoring::methods::ChemicalShiftAnisotropyEnergy
• ChemicalShiftData() : core::scoring::rna::chemical_shift::ChemicalShiftData
• ChemicalShiftEvaluator() : protocols::sparta::ChemicalShiftEvaluator
• ChemicalShiftEvaluatorCreator() : protocols::sparta::ChemicalShiftEvaluatorCreator
• ChemicalShiftScoringScheme() : core::sequence::ChemicalShiftScoringScheme
• ChemicalShiftSequence() : core::sequence::ChemicalShiftSequence
• ChemicalShiftSequenceCreator() : core::sequence::ChemicalShiftSequenceCreator
• chemshift_column() : protocols::abinitio::IterativeBase
• chemshift_compliance() : protocols::noesy_assign::PeakAssignment
• chi() : core::conformation::Residue , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::pack::task::operation::RotamerExplosion , core::pose::Pose , protocols::dna::DnaInterfaceMinMover , protocols::dna::DNABase , protocols::optimize_weights::PNatRotOptERotamerData , protocols::simple_moves::symmetry::SetupNCSMover , protocols::simple_moves::TaskAwareMinMover , protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• chi2max() : protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation
• chi2min() : protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation
• chi4E() : core::scoring::methods::ProClosureEnergy
• chi_2_proton_chi() : core::chemical::ResidueType
• chi_atoms() : core::chemical::ResidueType , core::conformation::Residue
• chi_clones() : core::conformation::symmetry::SymmetryInfo
• chi_dev() : protocols::comparative_modeling::Align_RotamerEvaluator
• chi_follows() : core::conformation::symmetry::SymmetryInfo
• chi_is_independent() : core::conformation::symmetry::SymmetryInfo
• chi_is_nonrotameric() : core::pack::dunbrack::DunbrackRotamerSampleData
• chi_matches_coords() : protocols::simple_moves::MinimalRotamer
• chi_mean() : core::pack::dunbrack::DunbrackRotamerMeanSD< S, P > , core::pack::dunbrack::DunbrackRotamerSampleData
• chi_poly_lookup() : core::scoring::hbonds::HBondDatabase
• chi_probability() : core::pack::dunbrack::DunbrackRotamerSampleData
• chi_rotamers() : core::chemical::ResidueType , core::conformation::Residue
• chi_sample() : protocols::match::upstream::FullChiSampleSet
• chi_samples() : protocols::match::upstream::FullChiSampleSet
• chi_sd() : core::pack::dunbrack::DunbrackRotamerMeanSD< S, P > , core::pack::dunbrack::DunbrackRotamerSampleData
• chi_torsions() : core::io::silent::RNA_SilentStruct
• chi_xx() : protocols::scoring::methods::pcs::PCS_tensor
• chi_xy() : protocols::scoring::methods::pcs::PCS_tensor
• chi_xz() : protocols::scoring::methods::pcs::PCS_tensor
• chi_yy() : protocols::scoring::methods::pcs::PCS_tensor
• chi_yz() : protocols::scoring::methods::pcs::PCS_tensor
• chidev() : core::pack::dunbrack::RotamerLibraryScratchSpace
• chidevpen() : core::pack::dunbrack::RotamerLibraryScratchSpace
• child() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• child_index() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• chimean() : core::pack::dunbrack::RotamerLibraryScratchSpace
• chinum() : protocols::simple_moves::sidechain_moves::SetChiMover
• ChiralMover() : protocols::simple_moves::chiral::ChiralMover
• chis_from_pose() : protocols::toolbox::pose_metric_calculators::RotamerRecovery
• chisamples_for_rotamer_and_chi() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• chisd() : core::pack::dunbrack::RotamerLibraryScratchSpace
• ChiSet() : core::pack::dunbrack::ChiSet
• chitip_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• chitip_atoms() : protocols::match::upstream::UpstreamResTypeGeometry
• ChiWellRmsdEvaluator() : protocols::simple_filters::ChiWellRmsdEvaluator
• ChiWellRmsdEvaluatorCreator() : protocols::simple_filters::ChiWellRmsdEvaluatorCreator
• choices() : protocols::genetic_algorithm::DiscreteRandomizer , protocols::genetic_algorithm::PositionSpecificRandomizer
• cholesky_bw() : protocols::simple_moves::BBGaussianMover
• cholesky_fw() : protocols::simple_moves::BBGaussianMover
• choose() : protocols::nonlocal::Chunk , protocols::nonlocal::Policy , protocols::nonlocal::SmoothPolicy , protocols::nonlocal::UniformPolicy
• choose_anchor_position() : protocols::hybridization::HybridizeFoldtreeDynamic , protocols::nonlocal::StarTreeBuilder
• choose_anchors() : protocols::hybridization::HybridizeFoldtreeDynamic
• choose_best_solution_based_on_score_function() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::swa::rna::RNA_AnalyticLoopCloser
• choose_cutpoint() : protocols::loops::Loop , protocols::star::Extender
• choose_cutpoints() : protocols::loops::Loops
• choose_database_filter() : protocols::features::ProteinSilentReport
• choose_desired_centroid() : protocols::ligand_docking::LigandBaseProtocol
• choose_effective_sequence_separation() : core::scoring::constraints::Constraint , core::scoring::constraints::MultiConstraint
• choose_fragment() : protocols::simple_moves::ConstraintFragmentMover , protocols::simple_moves::ClassicFragmentMover , protocols::simple_moves::SmoothFragmentMover , protocols::simple_moves::SmoothSymmetricFragmentMover
• choose_least_perturb_solution() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::swa::rna::RNA_AnalyticLoopCloser
• choose_n_best() : protocols::enzdes::PackRotamersMoverPartGreedy
• choose_next_pairing() : protocols::jumping::SheetBuilder
• choose_window_length() : protocols::simple_moves::ClassicFragmentMover
• choose_window_start() : protocols::simple_moves::ClassicFragmentMover
• Chunk() : protocols::nonlocal::Chunk
• chunk_coverage() : protocols::rna::RNA_ChunkLibrary
• chunk_key() : protocols::frag_picker::VallChunk
• chunk_set() : protocols::rna::RNA_ChunkLibrary
• ChunkSet() : protocols::rna::ChunkSet
• ChunkTrialMover() : protocols::hybridization::ChunkTrialMover
• Ci() : core::scoring::FACTSResidueInfo
• ci_1b_types() : core::scoring::ScoreFunction
• ci_2b_begin() : core::scoring::ScoreFunction
• ci_2b_end() : core::scoring::ScoreFunction
• ci_2b_intrares_begin() : core::scoring::ScoreFunction
• ci_2b_intrares_end() : core::scoring::ScoreFunction
• ci_2b_types() : core::scoring::ScoreFunction
• ci_lr_2b_methods_begin() : core::scoring::ScoreFunction
• ci_lr_2b_methods_end() : core::scoring::ScoreFunction
• ci_lr_2b_types() : core::scoring::ScoreFunction
• ciBR() : core::pack::annealer::FASTERAnnealer
• Circle() : core::scoring::packstat::Circle
• CircularGeneral1D_Func() : core::scoring::constraints::CircularGeneral1D_Func
• CircularHarmonicFunc() : core::scoring::constraints::CircularHarmonicFunc
• CircularPermutation() : protocols::fldsgn::CircularPermutation
• CircularPowerFunc() : core::scoring::constraints::CircularPowerFunc
• CircularSigmoidalFunc() : core::scoring::constraints::CircularSigmoidalFunc
• cis_omega() : core::util::ABEGO
• claim_accepted() : protocols::topology_broker::TopologyClaimer
• claimer() : protocols::topology_broker::TopologyBroker
• ClaimerMessage() : protocols::topology_broker::ClaimerMessage
• clash_check() : protocols::scoring::ImplicitFastClashCheck
• clash_check_test() : protocols::scoring::ImplicitFastClashCheck
• clash_check_trimer() : protocols::scoring::ImplicitFastClashCheck
• clash_count() : protocols::scoring::ImplicitFastClashCheck
• ClashCountCalculator() : protocols::toolbox::pose_metric_calculators::ClashCountCalculator
• clashes() : protocols::sic_dock::Rose
• clashes_naive() : protocols::sic_dock::Rose
• classic_mcm_protocol() : protocols::symmetric_docking::SymDockProtocol
• classic_protocol() : protocols::ligand_docking::LigandDockProtocol
• ClassicAbinitio() : protocols::abinitio::ClassicAbinitio
• ClassicFragmentMover() : protocols::simple_moves::ClassicFragmentMover
• ClassicGrid() : protocols::qsar::scoring_grid::ClassicGrid
• ClassicMatchAlgorithm() : protocols::match::downstream::ClassicMatchAlgorithm
• ClassicRelax() : protocols::relax::ClassicRelax
• classification() : core::io::pdb::HeaderInformation
• classify_onebody_enmeth() : core::scoring::MinimizationNode
• classify_twobody_enmeth() : core::scoring::MinimizationNode , core::scoring::MinimizationEdge
• clean_frag_cache() : core::fragment::FragmentIO
• clean_jumps() : protocols::abinitio::TemplateJumpSetup , protocols::jumping::BaseJumpSetup , protocols::jumping::JumpSetup , protocols::jumping::JumpSelector , protocols::jumping::ResiduePairJumpSetup , protocols::jumping::SheetBuilder
• clean_pose_store() : protocols::cluster::ClusterBase
• clean_residue_task() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• clean_up() : protocols::frag_picker::scores::ABEGO_SS_Score , protocols::frag_picker::scores::AmbigCSScore , protocols::frag_picker::scores::AtomBasedConstraintsScore , protocols::frag_picker::scores::CachingScoringMethod , protocols::frag_picker::scores::CSScore , protocols::frag_picker::scores::DisulfideDistance , protocols::frag_picker::scores::FragmentCrmsd , protocols::frag_picker::scores::FragmentCrmsdResDepth , protocols::frag_picker::scores::FragmentDME , protocols::frag_picker::scores::FragmentScoreManager , protocols::frag_picker::scores::GunnCostScore , protocols::frag_picker::scores::HydrophobicityProfileSimilarity , protocols::frag_picker::scores::HydrophobicitySimilarity , protocols::frag_picker::scores::JCoupling , protocols::frag_picker::scores::LAMBEGO_Similarity , protocols::frag_picker::scores::MidPhiOut , protocols::frag_picker::scores::MidPsiOut , protocols::frag_picker::scores::PartialSecondarySimilarity , protocols::frag_picker::scores::PCS_FragDistance , protocols::frag_picker::scores::Phi , protocols::frag_picker::scores::PhiPsiRmsd , protocols::frag_picker::scores::PhiPsiSquareWell , protocols::frag_picker::scores::ProfileScore , protocols::frag_picker::scores::ProfileScoreBlosum62 , protocols::frag_picker::scores::ProfileScoreDistWeight , protocols::frag_picker::scores::ProfileScoreL1 , protocols::frag_picker::scores::ProfileScoreStructL1 , protocols::frag_picker::scores::ProfileScoreSubMatrix , protocols::frag_picker::scores::Psi , protocols::frag_picker::scores::RamaScore , protocols::frag_picker::scores::RDCScore , protocols::frag_picker::scores::ScoreEValuator , protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::SolventAccessibility , protocols::frag_picker::scores::TalosSSSimilarity , protocols::frag_picker::scores::TorsionBinSimilarity
• clean_up_rna_two_body_energy_tables() : core::scoring::rna::RNA_PairwiseLowResolutionEnergy
• cleanup() : protocols::simple_moves::GreenPacker
• cleanup_after_job_completion() : protocols::jd2::JD2ResourceManagerJobInputter
• cleanup_pose() : protocols::swa::InputStreamWithResidueInfo
• cleanup_reqs() : protocols::wum2::EndPoint
• clear() : protocols::simple_filters::NeighborTypeFilter , protocols::simple_moves::BackboneMover , protocols::simple_moves::LoggedFragmentMover , protocols::toolbox::DecoySetEvaluation , protocols::toolbox::KClusterElement , protocols::toolbox::match_enzdes_util::EnzdesLoopsFile , protocols::wum::SilentStructStore , protocols::wum::WorkUnitQueue , protocols::wum2::WUQueue , core::chemical::ResidueSelector , core::chemical::sdf::MolData , core::conformation::Conformation , core::fragment::Frame , core::fragment::picking_old::concepts::Book< Pages > , core::fragment::picking_old::concepts::Library< Books > , core::graph::ArrayPool< T > , core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::SequenceMapping , core::io::sequence_comparation::DesignContrast , core::io::silent::SilentFileData , core::kinematics::AtomTree , core::kinematics::FoldTree , core::kinematics::MoveMap , core::kinematics::ResidueCoordinateChangeList , core::pack::annealer::SimAnnealerBase , core::pack::rotamer_set::WaterPackingInfo , core::pack::task::operation::DisallowIfNonnativeRLT , core::pack::task::operation::RestrictResidueToRepacking , core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::PreventRepacking , core::pack::task::TaskFactory , core::pose::datacache::SpecialSegmentsObserver , core::pose::datacache::ObserverCache , core::pose::metrics::PoseMetricContainer , core::pose::PDBPoseMap , core::pose::Pose , core::scoring::CenHBPotential , core::scoring::constraints::Constraints , core::scoring::constraints::ResidueConstraints , core::scoring::constraints::ConstraintSet , core::scoring::Energies , core::scoring::EMapVector , core::scoring::hbonds::HBondSet , core::scoring::NeighborList , core::scoring::SmoothScoreTermCoeffs , core::scoring::Strands , core::scoring::Hairpins , core::sequence::DP_Matrix , core::sequence::SequenceAlignment , protocols::abinitio::AbrelaxMover , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::canonical_sampling::TemperingBase , protocols::cluster::GatherPosesMover , protocols::cluster::Cluster , protocols::dna::DnaChains , protocols::evaluation::MetaPoseEvaluator , protocols::filters::CompoundFilter , protocols::filters::Filter , protocols::filters::FilterCollection , protocols::fldsgn::topology::BB_Pos , protocols::fldsgn::topology::BetaAlphaBetaMotifSet , protocols::fldsgn::topology::HelixPairingSet , protocols::fldsgn::topology::HSSTripletSet , protocols::fldsgn::topology::SheetSet , protocols::fldsgn::topology::StrandPairingSet , protocols::forge::build::BuildManager , protocols::frag_picker::BoundedCollector< StrictWeakOrdering > , protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering > , protocols::frag_picker::CandidatesCollector , protocols::frag_picker::GrabAllCollector , protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering > , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaCollector , protocols::frag_picker::quota::QuotaPool , protocols::frag_picker::quota::SecondaryStructurePool , protocols::frag_picker::scores::AdaptiveScoreHistogram , protocols::frag_picker::scores::ProfileScore , protocols::frag_picker::scores::ProfileScoreBlosum62 , protocols::frag_picker::scores::ProfileScoreDistWeight , protocols::frag_picker::scores::ProfileScoreL1 , protocols::frag_picker::scores::ProfileScoreStructL1 , protocols::frag_picker::scores::ProfileScoreSubMatrix , protocols::hotspot_hashing::HotspotStubSet , protocols::jd2::JD2ResourceManager , protocols::jumping::JumpSetup , protocols::jumping::ResiduePairJumpSetup , protocols::loops::Loops , protocols::match::Bool3DGrid , protocols::match::downstream::ActiveSiteGrid , protocols::moves::CompositionMover , protocols::moves::MoverContainer , protocols::moves::MoverStatistics , protocols::moves::PDBDumpMover , protocols::pockets::PClusterSet , protocols::pockets::PocketGrid , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::ResidueBBDofs , protocols::qsar::qsarMap , protocols::rosetta_scripts::ParsedProtocol
• clear_() : core::scoring::constraints::SOGFunc , core::scoring::constraints::SOGFunc_Impl
• clear_active_dofs() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• clear_active_pose_constraints() : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• clear_active_pose_constraints_for_block() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• clear_all() : protocols::swa::rna::RNA_LoopCloseSampler , protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• clear_at_inds() : protocols::match::downstream::AtomGeometrySecMatchRPE
• clear_atoms() : core::optimization::DOF_Node
• clear_blacklist() : protocols::wum::WorkUnitBase
• clear_cached_data() : protocols::design_opt::GreedyOptMutationMover
• clear_calculators() : core::pose::metrics::CalculatorFactory
• clear_channel_from_garbage_collector() : protocols::jd2::MpiFileBuffer
• clear_checkpoints() : protocols::abinitio::MembraneAbinitio , protocols::checkpoint::CheckPointer
• clear_comments() : core::io::silent::SilentStruct
• clear_compounds() : core::io::pdb::HeaderInformation
• clear_constraints() : protocols::forge::remodel::RemodelConstraintGenerator
• clear_current_job_output() : protocols::jd2::JobDistributor
• clear_data() : protocols::fldsgn::topology::SS_Info2 , protocols::motifs::BuildPosition , protocols::toolbox::KClusterElement
• clear_dCCdx_res_cache() : core::scoring::electron_density::ElectronDensity
• clear_dependencies() : protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager
• clear_design_taskset() : protocols::flxbb::FlxbbDesign
• clear_dof_nodes() : core::optimization::MinimizerMap
• clear_downstream_orientation_atoms() : protocols::match::MatcherTask
• clear_energies() : core::io::silent::SilentStruct , core::scoring::Energies , protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• clear_evaluators() : protocols::jd2::JobOutputter
• clear_events() : core::pose::datacache::LengthEventCollector
• clear_experimental_techniques() : core::io::pdb::HeaderInformation
• clear_extent_eval() : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• clear_extent_gen() : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• clear_external_geom_samplers() : protocols::match::downstream::ClassicMatchAlgorithm
• clear_filters() : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::match::output::MatchProcessor
• clear_fragment_eval() : core::fragment::picking_old::vall::VallLibrarian
• clear_fragment_gen() : core::fragment::picking_old::vall::VallLibrarian
• clear_fragments() : protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelLoopMover , protocols::loops::loop_mover::LoopMover
• clear_hash_map() : protocols::match::HitHasher
• clear_hbonds() : core::scoring::hbonds::HBondResPairMinData
• clear_history() : protocols::pack_daemon::MultistateFitnessFunction
• clear_info() : protocols::moves::Mover
• clear_initialization() : protocols::dna::DnaInterfacePacker
• clear_internals() : protocols::protein_interface_design::PatchdockReader
• clear_inverse_rotamers() : protocols::forge::constraints::InverseRotamersRCG
• clear_jumps() : protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::scoring::InterfaceInfo
• clear_keywords() : core::io::pdb::HeaderInformation
• clear_lib() : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• clear_match_data() : protocols::match::output::CloudPDBWriter
• clear_movesets() : protocols::rbsegment_relax::RBSegmentRelax
• clear_observers() : core::conformation::Conformation
• clear_parents() : protocols::genetic_algorithm::GeneticAlgorithm
• clear_poses() : protocols::moves::MonteCarlo
• clear_properties() : core::chemical::AtomType
• clear_rcgs() : protocols::forge::components::VarLengthBuild
• clear_residue_connections() : core::conformation::Residue
• clear_residue_maps() : core::chemical::ResidueTypeSet
• clear_rnl_pose() : protocols::enzdes::EnzdesScorefileFilter
• clear_rots() : protocols::motifs::BuildPosition
• clear_rv_infos() : protocols::forge::remodel::ResidueVicinityRCG
• clear_score() : protocols::moves::MoverStatistics
• clear_segments() : protocols::backrub::BackrubMover
• clear_serial_data() : protocols::wum::WorkUnitBase
• clear_setup_movers() : protocols::forge::components::VarLengthBuild
• clear_stored_constraints() : protocols::forge::remodel::RemodelConstraintGenerator
• clear_structure_map() : core::io::raw_data::RawFileData , core::io::silent::SilentFileData
• clear_suckers() : protocols::simple_moves::AddCavitiesMover
• clear_target_states() : protocols::toolbox::match_enzdes_util::InvrotTree
• clear_task() : protocols::simple_moves::DesignRepackMover
• clear_task_factory() : protocols::seeded_abinitio::SeedSetupMover , protocols::simple_moves::DesignRepackMover
• clear_title() : core::io::pdb::HeaderInformation
• clear_torsion_string_stack() : protocols::loops::loop_closure::kinematic_closure::KinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber
• clear_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
• clear_two_body_energy_for_edge() : core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph
• clear_user_provided_movers() : protocols::forge::components::VarLengthBuild
• clear_Vall() : core::fragment::picking_old::FragmentLibraryManager
• ClearConstraintsMover() : protocols::simple_moves::ClearConstraintsMover
• clearMask() : core::scoring::electron_density::ElectronDensity
• clearSmallPockets() : protocols::pockets::PocketGrid
• clip_to_nrchi_range() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• clone() : protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO , protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO , protocols::toolbox::task_operations::DesignAroundOperation , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LayerOperations , protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::ModifyAnnealer , protocols::toolbox::task_operations::PreventChainFromRepackingOperation , protocols::toolbox::task_operations::PreventResiduesFromRepackingOperation , protocols::toolbox::task_operations::ProteinCore , protocols::toolbox::task_operations::ProteinInterfaceDesignOperation , protocols::toolbox::task_operations::ReadResfileFromDB , protocols::toolbox::task_operations::RestrictByCalculatorsOperation , protocols::toolbox::task_operations::RestrictChainToRepackingOperation , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::toolbox::task_operations::RestrictInterGroupVectorOperation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::RestrictNonSurfaceToRepackingOperation , protocols::toolbox::task_operations::RestrictOperationsBase , protocols::toolbox::task_operations::RestrictResiduesToRepackingOperation , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation , protocols::toolbox::task_operations::RestrictToCDRH3Loop , protocols::toolbox::task_operations::DockingNoRepack1 , protocols::toolbox::task_operations::DockingNoRepack2 , protocols::toolbox::task_operations::RestrictToInterface , protocols::toolbox::task_operations::RestrictToInterfaceOperation , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation , protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors , protocols::toolbox::task_operations::RestrictToNeighborhoodOperation , protocols::toolbox::task_operations::RestrictToTerminiOperation , protocols::toolbox::task_operations::SelectBySASAOperation , protocols::toolbox::task_operations::SeqprofConsensusOperation , protocols::toolbox::task_operations::RestrictConservedLowDdgOperation , protocols::toolbox::task_operations::SetIGTypeOperation , protocols::toolbox::task_operations::ThreadSequenceOperation , protocols::topology_broker::AsymFoldandDockClaimer , protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::CutBiasClaimer , protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::DisulfJumpClaimer , protocols::topology_broker::DofClaim , protocols::topology_broker::SequenceClaim , protocols::topology_broker::BBClaim , protocols::topology_broker::JumpClaim , protocols::topology_broker::CutClaim , protocols::topology_broker::RootClaim , protocols::topology_broker::FibrilModelingClaimer , protocols::topology_broker::FoldandDockClaimer , protocols::topology_broker::FragmentClaimer , protocols::topology_broker::JumpClaimer , protocols::topology_broker::MembraneTopologyClaimer , protocols::topology_broker::MetalloClaimer , protocols::topology_broker::PcsEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::SequenceClaimer , protocols::topology_broker::StartStructClaimer , protocols::topology_broker::TemplateFragmentClaimer , protocols::topology_broker::TemplateJumpClaimer , protocols::topology_broker::TopologyClaimer , protocols::wum::DatabaseEntryWorkUnit , protocols::wum::WorkUnitBase , protocols::wum::WorkUnit_Wait , protocols::wum::WorkUnit_SilentStructStore , protocols::wum::WorkUnit_MoverWrapper , core::chemical::ResidueType , core::conformation::Conformation , core::conformation::Residue , core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetricConformation , core::conformation::symmetry::SymmetryInfo , core::fragment::BaseCacheUnit , core::fragment::BBTorsionAndAnglesSRFD , core::fragment::BBTorsionSRFD , core::fragment::ConstantLengthFragSet , core::fragment::MapCacheUnit< T > , core::fragment::VectorCacheUnit< T > , core::fragment::FragData , core::fragment::AnnotatedFragData , core::fragment::FragSet , core::fragment::FragSetCollection , core::fragment::Frame , core::fragment::IndependentBBTorsionSRFD , core::fragment::JumpingFrame , core::fragment::UpJumpSRFD , core::fragment::DownJumpSRFD , core::fragment::OrderedFragSet , core::fragment::picking_old::concepts::ExtentEvaluator< Bookmark, Ext > , core::fragment::picking_old::vall::eval::ABEGOEval , core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::eval::VallFragmentEval , core::fragment::picking_old::vall::gen::LengthGen , core::fragment::picking_old::vall::gen::SecStructGen , core::fragment::picking_old::vall::gen::VallFragmentGen , core::fragment::SecstructSRFD , core::fragment::SingleResidueFragData , core::grid::CartGrid< T > , core::id::CacheableAtomID_MapVector , core::import_pose::PDBSilentStruct , core::io::silent::BinaryProteinSilentStruct , core::io::silent::BinaryRNASilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreFileSilentStruct , core::io::silent::SilentStruct , core::kinematics::MoveMap , core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom , core::optimization::MinimizerOptions , core::pack::dunbrack::DunbrackConstraint , core::pack::dunbrack::DunbrackEnergy , core::pack::dunbrack::RotamerConstraint , core::pack::interaction_graph::HPatchEnergy , core::pack::interaction_graph::SurfaceEnergy , core::pack::rotamer_set::RotamerSetOperation , core::pack::rotamer_set::UnboundRotamersOperation , core::pack::rotamer_set::WaterPackingInfo , core::pack::task::operation::NoRepackDisulfides , core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::OptCysHG , core::pack::task::operation::OptH , core::pack::task::operation::ReplicateTask , core::pack::task::operation::ResFilter , core::pack::task::operation::AnyResFilter , core::pack::task::operation::AllResFilter , core::pack::task::operation::NoResFilter , core::pack::task::operation::ResidueTypeFilter , core::pack::task::operation::ResidueHasProperty , core::pack::task::operation::ResidueLacksProperty , core::pack::task::operation::ResidueName3Is , core::pack::task::operation::ResidueName3Isnt , core::pack::task::operation::ResidueIndexIs , core::pack::task::operation::ResidueIndexIsnt , core::pack::task::operation::ResiduePDBIndexIs , core::pack::task::operation::ResiduePDBIndexIsnt , core::pack::task::operation::ChainIs , core::pack::task::operation::ChainIsnt , 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::AddBehaviorRLT , core::pack::task::operation::DockingNoRepack1 , core::pack::task::operation::DockingNoRepack2 , core::pack::task::operation::RestrictToInterface , core::pack::task::operation::TaskOperation , core::pack::task::operation::RestrictToRepacking , core::pack::task::operation::RestrictResidueToRepacking , core::pack::task::operation::RestrictAbsentCanonicalAAS , core::pack::task::operation::DisallowIfNonnative , 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::SetRotamerCouplings , core::pack::task::operation::SetRotamerLinks , core::pack::task::operation::AppendRotamer , core::pack::task::operation::AppendRotamerSet , core::pack::task::operation::AppendResidueRotamerSet , core::pack::task::operation::PreserveCBeta , core::pack::task::operation::PreventRepacking , core::pack::task::operation::RestrictYSDesign , core::pack::task::operation::ExtraRotamers , core::pack::task::operation::ExtraChiCutoff , core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResfileCommand , core::pack::task::NATRO , core::pack::task::NATAA , core::pack::task::ALLAA , core::pack::task::ALLAAxc , core::pack::task::ALLAAwc , core::pack::task::PIKAA , core::pack::task::PIKNA , core::pack::task::PIKRNA , core::pack::task::NOTAA , core::pack::task::EMPTY , core::pack::task::POLAR , core::pack::task::APOLAR , core::pack::task::APOLA , core::pack::task::EX , core::pack::task::NC , core::pack::task::EX_CUTOFF , core::pack::task::USE_INPUT_SC , core::pack::task::AUTO , core::pack::task::SCAN , core::pack::task::TARGET , core::pack::task::NO_ADDUCTS , core::pack::task::FIX_HIS_TAUTOMER , core::pack::task::TaskFactory , core::pose::datacache::LengthEventCollector , core::pose::datacache::SpecialSegmentsObserver , core::pose::datacache::CacheableObserver , core::pose::datacache::CacheablePoseRawPtr , core::pose::datacache::PositionConservedResiduesStore , core::pose::metrics::PoseMetricCalculator , core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator , core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator , core::pose::metrics::simple_calculators::SasaCalculator , core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::ChemicalShiftAnisotropy , core::scoring::constraints::AmberPeriodicFunc , core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BigBinConstraint , core::scoring::constraints::BoundFunc , core::scoring::constraints::PeriodicBoundFunc , core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::constraints::CharmmPeriodicFunc , core::scoring::constraints::CircularGeneral1D_Func , core::scoring::constraints::CircularHarmonicFunc , core::scoring::constraints::CircularPowerFunc , core::scoring::constraints::CircularSigmoidalFunc , core::scoring::constraints::ConstantFunc , core::scoring::constraints::Constraint , core::scoring::constraints::CstEnergyContainer , core::scoring::constraints::Constraints , core::scoring::constraints::ConstraintsEnergy , core::scoring::constraints::ConstraintSet , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::CountViolFunc , core::scoring::constraints::CstMinimizationData , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::EtableFunc , core::scoring::constraints::FabConstraint , core::scoring::constraints::FadeFunc , core::scoring::constraints::FlatHarmonicFunc , core::scoring::constraints::Func , core::scoring::constraints::GaussianFunc , core::scoring::constraints::HarmonicFunc , core::scoring::constraints::IdentityFunc , core::scoring::constraints::KarplusFunc , core::scoring::constraints::KofNConstraint , core::scoring::constraints::LinearPenaltyFunction , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::MinMultiHarmonicFunc , core::scoring::constraints::MixtureFunc , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NamedAtomPairConstraint , core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::PeriodicFunc , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::ResidueTypeLinkingConstraint , core::scoring::constraints::ScalarWeightedFunc , core::scoring::constraints::SequenceProfileConstraint , core::scoring::constraints::SigmoidFunc , core::scoring::constraints::SiteConstraint , core::scoring::constraints::SiteConstraintResidues , core::scoring::constraints::SkipViolFunc , core::scoring::constraints::SoedingFunc , core::scoring::constraints::SOGFunc , core::scoring::constraints::SplineFunc , core::scoring::constraints::SquareWell2Func , core::scoring::constraints::SquareWellFunc , core::scoring::constraints::SumFunc , core::scoring::constraints::TopOutFunc , core::scoring::constraints::USOGFunc , core::scoring::ContextGraph , core::scoring::custom_pair_distance::RespairInteractions , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::custom_pair_distance::DistanceFunc , core::scoring::DenseEnergyContainer , core::scoring::DipolarCoupling , core::scoring::disulfides::CentroidDisulfideEnergy , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::Cb_Distance_Func , core::scoring::disulfides::Cen_Distance_Func , core::scoring::disulfides::CaCbCb_Angle_Func , core::scoring::disulfides::NCaCaC_Dihedral_Func , core::scoring::disulfides::CaCbCbCa_Dihedral_Func , core::scoring::disulfides::DisulfideMatchingEnergy , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::DisulfMinData , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::disulfides::CBSG_Dihedral_Func , core::scoring::disulfides::SGSG_Dihedral_Func , core::scoring::disulfides::CB_Angle_Func , core::scoring::disulfides::SG_Dist_Func , core::scoring::dna::BasePartner , core::scoring::dna::DNAChiEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::DockingScoreFunction , core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density::FastDensEnergy , core::scoring::electron_density::PattersonCorrEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy , core::scoring::Energies , core::scoring::CenListInfo , core::scoring::etable::CoarseEtableEnergy , core::scoring::etable::TableLookupEtableEnergy , core::scoring::etable::AnalyticEtableEnergy , core::scoring::FACTSResidueInfo , core::scoring::FACTSPoseInfo , core::scoring::FACTSRotamerSetInfo , core::scoring::GenBornResidueInfo , core::scoring::GenBornPoseInfo , core::scoring::GenBornRotamerSetInfo , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::hackaro::HackAroEnergy , core::scoring::hackelec::HackElecEnergy , core::scoring::hackelec::HackElecEnergyAroAll , core::scoring::hackelec::HackElecEnergyAroAro , core::scoring::hackelec::RNAHackElecEnergy , core::scoring::hbonds::HBondResidueMinData , core::scoring::hbonds::HBondResPairMinData , core::scoring::hbonds::HBondEnergy , core::scoring::hbonds::HBondSet , core::scoring::interface::DDPscore , core::scoring::LREnergyContainer , core::scoring::Membrane_FAEmbed , core::scoring::MembraneEmbed , core::scoring::MembraneTopology , core::scoring::methods::BurialEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::ChainbreakEnergy , core::scoring::methods::ChemicalShiftAnisotropyEnergy , core::scoring::methods::ContactOrderEnergy , core::scoring::methods::CSD_TorsionEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::DipolarCouplingEnergy , core::scoring::methods::DirectReadoutEnergy , core::scoring::methods::DistanceChainbreakEnergy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::EnvEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::HybridVDW_Energy , core::scoring::methods::LinearChainbreakEnergy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::LKB_ResidueInfo , core::scoring::methods::LKB_ResiduesInfo , core::scoring::methods::LK_CosThetaEnergy , core::scoring::methods::LK_SigmoidalFunc , core::scoring::methods::LK_hack , core::scoring::methods::MembraneCbetaEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MembraneEnvEnergy , core::scoring::methods::MembraneEnvPenalties , core::scoring::methods::MembraneEnvSmoothEnergy , core::scoring::methods::MembraneLipo , core::scoring::methods::MetalloPlacementEnergy , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::NMerPSSMEnergy , core::scoring::methods::NMerRefEnergy , core::scoring::methods::OmegaTetherEnergy , core::scoring::methods::P_AA_Energy , core::scoring::methods::P_AA_pp_Energy , core::scoring::methods::PackStatEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::PeptideBondEnergy , core::scoring::methods::pHEnergy , core::scoring::methods::PBLifetimeCache , core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::RamachandranEnergy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::ReferenceEnergy , core::scoring::methods::ReferenceEnergyNoncanonical , core::scoring::methods::ResidualDipolarCouplingEnergy , core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl , core::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments , core::scoring::methods::RG_Energy , core::scoring::methods::RG_MinData , core::scoring::methods::RG_Energy_Fast , core::scoring::methods::RMS_Energy , core::scoring::methods::SA_Energy , core::scoring::methods::SecondaryStructureEnergy , core::scoring::methods::SequenceDependentRefEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::SmoothEnvEnergy , core::scoring::methods::SuckerEnergy , core::scoring::methods::SymmetricLigandEnergy , core::scoring::methods::UnfoldedStateEnergy , core::scoring::methods::VDW_Energy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::methods::WaterAdductIntraEnergy , core::scoring::methods::YHHPlanarityEnergy , core::scoring::MinScoreScoreFunction , core::scoring::NeighborList , core::scoring::nv::NVscore , core::scoring::OneToAllEnergyContainer , core::scoring::orbitals::OrbitalsScore , core::scoring::packing::HolesEnergy , core::scoring::packing::HolesEnergyRes , core::scoring::packing::SurfEnergy , core::scoring::packing::SurfVolEnergy , core::scoring::PeptideBondedEnergyContainer , core::scoring::ResidualDipolarCoupling , core::scoring::ResidualDipolarCoupling_Rohl , core::scoring::ResidueNblistData , core::scoring::ResiduePairNeighborList , core::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergy , core::scoring::rna::RG_Energy_RNA , core::scoring::rna::RNA_BaseBaseEnergy , core::scoring::rna::RNA_BulgeEnergy , core::scoring::rna::RNA_CentroidInfo , core::scoring::rna::RNA_DataBackboneEnergy , core::scoring::rna::RNA_DataInfo , core::scoring::rna::RNA_FA_Stack , core::scoring::rna::RNA_FilteredBaseBaseInfo , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_FullAtomVDW_BasePhosphate , core::scoring::rna::RNA_LJ_BaseEnergy , core::scoring::rna::RNA_Mg_Energy , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::RNA_RawBaseBaseInfo , core::scoring::rna::RNA_ScoringInfo , core::scoring::rna::RNA_SugarCloseEnergy , core::scoring::rna::RNA_TorsionEnergy , core::scoring::rna::RNA_VDW_Energy , core::scoring::saxs::FastSAXSEnergy , core::scoring::saxs::SAXSEnergy , core::scoring::ScoreFunction , core::scoring::SigmoidWeightedCenList< T > , core::scoring::solid_surface::SurfaceEnergies , core::scoring::SS_Info , core::scoring::SS_Killhairpins_Info , core::scoring::sym_e::symEnergy , core::scoring::symmetry::NBListCache , core::scoring::symmetry::SymmetricEnergies , core::scoring::symmetry::SymmetricScoreFunction , core::scoring::TenANeighborGraph , core::scoring::trie::TrieCollection , core::scoring::TwelveANeighborGraph , core::sequence::CacheableSequenceProfile , core::sequence::ChemicalShiftScoringScheme , core::sequence::ChemicalShiftSequence , core::sequence::CompassScoringScheme , core::sequence::CompositeScoringScheme , core::sequence::CompositeSequence , core::sequence::DPScoringScheme , core::sequence::L1ScoringScheme , core::sequence::MatrixScoringScheme , core::sequence::PairScoringScheme , core::sequence::ProfSimScoringScheme , core::sequence::ScoringScheme , core::sequence::Sequence , core::sequence::SequenceAlignment , core::sequence::SequenceProfile , core::sequence::SimpleScoringScheme , protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::DomainAssembly , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::JumpingFoldConstraints , protocols::abinitio::KinematicAbinitio , protocols::abinitio::JumpingFoldConstraintsWrapper , protocols::abinitio::MembraneAbinitio , protocols::analysis::InterfaceAnalyzerMover , protocols::anchored_design::AnchoredDesignMover , protocols::anchored_design::AnchorMoversData , protocols::antibody::AntibodyModeler , protocols::ub_e2c::ubi_e2c_modeler , protocols::antibody2::AntibodyModelerProtocol , protocols::antibody2::GraftCDRLoopsProtocol , protocols::antibody2::H3PerturbCCD , protocols::antibody2::H3RefineCCD , protocols::antibody2::LHRepulsiveRamp , protocols::antibody2::LHRepulsiveRampLegacy , protocols::antibody2::LHSnugFitLegacy , protocols::antibody2::RefineOneCDRLoop , protocols::antibody2::SnugDock , protocols::antibody2::SnugDockProtocol , protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::PDBTrajectoryRecorder , protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::FixedTemperatureController , protocols::canonical_sampling::TrialCounterObserver , protocols::cluster::EnsembleConstraints_Simple , protocols::cluster::ClusterPhilStyle , protocols::cluster::ClusterPhilStyle_Loop , protocols::cluster::AssignToClustersMover , protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::comparative_modeling::features::ResidueFeature , protocols::comparative_modeling::features::SSFeature , protocols::comparative_modeling::features::TorsionFeature , protocols::comparative_modeling::IgnoreSubsetConstraintSet , protocols::comparative_modeling::LoopRelaxMover , protocols::constraints_additional::AmbiguousMultiConstraint , protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::MaxSeqSepConstraintSet , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::contact_map::ContactMap , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::dna::DesignProteinBackboneAroundDNA , protocols::dna::DnaChains , protocols::dna::DnaInterfaceFinder , protocols::dna::DnaInterfaceMinMover , protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::DnaInterfacePacker , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::SeparateDnaFromNonDna , protocols::dna::WatsonCrickRotamerCouplings , protocols::docking::DockingLowResFilter , protocols::docking::DockingHighResFilter , protocols::docking::DockingHighResLegacy , protocols::docking::DockingInitialPerturbation , protocols::docking::DockingLowRes , protocols::docking::DockingLowResEnsemble , protocols::docking::DockingProtocol , protocols::docking::DockMCMCycle , protocols::docking::DockMCMProtocol , protocols::docking::DockSetupMover , protocols::docking::TemperedDocking , protocols::electron_density::SetupForDensityScoringMover , protocols::enzdes::AddOrRemoveMatchCsts , protocols::enzdes::BackboneSampler , protocols::enzdes::PredesignPerturbMover , protocols::enzdes::SetCatalyticResPackBehavior , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::enzdes::AddRigidBodyLigandConfs , protocols::enzdes::AddLigandMotifRotamers , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::EnzScoreFilter , protocols::enzdes::DiffAtomSasaFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::features::ReportToDB , protocols::filters::TrueFilter , protocols::filters::FalseFilter , protocols::filters::StochasticFilter , protocols::filters::CompoundFilter , protocols::filters::CombinedFilter , protocols::filters::MoveBeforeFilter , protocols::filters::IfThenFilter , protocols::filters::CalculatorFilter , protocols::filters::ContingentFilter , protocols::filters::Filter , protocols::filters::HeavyAtomFilter , protocols::filters::ReplicateFilter , protocols::filters::TimeFilter , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::NcontactsCalculator , protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::fldsgn::SheetConstraintsRCG , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::HelixPairingSet , protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::SS_Info2 , protocols::fldsgn::topology::StrandPairing , protocols::fldsgn::topology::StrandPairingSet , protocols::flexpep_docking::FlexPepDockingFlags , protocols::flexpep_docking::FlexPepDockingProtocol , protocols::flxbb::FilterStructs , protocols::flxbb::FilterStructs_Packstat , protocols::flxbb::FilterStructs_TotalCharge , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::flxbb::LayerDesignOperation , protocols::flxbb::CombinedTaskOperation , protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::RelativeConnectRight , protocols::forge::build::RelativeSequencePosition , protocols::forge::build::CountFromLeft , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::constraints::InverseRotamersRCG , protocols::forge::constraints::InvrotTreeRCG , protocols::forge::constraints::NtoC_RCG , protocols::forge::constraints::RemoveCsts , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::forge::remodel::RemodelRotamerLinks , protocols::forge::remodel::ResidueVicinityRCG , protocols::frag_picker::nonlocal::NonlocalFrags , protocols::frag_picker::scores::FragmentScoreMap , protocols::genetic_algorithm::EntityElement , protocols::genetic_algorithm::Entity , protocols::hotspot_hashing::movers::PlaceSurfaceProbe , protocols::hotspot_hashing::SearchPatternRotSetOp , protocols::hotspot_hashing::AddSearchPatternRotSetOp , protocols::hybridization::CartesianSampler , protocols::hybridization::HybridizeProtocol , protocols::hybridization::TemplateHistory , protocols::idealize::IdealizeMover , core::scoring::constraints::ChainbreakDistFunc , protocols::ligand_docking::AddHydrogens , protocols::ligand_docking::AtomCountFilter , protocols::ligand_docking::ChainExistsFilter , protocols::ligand_docking::CompleteConnectionsFilter , protocols::ligand_docking::CompoundTranslate , protocols::ligand_docking::FinalMinimizer , protocols::ligand_docking::GrowLigand , protocols::ligand_docking::HBondAcceptorFilter , protocols::ligand_docking::HBondDonorFilter , protocols::ligand_docking::HeavyAtomFilter , protocols::ligand_docking::HighResDocker , protocols::ligand_docking::InterfaceScoreCalculator , protocols::ligand_docking::LigandDesign , protocols::ligand_docking::MinimizeBackbone , protocols::ligand_docking::MolarMassFilter , 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::ligand_docking::Transform , protocols::ligand_docking::Translate , protocols::loop_build::LoopMover_SlidingWindow , protocols::loophash::FastGapMover , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashLibrary , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashRelaxProtocol , protocols::loophash::Mover_LoopHashRefine , protocols::loophash::WorkUnit_LoopHash , protocols::loops::FoldTreeFromLoops , protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD , protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves , protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::loops::loop_mover::refine::RepackTrial , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::LoopRebuild , protocols::loops::loops_definers::LoopsDatabaseDefiner , protocols::loops::loops_definers::LoopsDefiner , protocols::loops::loops_definers::LoopsExplicitDefiner , protocols::loops::loops_definers::LoopsFileDefiner , protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue , protocols::match::MatcherMover , protocols::match::output::WriteUpstreamCoordinateKinemage , protocols::match::upstream::ProteinUpstreamBuilder , protocols::match::upstream::UpstreamBuilder , protocols::medal::MedalExchangeMover , protocols::medal::MedalMover , protocols::motifs::BuildPosition , protocols::motifs::Motif , protocols::motifs::MotifDnaPacker , protocols::motifs::MotifHit , protocols::moves::CyclicMover , protocols::moves::DsspMover , protocols::moves::IfMover , protocols::moves::IteratedConvergenceMover , protocols::moves::Mover , protocols::moves::SequenceMover , protocols::moves::RandomMover , protocols::moves::CycleMover , protocols::moves::NullMover , protocols::moves::RampingMover , protocols::moves::StructureRestrictor , protocols::moves::MonteCarloUtil , protocols::multistate_design::MultiStateEntity< T > , protocols::multistate_design::PosType , protocols::noesy_assign::Resonance , protocols::nonlocal::HelixRotate , protocols::nonlocal::SheetTranslate , protocols::nonlocal::SingleFragmentMover , protocols::optimize_weights::ScaleAnnealerTemperatureOperation , protocols::pb_potential::SetupPoissonBoltzmannPotential , protocols::pockets::PocketConstraint , protocols::protein_interface_design::filters::AtomicContactCountFilter , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::InterfaceHolesFilter , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::filters::StubScoreLoopsFilter , protocols::protein_interface_design::filters::Torsion , protocols::protein_interface_design::movers::AddChainBreak , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots , protocols::protein_interface_design::movers::BackrubDDMover , protocols::protein_interface_design::movers::BestHotspotCstMover , protocols::protein_interface_design::movers::BuildAlaPose , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::protein_interface_design::movers::DisulfideMover , protocols::protein_interface_design::movers::DockAndRetrieveSidechains , protocols::protein_interface_design::movers::FavorNativeResiduePreCycle , protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycle , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::protein_interface_design::movers::HotspotHasherMover , protocols::protein_interface_design::movers::InterfaceRecapitulationMover , protocols::protein_interface_design::movers::LoopFinder , protocols::protein_interface_design::movers::LoopLengthChange , protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopOver , protocols::protein_interface_design::movers::LoopRemodel , protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::NullDesignMover , protocols::protein_interface_design::movers::PeptideStapleDesignMover , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlacementMinimizationMover , protocols::protein_interface_design::movers::PlaceOnLoop , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover , protocols::protein_interface_design::movers::PrepackMover , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::protein_interface_design::movers::RandomMutation , protocols::protein_interface_design::movers::RepackMinimize , protocols::protein_interface_design::movers::SaveAndRetrieveSidechains , protocols::protein_interface_design::movers::SetAtomTree , protocols::protein_interface_design::movers::SetTemperatureFactor , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover , protocols::protein_interface_design::movers::ShoveResidueMover , protocols::protein_interface_design::movers::SpinMover , protocols::protein_interface_design::movers::Splice , protocols::protein_interface_design::movers::SubroutineMover , protocols::protein_interface_design::movers::TaskAwareCsts , protocols::protein_interface_design::movers::TryRotamers , protocols::protein_interface_design::movers::VLB , protocols::qsar::RenderGridsToKinemage , protocols::qsar::scoring_grid::GridInitMover , protocols::rbsegment_relax::FragInsertAndAlignMover , protocols::rbsegment_relax::HelicalGaussianMover , protocols::rbsegment_relax::SequenceShiftMover , protocols::rbsegment_relax::GaussianRBSegmentMover , protocols::rbsegment_relax::StrandTwistingMover , protocols::relax::CentroidRelax , protocols::relax::ClassicRelax , protocols::relax::FastRelax , protocols::relax::MiniRelax , protocols::relax::WorkUnit_BatchRelax , protocols::relax::WorkUnit_BatchRelax_and_PostRescore , protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::rigid::RollMover , protocols::rna::MultipleDomainMover , protocols::rna::RNA_DeNovoProtocol , protocols::rna::RNA_HelixAssembler , protocols::rna::RNA_LoopCloser , protocols::rna::RNA_Minimizer , protocols::rna::RNA_SecStructInfo , protocols::rosetta_scripts::ParsedProtocol , protocols::rosetta_scripts::SavePoseMover , protocols::rotamer_recovery::RotamerRecoveryMover , protocols::scoring::InterfaceInfo , protocols::scoring::methods::EnsembleEnergy , protocols::scoring::methods::InterchainEnvEnergy , protocols::scoring::methods::InterchainPairEnergy , protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcs::PCS_Energy , protocols::scoring::methods::pcs2::PcsDataCenterManager , protocols::scoring::methods::pcs2::PcsEnergy , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments , protocols::scoring::methods::saxs::PDDFEnergy , protocols::scoring::methods::SpecialRotamerEnergy , protocols::scoring::ResidualDipolarCouplingRigidSegments , protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::CoordinateCst , protocols::seeded_abinitio::DefineMovableLoops , protocols::seeded_abinitio::GrowPeptides , protocols::seeded_abinitio::PlaceFragments , protocols::seeded_abinitio::SeedFoldTree , protocols::seeded_abinitio::SeedSetupMover , protocols::seeded_abinitio::SegmentHybridizer , protocols::seeded_abinitio::SwapSegment , protocols::simple_filters::AbinitioBaseFilter , protocols::simple_filters::AlaScan , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::COFilter , protocols::simple_filters::ConservedPosMutationFilter , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::DdgFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ExpiryFilter , protocols::simple_filters::FileExistFilter , protocols::simple_filters::FileRemoveFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterfaceBindingEnergyDensityFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::NeighborTypeFilter , protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::Operator , protocols::simple_filters::PackerNeighborGraphFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::PDDFScoreFilter , protocols::simple_filters::PoseInfoFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::ReportFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::ResidueCountFilter , protocols::simple_filters::ResidueDistanceFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_filters::ResiduesInInterfaceFilter , protocols::simple_filters::RGFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::SAXSScoreFilter , protocols::simple_filters::ScoreCutoffFilter , protocols::simple_filters::ScoreTypeFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SheetFilter , protocols::simple_filters::SidechainRmsdFilter , protocols::simple_filters::Sigmoid , protocols::simple_filters::SymmetricMotifFilter , protocols::simple_filters::TerminusDistanceFilter , protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::simple_moves::SmallMover , protocols::simple_moves::ShearMover , protocols::simple_moves::carbohydrates::RingConformationMover , protocols::simple_moves::ClearConstraintsMover , protocols::simple_moves::ConsensusDesignMover , protocols::simple_moves::ConstrainToIdealMover , protocols::simple_moves::ConstraintSetMover , protocols::simple_moves::CutChainMover , protocols::simple_moves::ddG , protocols::simple_moves::DesignRepackMover , protocols::simple_moves::DumpPdb , protocols::simple_moves::ExtendedPoseMover , protocols::simple_moves::FavorSequenceProfile , protocols::simple_moves::ForceDisulfidesMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::GroupDiscriminator , protocols::simple_moves::UserDefinedGroupDiscriminator , protocols::simple_moves::ChainGroupDiscriminator , protocols::simple_moves::HelicalPeptideLengthMover , protocols::simple_moves::LoadPDBMover , protocols::simple_moves::LoadUnboundRotMover , protocols::simple_moves::MakePolyXMover , protocols::simple_moves::MembraneTopology , protocols::simple_moves::MinMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::ModifyVariantTypeMover , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloTest , protocols::simple_moves::MutateResidue , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::PDBReloadMover , protocols::simple_moves::PeptideStapleMover , protocols::simple_moves::RepackSidechainsMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::SaneMinMover , protocols::simple_moves::ScoreMover , protocols::simple_moves::SequenceProfileMover , protocols::simple_moves::SetTorsion , protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover , protocols::simple_moves::sidechain_moves::SetChiMover , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::SuperimposeMover , protocols::simple_moves::SwitchChainOrderMover , protocols::simple_moves::SwitchResidueTypeSetMover , protocols::simple_moves::symmetry::DetectSymmetry , protocols::simple_moves::symmetry::SetupForSymmetryMover , protocols::simple_moves::symmetry::ExtractAsymmetricUnitMover , protocols::simple_moves::symmetry::ExtractAsymmetricPoseMover , protocols::simple_moves::symmetry::SetupNCSMover , protocols::simple_moves::symmetry::SymMinMover , protocols::simple_moves::symmetry::SymPackRotamersMover , protocols::simple_moves::TaskAwareMinMover , protocols::star::StarAbinitio , protocols::surface_docking::SurfaceParameters , protocols::swa::monte_carlo::SubToFullInfo , protocols::swa::rna::RNA_AnalyticLoopCloser , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::symmetric_docking::SymDockProtocol , protocols::symmetric_docking::SymRestrictTaskForDocking , protocols::toolbox::AllowInsert , protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver , protocols::toolbox::match_enzdes_util::InvrotCollector , protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::CatPiCalculator , protocols::toolbox::pose_metric_calculators::ChargeCalculator , protocols::toolbox::pose_metric_calculators::ClashCountCalculator , protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator , protocols::toolbox::pose_metric_calculators::ExplicitWaterUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::toolbox::pose_metric_calculators::HPatchCalculator , protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator , protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator , protocols::toolbox::pose_metric_calculators::PackstatCalculator , protocols::toolbox::pose_metric_calculators::PiPiCalculator , protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator , protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator , protocols::toolbox::pose_metric_calculators::SaltBridgeCalculator , protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::SurfaceCalculator , protocols::toolbox::DummyClass , protocols::toolbox::SF_Replica
• clone_cache_data() : core::fragment::Frame
• clone_calculators() : core::pose::metrics::PoseMetricContainer
• clone_scorefxn() : protocols::rna::RNA_Minimizer
• clone_with_frags() : core::fragment::Frame
• clone_with_new_sequence_numbering() : core::conformation::PseudoBondCollection
• clone_with_template() : core::fragment::Frame
• close() : protocols::dna::DnaNeighbor , protocols::jd2::SingleFileBuffer
• close_all_loops() : protocols::rna::MultipleDomainMover
• close_at_all_cutpoints() : protocols::coarse_rna::CoarseRNA_LoopCloser
• close_at_cutpoint() : protocols::swa::rna::RNA_AnalyticLoopCloser
• close_channel() : protocols::jd2::MpiFileBuffer
• close_file() : protocols::jd2::MpiFileBuffer
• close_gaps() : protocols::loophash::LoopHashSampler
• close_loops() : protocols::abinitio::AbrelaxApplication
• close_loops_carefully() : protocols::rna::RNA_LoopCloser
• close_one_loop_stem() : protocols::antibody::CloseOneMover
• close_the_loop() : protocols::coarse_rna::CoarseRNA_LoopCloser
• close_with_idealization() : protocols::abinitio::AbrelaxMover
• CloseFold() : protocols::seeded_abinitio::CloseFold
• CloseOneCDRLoop() : protocols::antibody2::CloseOneCDRLoop
• CloseOneMover() : protocols::antibody::CloseOneMover
• closest_interface_residue() : protocols::scoring::Interface , protocols::scoring::InterfaceInfo
• closest_orient_atoms_msd() : protocols::enzdes::ModifyStoredRBConfs
• closest_state_on_alt_bb() : protocols::flexpack::interaction_graph::FlexbbNode
• closure() : protocols::simple_moves::BBConRotMover
• closure_fragments() : protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• closure_protocol() : protocols::abinitio::AbrelaxMover , protocols::abinitio::KinematicAbinitio
• CloudPDBWriter() : protocols::match::output::CloudPDBWriter
• cluster() : protocols::abinitio::IterativeBase , protocols::cluster::APCluster , protocols::comparative_modeling::AlignmentClustering , protocols::hotspot_hashing::HotspotStubSet , protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::StepWiseClusterer , protocols::toolbox::ClusterBase , protocols::toolbox::KCluster
• Cluster() : protocols::cluster::Cluster
• cluster_loop() : protocols::forge::remodel::RemodelAccumulator
• Cluster_Member() : protocols::swa::rna::Cluster_Member
• cluster_pose() : protocols::forge::remodel::RemodelAccumulator
• cluster_pose_data_list() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler
• cluster_switch() : protocols::forge::remodel::RemodelAccumulator
• cluster_with_auto_tune() : protocols::swa::StepWiseClusterer
• ClusterBase() : protocols::cluster::ClusterBase , protocols::toolbox::ClusterBase
• clustered_best_poses() : protocols::forge::remodel::RemodelAccumulator
• clustered_pose_list() : protocols::swa::StepWiseClusterer
• clustered_top_poses() : protocols::forge::remodel::RemodelAccumulator
• clusterlist() : protocols::toolbox::ClusterBase
• ClusterOptions() : protocols::toolbox::ClusterOptions
• ClusterPhilStyle() : protocols::cluster::ClusterPhilStyle , protocols::toolbox::ClusterPhilStyle
• ClusterPhilStyle_Loop() : protocols::cluster::ClusterPhilStyle_Loop
• clusterPockets() : protocols::pockets::PocketGrid
• CM_SuggestFixResidue() : protocols::topology_broker::RigidChunkClaimer::CM_SuggestFixResidue
• cmd_accept_to_best() : protocols::relax::FastRelax
• cmd_line_csts() : protocols::comparative_modeling::LoopRelaxMover
• cmdline_options_activated() : protocols::noesy_assign::NoesyModule
• CmdLineData() : protocols::topology_broker::CmdLineData
• cmp() : core::scoring::packstat::Event
• coarse_nchi() : core::coarse::Translator
• CoarseEtable() : core::coarse::CoarseEtable
• CoarseEtableEnergy() : core::scoring::etable::CoarseEtableEnergy
• CoarseRNA_DeNovoProtocol() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• CoarseRNA_Fragments() : protocols::coarse_rna::CoarseRNA_Fragments
• CoarseRNA_LoopCloser() : protocols::coarse_rna::CoarseRNA_LoopCloser
• CoarseRotamer() : core::pack::dunbrack::CoarseRotamer
• CoarseRotamerSet() : core::pack::dunbrack::CoarseRotamerSet
• CoarseSingleResidueLibrary() : core::pack::dunbrack::CoarseSingleResidueLibrary
• coarsify() : core::coarse::Translator , core::coarse::TranslatorSet , core::pack::dunbrack::CoarseSingleResidueLibrary
• COFilter() : protocols::simple_filters::COFilter
• collect() : protocols::abinitio::HedgeArchive
• collect_all_inverse_rotamers() : protocols::toolbox::match_enzdes_util::InvrotTarget , protocols::toolbox::match_enzdes_util::InvrotTree , protocols::toolbox::match_enzdes_util::InvrotTreeNode , protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase
• collect_alternative_decoys() : protocols::abinitio::IterativeBase
• collect_ddG_of_binding_data() : protocols::optimize_weights::IterativeOptEDriver
• collect_ddG_of_mutation_data() : protocols::optimize_weights::IterativeOptEDriver
• collect_decoy_discrimination_data() : protocols::optimize_weights::IterativeOptEDriver
• collect_dG_of_binding_data() : protocols::optimize_weights::IterativeOptEDriver
• collect_hedge_structures() : protocols::abinitio::IterativeBase
• collect_hedgeing_decoys_from_batches() : protocols::abinitio::IterativeBase
• collect_HN_S2_and_EF() : protocols::sparta::PDB
• collect_ligand_discrimination_data() : protocols::optimize_weights::IterativeOptEDriver
• collect_rotamer_energies() : protocols::optimize_weights::IterativeOptEDriver
• collect_rotamer_energies_from_slave_cpu() : protocols::optimize_weights::IterativeOptEDriver
• collect_rotamer_energies_from_slave_cpus() : protocols::optimize_weights::IterativeOptEDriver
• collect_rotamer_recovery_data_from_slave_cpu() : protocols::optimize_weights::IterativeOptEDriver
• collect_rotamer_recovery_data_from_slave_cpus() : protocols::optimize_weights::IterativeOptEDriver
• collect_sequence_recovery_data_from_slave_cpu() : protocols::optimize_weights::IterativeOptEDriver
• collect_sequence_recovery_data_from_slave_cpus() : protocols::optimize_weights::IterativeOptEDriver
• collect_target_statistics() : protocols::noesy_assign::PeakCalibrator
• collect_upperbound_statistics() : protocols::noesy_assign::PeakCalibrator , protocols::noesy_assign::StructureDependentPeakCalibrator , protocols::noesy_assign::StructureIndependentPeakCalibrator
• collectInsertionPose() : protocols::forge::remodel::RemodelData
• collision_check_id_2_restype_id() : protocols::toolbox::match_enzdes_util::LigandConformer
• colonyE() : protocols::hotspot_hashing::HotspotStubSet
• ColorGradient() : protocols::qsar::ColorGradient
• cols() : core::sequence::DP_Matrix
• CoM() : protocols::pockets::FingerprintBase
• com() : protocols::features::helixAssembly::HelicalFragment
• combine() : protocols::noesy_assign::Resonance
• combine_movemaps() : protocols::grafting::GraftMoverBase
• combine_ratio() : protocols::topology_broker::ConstraintClaimer
• Combine_Tags_Info() : protocols::swa::rna::Combine_Tags_Info
• combine_xyz_lists() : protocols::pockets::NonPlaidFingerprint
• CombineChainsMover() : protocols::domain_assembly::CombineChainsMover
• CombinedConstraintEvaluator() : protocols::constraints_additional::CombinedConstraintEvaluator
• CombinedConstraintEvaluatorCreator() : protocols::constraints_additional::CombinedConstraintEvaluatorCreator
• CombinedFilter() : protocols::filters::CombinedFilter
• CombinedTaskOperation() : protocols::flxbb::CombinedTaskOperation
• command_string() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• commands_for_residue() : core::pack::task::ResfileContents
• comment() : core::sequence::SequenceAlignment
• comment_from_line() : core::io::silent::SilentStruct
• comment_line() : core::io::silent::SilentFileData
• comment_lines() : core::io::silent::SilentFileData
• comments() : core::sequence::SequenceAlignment
• commit_alt_bb_substitution() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• commit_change() : core::pack::interaction_graph::SimpleEdge , core::pack::interaction_graph::SimpleNode , core::pack::interaction_graph::SimpleInteractionGraph
• commit_change_no_res_pointer_update() : core::pack::interaction_graph::SimpleNode
• commit_considered_backbone_move() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• commit_considered_substitution() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistNode , core::pack::interaction_graph::SymmMinimalistInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbNode , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• commit_considered_substitution_surface() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• commit_relaxation() : core::pack::interaction_graph::FASTERInteractionGraph
• compact_bbindex() : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• compare() : protocols::loophash::BackboneSegment
• compare_input_pose_geometry_to_reference() : protocols::simple_moves::GreenPacker
• compare_RNA_char() : protocols::rna::RNA_Fragments
• compare_RNA_secstruct() : protocols::rna::RNA_Fragments
• compare_SizeRealPairs() : protocols::enzdes::EnzdesFlexibleRegion
• compare_to_native() : protocols::enzdes::DesignVsNativeComparison
• CompareByScoreCombination() : protocols::frag_picker::CompareByScoreCombination
• CompareScoreComponent() : protocols::frag_picker::CompareScoreComponent
• CompareTags() : protocols::jd2::CompareTags
• CompareTotalScore() : protocols::frag_picker::CompareTotalScore
• CompassScoringScheme() : core::sequence::CompassScoringScheme
• compatibility_check() : protocols::forge::build::BuildManager
• compatible() : protocols::match::upstream::ScaffoldBuildPoint , protocols::match::downstream::DownstreamBuilder , protocols::abinitio::PairingStatEntry , protocols::abinitio::AlternativePairings , protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::match::upstream::OriginalBackboneBuildPoint , protocols::match::upstream::ProteinUpstreamBuilder , protocols::match::upstream::ScaffoldBuildPoint , protocols::match::upstream::UpstreamBuilder
• compatible_with() : protocols::forge::build::BuildInstruction
• compatible_with_current_format() : protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::PeakFileFormat_Base
• complete() : protocols::genetic_algorithm::GeneticAlgorithm
• complete_deltaE_prediction_for_bbmove() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• complete_partial_state_assignment() : core::pack::interaction_graph::FASTERNode , protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• complete_state_assignment() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , core::pack::interaction_graph::LinearMemNode
• CompleteConnectionsFilter() : protocols::ligand_docking::CompleteConnectionsFilter
• completed() : protocols::jd2::Job
• CompletionMessage() : protocols::jd2::archive::MPIArchiveJobDistributor::CompletionMessage
• component() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• components_moved_by_jump() : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• compose_atoms() : core::chemical::sdf::MolWriter
• compose_bonds() : core::chemical::sdf::MolWriter
• compose_ctab() : core::chemical::sdf::MolWriter
• compose_metadata() : core::chemical::sdf::MolWriter
• compose_nbr_atom() : core::chemical::sdf::MolWriter
• compose_typeinfo() : core::chemical::sdf::MolWriter
• ComposeSearchPatterns() : protocols::hotspot_hashing::ComposeSearchPatterns
• CompositeFragmentSelector() : protocols::frag_picker::CompositeFragmentSelector
• CompositeScoringScheme() : core::sequence::CompositeScoringScheme
• CompositeSequence() : core::sequence::CompositeSequence
• CompositeSequenceCreator() : core::sequence::CompositeSequenceCreator
• CompositionMover() : protocols::moves::CompositionMover
• compound_in_progress() : core::io::pdb::HeaderInformation
• compound_token_to_string() : core::io::pdb::HeaderInformation
• CompoundFilter() : protocols::filters::CompoundFilter
• compounds() : core::io::pdb::HeaderInformation
• CompoundTranslate() : protocols::ligand_docking::CompoundTranslate
• compprob() : core::scoring::packstat::PackingScore
• compute() : core::scoring::dna::TorsionFourierComponent , core::scoring::dssp::Dssp , core::scoring::dssp::StrandPairingSet , core::scoring::packstat::LeeRichards , protocols::abinitio::PairingStatistics , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::EnzScoreFilter , protocols::enzdes::DiffAtomSasaFilter , protocols::filters::CompoundFilter , protocols::filters::CombinedFilter , protocols::filters::IfThenFilter , protocols::filters::ReplicateFilter , protocols::filters::TimeFilter , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::MatchResidues , protocols::protein_interface_design::filters::AtomicContactCountFilter , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::InterfaceHolesFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::filters::Torsion , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::DdgFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::FileExistFilter , protocols::simple_filters::FileRemoveFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::NeighborTypeFilter , protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::Operator , protocols::simple_filters::PackStatFilter , protocols::simple_filters::PoseInfoFilter , protocols::simple_filters::ReportFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::ResidueCountFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_filters::ResiduesInInterfaceFilter , protocols::simple_filters::ScoreTypeFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SidechainRmsdFilter , protocols::simple_filters::Sigmoid , protocols::simple_filters::SymmetricMotifFilter , protocols::simple_filters::TerminusDistanceFilter , protocols::toolbox::ClusterPhilStyle , protocols::toolbox::task_operations::LayerOperations , protocols::fldsgn::filters::FragQualFilter , protocols::toolbox::SelectResiduesByLayer , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::ResidueDistanceFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::InterfaceBindingEnergyDensityFilter , protocols::simple_filters::ExpiryFilter , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::jumping::SameStrand , protocols::filters::CalculatorFilter , protocols::enzdes::RepackWithoutLigandFilter , core::scoring::packstat::Slice
• compute_absent_energies() : protocols::simple_moves::GreenPacker
• compute_absent_lrci_energies_for_residue_pair() : protocols::simple_moves::GreenPacker
• compute_absent_srci_energies_for_residue_pair() : protocols::simple_moves::GreenPacker
• compute_aggregate_score() : protocols::pack_daemon::MultistateFitnessFunction
• compute_altbbconf_alternate_state_energy() : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• compute_anchor_transform() : protocols::features::LoopAnchorFeatures
• compute_atom_angles() : protocols::features::LoopAnchorFeatures
• compute_average_distances() : protocols::noesy_assign::FragsToAtomDist
• compute_average_structure() : protocols::toolbox::DecoySetEvaluation
• compute_beta_topology() : protocols::abinitio::IterativeBase
• compute_bias() : protocols::rigid::RigidBodyMotionMover
• compute_Boltzmann_weight() : protocols::simple_filters::RotamerBoltzmannWeight
• compute_cb_frame() : protocols::match::upstream::ProteinUpstreamBuilder
• compute_centroid_environment() : core::scoring::EnvPairPotential , core::scoring::SmoothEnvPairPotential
• compute_chi() : core::scoring::saxs::SAXSEnergy , protocols::scoring::methods::saxs::PDDFEnergy
• compute_chi_with_fit() : core::scoring::saxs::SAXSEnergy
• compute_comb() : protocols::fldsgn::MatchResidues
• compute_cores() : protocols::abinitio::IterativeBase
• compute_csascore() : core::scoring::ChemicalShiftAnisotropy
• compute_d2() : protocols::simple_filters::SymmetricMotifFilter
• compute_dcentroid_environment() : core::scoring::SmoothEnvPairPotential
• compute_dcscore() : core::scoring::DipolarCoupling
• compute_derivatives() : core::scoring::packstat::Slice
• compute_designable_neighbors() : protocols::enzdes::PackRotamersMoverPartGreedy
• compute_dipscore() : core::scoring::ResidualDipolarCoupling
• compute_dipscore_nls() : core::scoring::ResidualDipolarCoupling
• compute_dipscore_nlsDa() : core::scoring::ResidualDipolarCoupling
• compute_dipscore_nlsDaR() : core::scoring::ResidualDipolarCoupling
• compute_dipscore_nlsR() : core::scoring::ResidualDipolarCoupling
• compute_dist_map() : core::kinematics::ShortestPathInFoldTree
• compute_distance_histogram() : core::scoring::saxs::SAXSEnergy
• compute_distance_matrix() : protocols::toolbox::DecoySetEvaluation
• compute_energies() : core::pack::rotamer_set::symmetry::SymmetricRotamerSets , protocols::features::StructureScoresFeatures , protocols::simple_moves::GreenPacker , core::pack::rotamer_set::RotamerSets
• compute_energy() : core::pack::interaction_graph::SimpleEdge
• compute_energy_for_assignment() : protocols::pack_daemon::PackDaemon , protocols::pack_daemon::DaemonSet
• compute_entropy_reduction() : protocols::simple_filters::RotamerBoltzmannWeight
• compute_events() : core::scoring::packstat::Slice
• compute_fa_projection() : core::scoring::Membrane_FAPotential
• compute_fractions() : core::fragment::SecondaryStructure
• compute_fragment_bias() : protocols::hybridization::CartesianSampler
• compute_func() : core::scoring::constraints::SoedingFunc
• compute_grid_constant() : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• compute_gunn() : protocols::frag_picker::scores::GunnCost , protocols::simple_moves::GunnCost
• compute_Hbonds_for_residue() : protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator
• compute_insert_pos() : protocols::abinitio::AllResiduesChanged , protocols::hybridization::AllResiduesChanged , protocols::abinitio::AllResiduesChanged
• compute_intensities() : core::scoring::saxs::SAXSEnergy
• compute_interface() : protocols::scoring::InterchainPotential
• compute_interface_delta_hbond_unsat() : protocols::analysis::InterfaceAnalyzerMover
• compute_interface_energy() : protocols::analysis::InterfaceAnalyzerMover
• compute_interface_packstat() : protocols::analysis::InterfaceAnalyzerMover
• compute_interface_sc() : protocols::analysis::InterfaceAnalyzerMover
• compute_jumpout_diff() : core::scoring::geometric_solvation::DatabaseOccSolEne
• compute_L1() : core::scoring::saxs::SAXSEnergy , protocols::scoring::methods::saxs::PDDFEnergy
• compute_ligand_natoms() : protocols::pockets::PlaidFingerprint
• compute_ligand_resnum() : protocols::pockets::PlaidFingerprint
• compute_matching_energy() : core::scoring::disulfides::DisulfideMatchingPotential
• compute_max_branch_depth() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• compute_membrane_embedding() : core::scoring::MembranePotential
• compute_metrics_for_residue_subset() : protocols::enzdes::EnzdesScorefileFilter
• compute_model_weights() : protocols::abinitio::PairingStatistics
• compute_modified_ddG() : protocols::simple_filters::RotamerBoltzmannWeight
• compute_Nk() : protocols::noesy_assign::PeakAssignmentResidueMap
• compute_normalization() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• compute_number_cavities() : protocols::vip::VIP_Mover
• compute_one_body_energies() : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubset , core::pack::rotamer_set::symmetry::SymmetricRotamerSets , core::pack::rotamer_set::symmetry::SymmetricRotamerSet_ , core::pack::rotamer_set::RotamerSet
• compute_one_body_energies_for_otf_ig() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• compute_one_body_energy_maps() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSubset , core::pack::rotamer_set::RotamerSet_
• compute_onebody_interactions_with_background() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• compute_pair_energy_for_alternate_state() : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• compute_pair_energy_for_current_state() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , core::pack::interaction_graph::LinearMemNode
• compute_pairwise_score() : protocols::scoring::ResidualDipolarCouplingRigidSegments
• compute_pddf() : protocols::scoring::methods::saxs::PDDFEnergy
• compute_pddf_without_ff() : protocols::scoring::methods::saxs::PDDFEnergy
• compute_per_residue_probabilities() : protocols::medal::MedalMover
• compute_polar_group_sol_energy() : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• compute_pose_hpatch_score() : core::pack::interaction_graph::SurfacePotential
• compute_pose_surface_energy() : core::pack::interaction_graph::SurfacePotential
• compute_proline_correction_energies_for_otf_graph() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::symmetry::SymmetricRotamerSets
• compute_proposal_density() : protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover
• compute_reference_intragroup_rpes() : protocols::simple_moves::GreenPacker
• compute_residue() : protocols::simple_filters::NMerPSSMEnergyFilter
• compute_residue_surface_energy() : core::pack::interaction_graph::SurfacePotential
• compute_rmsd() : protocols::comparative_modeling::LoopRelaxMover
• compute_rotamer_energies_for_assigned_pdbs() : protocols::optimize_weights::IterativeOptEDriver
• compute_rotamer_pair_energy() : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SymmOnTheFlyNode
• compute_rotamers_around_ligands() : protocols::optimize_weights::IterativeOptEDriver
• compute_rotdensities() : protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover
• compute_samebbconf_alternate_state_energy_first_node() : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• compute_samebbconf_alternate_state_energy_second_node() : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• compute_separated_sasa() : protocols::analysis::InterfaceAnalyzerMover
• compute_smooth_nb() : core::scoring::packing::PoseBalls
• compute_sr_one_body_energies_for_flexsets() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• compute_state_energies() : protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::MPIMultistateFitnessFunction
• compute_surface() : core::scoring::packstat::Slice
• compute_surrounding_sasa() : core::scoring::packstat::MultiProbePerSphereAccumulator
• compute_swap_trim_CSPs() : protocols::ub_e2c::ubi_e2c_modeler
• compute_symm_rotations() : core::scoring::electron_density::ElectronDensity
• compute_tempered_rotamer_probabilities() : protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover
• compute_tensor_stats() : core::scoring::ResidualDipolarCoupling
• compute_total_score() : protocols::scoring::ResidualDipolarCouplingRigidSegments
• compute_transform_and_write_to_db() : protocols::features::LoopAnchorFeatures
• compute_trim_CSPs() : protocols::ub_e2c::ubi_e2c_modeler
• compute_zero_intensity() : core::scoring::saxs::SAXSEnergy
• computeAllBoltz() : protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• computeBoltzSum() : protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• computeBoltzWeight() : protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• computeCrystParams() : core::scoring::electron_density::ElectronDensity , core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• computeGradient() : protocols::viewer::triangleIterator
• computeGradients() : core::scoring::electron_density::ElectronDensity
• computeGunnTuples() : protocols::frag_picker::scores::GunnCostScore
• computeStats() : core::scoring::electron_density::ElectronDensity
• ComputeTotalDistCst() : protocols::abinitio::ComputeTotalDistCst
• ConcurrencyTest() : protocols::features::helixAssembly::ConcurrencyTest
• ConcurrencyTestCreator() : protocols::features::helixAssembly::ConcurrencyTestCreator
• conditional_erase() : core::pose::PDBPoseMap
• conditionally_add_edge() : core::scoring::ContextGraph , core::scoring::TenANeighborGraph , core::scoring::TwelveANeighborGraph
• conf_size() : protocols::docking::DockingEnsemble
• confidence() : core::fragment::SecondaryStructure
• configure_new_scorefunction() : protocols::optimize_weights::IterativeOptEDriver
• confirm_sequence() : protocols::forge::remodel::RemodelMover
• conformation() : core::pose::Pose
• Conformation() : core::conformation::Conformation
• conformation() : core::pose::Pose
• conformation_energy() : core::scoring::constraints::Constraints
• ConformationEvent() : core::pose::signals::ConformationEvent
• ConformationViewer() : protocols::viewer::ConformationViewer
• ConformationXYZ() : core::scoring::constraints::ConformationXYZ
• ConformerSwitchMover() : protocols::docking::ConformerSwitchMover
• conn_dat() : core::scoring::etable::etrie::CountPairDataGeneric
• conn_dist() : core::scoring::etable::etrie::CountPairData_1_2 , core::scoring::etable::etrie::CountPairData_1_3 , core::scoring::etable::etrie::CountPairDataGeneric , core::scoring::etable::etrie::CountPairData_1_1
• connect_atom() : core::conformation::Residue
• connect_map() : core::conformation::Residue
• connected() : core::kinematics::FoldTree
• connected_components() : protocols::match::HitNeighborFinder
• connected_residue_at_resconn() : core::conformation::Residue
• connection_distance() : core::conformation::Residue
• connection_exists_to_residue() : core::scoring::trie::RotamerTrieBase
• connection_id_for_residue() : core::scoring::trie::RotamerTrieBase
• connection_incomplete() : core::conformation::Residue
• connection_index() : core::scoring::mm::MMBondAngleResidueTypeParam
• connection_pair() : core::scoring::mm::MMBondAngleResidueTypeParam
• connection_table_length() : core::chemical::sdf::CtabBase
• connection_table_line() : core::chemical::sdf::CtabBase
• connection_theta0() : core::scoring::mm::MMBondAngleResidueTypeParam
• connection_use_theta0() : core::scoring::mm::MMBondAngleResidueTypeParam
• ConnectionEvent() : core::conformation::signals::ConnectionEvent
• connections() : protocols::rna::RNA_StructureParameters
• connections_match() : core::conformation::Residue
• connections_to_residue() : core::conformation::Residue
• ConnectRight() : protocols::forge::build::ConnectRight
• connid() : core::chemical::ResConnID
• connid_for_entry_connpoint() : core::scoring::trie::CPDataCorrespondence
• ConsensusDesignMover() : protocols::simple_moves::ConsensusDesignMover
• ConservedPosMutationFilter() : protocols::simple_filters::ConservedPosMutationFilter
• consider_alternate_state() : core::pack::interaction_graph::HPatchNode< V, E, G >
• consider_backbone_move() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• consider_bbmove_w_state_substitution() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• consider_substitution() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph
• considering_alternate_state() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode
• consolidate_matches() : protocols::match::MatcherTask
• const_begin() : core::graph::EdgeList
• const_edge() : core::graph::EdgeListElement
• const_edge_list_begin() : core::graph::Graph , core::graph::Node
• const_edge_list_end() : core::graph::Node , core::graph::Graph
• const_end() : core::graph::EdgeList
• const_full_to_sub() : protocols::swa::rna::StepWiseRNA_JobParameters
• const_iterator() : core::io::raw_data::RawFileData::const_iterator , core::io::silent::SilentFileData::const_iterator
• const_last() : core::graph::EdgeList
• const_lower_edge_list_begin() : core::graph::Node
• const_lower_edge_list_end() : core::graph::Node
• const_neighbor_iterator_begin() : core::scoring::constraints::CstEnergyContainer , core::scoring::DenseEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::LREnergyContainer , core::scoring::OneToAllEnergyContainer , core::scoring::PeptideBondedEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer
• const_neighbor_iterator_end() : core::scoring::constraints::CstEnergyContainer , core::scoring::DenseEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::LREnergyContainer , core::scoring::OneToAllEnergyContainer , core::scoring::PeptideBondedEnergyContainer
• const_next() : core::graph::EdgeListElement
• const_previous() : core::graph::EdgeListElement
• const_residues() : core::conformation::Conformation
• const_state() : protocols::wum2::WorkUnit_ElScripts
• const_states() : protocols::multistate_design::MultiStateFitnessFunction
• const_sub_to_full() : protocols::swa::rna::StepWiseRNA_JobParameters
• const_upper_edge_list_begin() : core::graph::Node , core::graph::UEVertex< V, E >
• const_upper_edge_list_end() : core::graph::Node , core::graph::UEVertex< V, E >
• const_upper_neighbor_iterator_begin() : core::scoring::constraints::CstEnergyContainer , core::scoring::DenseEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::OneToAllEnergyContainer , core::scoring::PeptideBondedEnergyContainer , core::scoring::LREnergyContainer
• const_upper_neighbor_iterator_end() : core::scoring::constraints::CstEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::OneToAllEnergyContainer , core::scoring::PeptideBondedEnergyContainer , core::scoring::LREnergyContainer , core::scoring::DenseEnergyContainer
• ConstAbinitioMoverWeight() : protocols::topology_broker::weights::ConstAbinitioMoverWeight
• ConstantConstraint() : core::scoring::constraints::ConstantConstraint
• ConstantFunc() : core::scoring::constraints::ConstantFunc
• ConstantLengthFragSet() : core::fragment::ConstantLengthFragSet
• ConstantLengthFragSetIterator_() : core::fragment::ConstantLengthFragSetIterator_
• ConstPattern() : protocols::hotspot_hashing::ConstPattern
• constrain_coords() : protocols::relax::RelaxProtocolBase
• constrain_relax_segments() : protocols::relax::RelaxProtocolBase
• constrain_relax_to_native_coords() : protocols::relax::RelaxProtocolBase
• constrain_relax_to_start_coords() : protocols::relax::RelaxProtocolBase
• constrained_lig_atoms() : protocols::enzdes::EnzdesConstraintReporter
• constrained_nonligand_atoms() : protocols::enzdes::EnzdesConstraintReporter
• Constraint() : core::scoring::constraints::Constraint
• constraint_energy() : protocols::enzdes::LigInterfaceEnergyFilter
• constraint_file() : protocols::simple_moves::ConstraintSetMover
• constraint_set() : core::pose::Pose , protocols::simple_moves::ConstraintSetMover
• ConstraintClaimer() : protocols::topology_broker::ConstraintClaimer
• ConstraintCreator() : core::scoring::constraints::ConstraintCreator
• ConstraintEdge() : core::scoring::constraints::ConstraintEdge
• ConstraintedOptimizationWeightFunc() : protocols::optimize_weights::ConstraintedOptimizationWeightFunc
• ConstraintEvaluator() : protocols::constraints_additional::ConstraintEvaluator
• ConstraintEvaluatorCreator() : protocols::constraints_additional::ConstraintEvaluatorCreator
• ConstraintEvaluatorWrapper() : protocols::topology_broker::ConstraintEvaluatorWrapper
• ConstraintEvaluatorWrapperCreator() : protocols::topology_broker::ConstraintEvaluatorWrapperCreator
• ConstraintFactory() : core::scoring::constraints::ConstraintFactory
• ConstraintFileRCG() : protocols::forge::constraints::ConstraintFileRCG
• ConstraintFragmentMover() : protocols::simple_moves::ConstraintFragmentMover
• ConstraintFragmentSampler() : protocols::abinitio::ConstraintFragmentSampler
• ConstraintGraph() : core::scoring::constraints::ConstraintGraph
• ConstraintIO() : core::scoring::constraints::ConstraintIO
• ConstraintNode() : core::scoring::constraints::ConstraintNode
• ConstrainToIdealMover() : protocols::simple_moves::ConstrainToIdealMover
• ConstraintRegistrator() : core::scoring::constraints::ConstraintRegistrator< T >
• Constraints() : core::scoring::constraints::Constraints
• constraints() : core::scoring::constraints::Constraints , core::scoring::constraints::CstMinimizationData , protocols::abinitio::FoldConstraints , protocols::abinitio::Template , protocols::hotspot_hashing::HotspotStubSet , protocols::abinitio::ConstraintFragmentSampler
• Constraints() : core::scoring::constraints::Constraints
• constraints_only() : protocols::idealize::IdealizeMover
• ConstraintScoreCutoffFilter() : protocols::simple_filters::ConstraintScoreCutoffFilter
• ConstraintsEnergy() : core::scoring::constraints::ConstraintsEnergy
• ConstraintSet() : core::scoring::constraints::ConstraintSet
• ConstraintSetMover() : protocols::simple_moves::ConstraintSetMover
• construct() : boost::unordered_object_pool< T, UserAllocator >
• construct_and_dump_outpose() : protocols::enzdes::PoseFoundResiduesCombination
• construct_rotamer_trie() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• ConstScore() : protocols::frag_picker::scores::ConstScore
• Contact() : protocols::contact_map::Contact , protocols::frag_picker::Contact
• contact() : protocols::dna::DnaNeighbor
• contact_buried_problematic_res() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• contact_distance() : protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::NcontactsCalculator
• contact_list() : protocols::scoring::Interface
• contact_order() : core::scoring::dssp::StrandPairing , protocols::abinitio::PairingStatEntry
• ContactCounts() : protocols::frag_picker::ContactCounts
• ContactMap() : protocols::contact_map::ContactMap
• ContactMapEvaluator() : protocols::simple_filters::ContactMapEvaluator
• ContactMapEvaluatorCreator() : protocols::simple_filters::ContactMapEvaluatorCreator
• ContactOrderEnergy() : core::scoring::methods::ContactOrderEnergy
• ContactPartner() : protocols::contact_map::ContactPartner
• contacts() : protocols::sic_dock::Rose
• contacts_naive() : protocols::sic_dock::Rose
• contains() : core::scoring::dssp::StrandPairing , core::scoring::packstat::Circle , core::scoring::packstat::Octree2D , protocols::forge::build::Interval , protocols::dna::DnaChains
• contains_atom_type() : core::chemical::CSDAtomTypeSet , core::chemical::MMAtomTypeSet
• contains_bond_length() : core::chemical::IdealBondLengthSet
• contains_catalytic_res() : protocols::enzdes::EnzdesFlexibleRegion
• contains_element_type() : core::chemical::ElementSet
• contains_position() : protocols::toolbox::match_enzdes_util::EnzdesCstCache , protocols::toolbox::match_enzdes_util::EnzdesCstParamCache , protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache , protocols::toolbox::match_enzdes_util::EnzConstraintIO
• contains_seqpos() : core::fragment::Frame
• contents_in_pose_store() : protocols::forge::remodel::RemodelAccumulator
• context_graph() : core::scoring::Energies
• context_graphs() : core::scoring::Energies
• ContextDependentLRTwoBodyEnergy() : core::scoring::methods::ContextDependentLRTwoBodyEnergy
• ContextDependentOneBodyEnergy() : core::scoring::methods::ContextDependentOneBodyEnergy
• ContextDependentTwoBodyEnergy() : core::scoring::methods::ContextDependentTwoBodyEnergy
• ContextGraph() : core::scoring::ContextGraph
• ContextIndependentGeometricSolEnergy() : core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy
• ContextIndependentLRTwoBodyEnergy() : core::scoring::methods::ContextIndependentLRTwoBodyEnergy
• ContextIndependentOneBodyEnergy() : core::scoring::methods::ContextIndependentOneBodyEnergy
• ContextIndependentTwoBodyEnergy() : core::scoring::methods::ContextIndependentTwoBodyEnergy
• ContingentFilter() : protocols::filters::ContingentFilter
• continue_slide() : protocols::simple_moves::symmetry::SymmetrySlider
• ContinuousRotamerSet() : core::pack::rotamer_set::ContinuousRotamerSet
• ContinuousRotamerSets() : core::pack::rotamer_set::ContinuousRotamerSets
• control_grid_param() : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::scoring::methods::pcs2::PcsGridSearchParameter
• controlling_chi_for_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• converged() : protocols::optimize_weights::IterativeOptEDriver
• convert_based_on_match_type() : protocols::rna::RNA_Fragments
• convert_GeomSampleInfo_to_FuncOP() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• convert_matrix_to_xyz() : protocols::hybridization::TMalign
• convert_profile_to_probs() : core::sequence::SequenceProfile
• convert_silent_file_to_pose_data_list() : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• convert_to_centroid() : protocols::swa::protein::StepWiseProteinScreener , protocols::swa::StepWiseScreener
• convert_vector_to_xyz() : protocols::hybridization::TMalign
• convert_xyz_to_matrix() : protocols::hybridization::TMalign
• convert_xyz_to_vector() : protocols::hybridization::TMalign
• convert_xyz_v_to_vectors() : protocols::hybridization::TMalign
• convertPSERtoASP() : protocols::flexpep_docking::FlexPepDockingAbInitio
• convertPSERtoGLU() : protocols::flexpep_docking::FlexPepDockingAbInitio
• cool() : core::pack::annealer::MultiCoolAnnealer
• coord() : core::pack::scmin::ResidueAtomTreeCollectionMomento , protocols::match::downstream::TargetRotamerCoords
• coord2key() : protocols::canonical_sampling::HamiltonianExchange
• coord_sdev() : protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots
• CoordConstraintClaimer() : protocols::topology_broker::CoordConstraintClaimer
• coordinate_cacher() : protocols::match::output::PDBWriter
• coordinate_constraint_energy() : core::scoring::constraints::ConstraintEdge
• coordinate_constraint_weight() : protocols::idealize::IdealizeMover
• coordinate_for_nonchi_atom_in_ideal_frame() : protocols::match::upstream::UpstreamResTypeGeometry
• coordinate_in_D3_frame() : protocols::toolbox::match_enzdes_util::LigandConformer
• coordinate_in_global_frame() : protocols::toolbox::match_enzdes_util::LigandConformer
• CoordinateConstraint() : core::scoring::constraints::CoordinateConstraint
• CoordinateConstraintCreator() : core::scoring::constraints::CoordinateConstraintCreator
• CoordinateConstraintKC() : protocols::abinitio::CoordinateConstraintKC
• CoordinateCst() : protocols::seeded_abinitio::CoordinateCst
• coordinates_from_hit() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• coordinates_from_orientation() : protocols::toolbox::match_enzdes_util::LigandConformer
• Coordinates_Tetrahedral_bondedto3atoms_helper() : core::chemical::orbitals::AssignOrbitals
• Coordinates_TriganolPlanar_bondedto1atom_helper() : core::chemical::orbitals::AssignOrbitals
• CoordinatesDihedral() : core::scoring::orbitals::OrbitalsAssigned
• CoordinatesTetrahedral() : core::scoring::orbitals::OrbitalsAssigned
• coords() : protocols::ligand_docking::StartFrom , core::io::silent::RNA_SilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::grid::CartGrid< T > , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::pose::MiniPose , protocols::toolbox::DecoySetEvaluation , protocols::toolbox::KClusterData , core::io::silent::ProteinSilentStruct_Template< T > , core::pose::UnrecognizedAtomRecord , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• coordTransformFromThreePoints() : protocols::rbsegment_relax::RBSegmentMover
• copy() : protocols::docking::TemperedDocking , core::pack::interaction_graph::RotamerDots , core::pose::PDBInfo , protocols::docking::DockSetupMover
• copy_alternate_to_current() : protocols::flexpack::interaction_graph::FlexbbNode , protocols::flexpack::interaction_graph::FlexbbEdge
• copy_array_contents() : core::graph::ArrayPoolElement< T >
• copy_bb_donor_acceptor_arrays() : core::scoring::hbonds::HBondSet
• Copy_CCD_torsions() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• Copy_CCD_torsions_general() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• copy_connectivity() : core::graph::Graph
• copy_context_graphs() : core::scoring::Energies
• copy_coord() : protocols::toolbox::KMedoid
• copy_coordinates() : protocols::frag_picker::DiversifyCrmsdByClustering , protocols::frag_picker::DiversifyCrmsdSelector
• copy_coords() : core::pack::scmin::ResidueAtomTreeCollectionMomento , core::kinematics::AtomTree , core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom , protocols::swa::protein::StepWiseProteinScreener , protocols::swa::StepWiseScreener
• copy_data() : protocols::simple_moves::carbohydrates::RingConformationMover , core::chemical::carbohydrates::CarbohydrateInfo
• copy_dna_chains() : protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::RestrictDesignToProteinDNAInterface
• copy_dofs_from_pose() : core::optimization::CartesianMinimizerMap , core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap
• copy_dofs_to_pose() : core::optimization::symmetry::SymMinimizerMap , core::optimization::CartesianMinimizerMap , core::optimization::MinimizerMap
• copy_from() : core::scoring::TenANeighborEdge , core::scoring::etable::MembEtable , core::scoring::constraints::Constraints , core::pack::interaction_graph::SimpleNode , core::graph::Node , core::pack::interaction_graph::SimpleEdge , core::scoring::constraints::ConstraintEdge , core::scoring::EnergyNode , core::scoring::MinimizationNode , core::scoring::MinimizationEdge , core::scoring::TenANeighborNode , core::scoring::TwelveANeighborNode , core::graph::Edge , core::graph::UpperEdgeGraph< V, E > , core::scoring::constraints::ConstraintNode , core::scoring::EnergyEdge , core::scoring::etable::MembEtable , core::scoring::TwelveANeighborEdge
• copy_from_ref() : protocols::scoring::methods::pcs::PCS_tensor
• copy_hit() : protocols::match::upstream_hit , protocols::match::downstream_hit
• copy_interface() : protocols::dna::RestrictDesignToProteinDNAInterface
• copy_length_events() : core::pose::datacache::LengthEventCollector
• copy_lr_energy_containers() : core::scoring::Energies
• copy_native_packertask_logic() : protocols::optimize_weights::IterativeOptEDriver
• copy_native_structure() : protocols::abinitio::AbrelaxApplication
• copy_nblists() : core::scoring::Energies
• copy_next_pose_segment() : protocols::swa::InputStreamWithResidueInfo
• copy_old_data_into_new_table() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• copy_operations() : core::pack::task::TaskFactory
• copy_residue_connections() : core::conformation::Residue
• copy_residue_connections_from() : core::conformation::Residue
• copy_rna_chi() : protocols::swa::StepWisePoseSetup
• copy_scores() : core::io::silent::SilentStruct
• copy_segment() : core::conformation::Conformation , core::pose::Pose
• copy_sidechains() : protocols::comparative_modeling::LoopRelaxMover
• copy_stretch() : protocols::simple_filters::RelativePoseFilter
• copy_structure() : protocols::abinitio::AbrelaxApplication
• copy_suite_torsion() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler
• copy_targeted_dna() : protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::RestrictDesignToProteinDNAInterface
• copy_values() : core::scoring::rna::RNA_RawBaseBaseInfo
• copy_without_output() : protocols::jd2::Job
• copying_side_chains() : protocols::seeded_abinitio::SwapSegment
• COradius() : core::scoring::FACTSResidueInfo
• core() : protocols::abinitio::IterativeBase
• CoreDunbrackFilter() : protocols::fldsgn::filters::CoreDunbrackFilter
• corners() : protocols::match::Bool3DGrid
• correct_arrays_for_symmetry() : core::scoring::symmetry::SymmetricScoreFunction
• correct_finalize_score() : core::scoring::symmetry::SymmetricScoreFunction
• correct_jump_atoms_for_fragments() : protocols::jumping::JumpSample
• correct_termini_derivatives() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
• CorrectionVisitor() : protocols::sic_dock::CorrectionVisitor
• correctly_copy_HO2star_positions() : protocols::swa::rna::StepWiseRNA_PoseSetup
• correspondence() : protocols::pack_daemon::PackDaemon
• corresponding_res_block() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• cosAHD_fade_lookup() : core::scoring::hbonds::HBondDatabase
• cosAHD_long_poly_lookup() : core::scoring::hbonds::HBondDatabase
• cosAHD_short_poly_lookup() : core::scoring::hbonds::HBondDatabase
• cosBAH_fade_lookup() : core::scoring::hbonds::HBondDatabase
• cosBAH_long_poly_lookup() : core::scoring::hbonds::HBondDatabase
• cosBAH_short_poly_lookup() : core::scoring::hbonds::HBondDatabase
• could_be_accepted() : protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::SecondaryStructurePool , protocols::frag_picker::quota::QuotaPool
• could_not_create_resource_error_message() : protocols::loops::LoopsFileFallbackConfiguration
• count() : core::scoring::etable::count_pair::CountPairIntraResC4 , core::scoring::etable::count_pair::CountPairFunction , core::import_pose::atom_tree_diffs::AtomTreeDiff , core::scoring::etable::count_pair::CountPairGeneric , core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairIntraResC3 , core::scoring::etable::count_pair::CountPairNone , core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairAll , core::sequence::CompositeScoringScheme
• count_accepted() : protocols::moves::TrialCounter , protocols::canonical_sampling::MultiTemperatureTrialCounter
• count_assignments() : protocols::noesy_assign::CrossPeakList
• count_at_path_distance() : core::scoring::etable::count_pair::CountPairCrossover4 , core::scoring::etable::count_pair::CountPairCrossover3
• count_atoms() : core::scoring::APBSWrapper
• count_atoms_in_common() : core::scoring::trie::RotamerDescriptor< AT, CPDAT >
• count_candidates() : protocols::frag_picker::quota::QuotaPool , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::CandidatesCollector , protocols::frag_picker::GrabAllCollector , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::SecondaryStructurePool , protocols::frag_picker::BoundedCollector< StrictWeakOrdering > , protocols::frag_picker::quota::QuotaCollector , protocols::frag_picker::quota::SecondaryStructurePool
• count_components() : protocols::frag_picker::scores::FragmentScoreManager
• count_connected_components_and_initialize_vertex_groups() : core::pack::interaction_graph::InteractionGraphBase
• count_dynamic_memory() : core::pack::interaction_graph::FASTERInteractionGraph , protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::flexpack::interaction_graph::FlexbbInteractionGraph , core::scoring::TwelveANeighborEdge , core::scoring::TenANeighborNode , core::scoring::EnergyGraph , core::scoring::constraints::ConstraintGraph , core::pack::interaction_graph::SymmOnTheFlyEdge , core::pack::interaction_graph::SymmMinimalistNode , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::FirstClassNode< V, E, G > , protocols::flexpack::interaction_graph::FlexbbNode , protocols::flexpack::interaction_graph::FlexbbEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::graph::Node , core::pack::interaction_graph::FirstClassEdge< V, E, G > , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::SimpleNode , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::SymmMinimalistInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyNode , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , core::scoring::ContextGraph , core::scoring::EnergyEdge , core::scoring::MinimizationNode , core::scoring::TenANeighborEdge , core::scoring::TenANeighborGraph , core::scoring::TwelveANeighborNode , core::scoring::TwelveANeighborGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbNode , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , protocols::flexpack::interaction_graph::OTFFlexbbEdge , core::graph::Edge , core::graph::Graph , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SimpleEdge , core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::scoring::constraints::ConstraintNode , core::scoring::constraints::ConstraintEdge , core::scoring::EnergyNode , core::scoring::MinimizationEdge , core::scoring::MinimizationGraph , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbEdge
• count_energy_drop() : protocols::moves::TrialCounter , protocols::canonical_sampling::MultiTemperatureTrialCounter
• count_energy_to_node_in_my_fragtotalE() : protocols::flexpack::interaction_graph::FlexbbNode
• count_ff() : core::scoring::saxs::FormFactorManager
• count_file_reads() : protocols::pack_daemon::DynamicAggregateFunction
• count_fixed_residues() : core::kinematics::FoldTree
• count_inserted() : protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering > , protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• count_moveable_residues() : protocols::forge::remodel::RemodelLoopMover
• count_n_matches() : protocols::match::MatchCounter
• count_ntrial() : protocols::flxbb::FilterStructs
• count_num_covered() : core::pack::interaction_graph::DotSphere
• count_num_npd_properties() : protocols::pack_daemon::DynamicAggregateFunction
• count_pools() : protocols::frag_picker::quota::QuotaCollector , protocols::frag_picker::quota::QuotaConfig
• count_query_ss() : protocols::frag_picker::FragmentPicker
• count_removed_structures() : protocols::jd2::archive::ArchiveBase
• count_rotamer() : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• count_rotamer_as_native() : protocols::optimize_weights::PNatRotOptEPositionData
• count_scoring_atoms() : core::scoring::saxs::SAXSEnergy
• count_static_memory() : core::pack::interaction_graph::SymmLinearMemNode , core::scoring::TwelveANeighborGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbEdge , core::pack::interaction_graph::SymmOnTheFlyEdge , core::scoring::ContextGraph , core::scoring::constraints::ConstraintNode , core::scoring::MinimizationNode , core::scoring::MinimizationEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::scoring::TwelveANeighborNode , core::scoring::MinimizationGraph , core::scoring::EnergyEdge , core::scoring::constraints::ConstraintEdge , core::pack::interaction_graph::SymmMinimalistInteractionGraph , core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::SimpleEdge , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DensePDNode , core::graph::Edge , protocols::flexpack::interaction_graph::MinimalistFlexbbNode , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::SimpleNode , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::graph::Node , core::graph::Graph , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistNode , core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::SymmOnTheFlyNode , core::scoring::constraints::ConstraintGraph , core::scoring::EnergyNode , core::scoring::EnergyGraph , core::scoring::TenANeighborNode , core::scoring::TenANeighborEdge , core::scoring::TenANeighborGraph , core::scoring::TwelveANeighborEdge , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• count_structure() : protocols::jd2::archive::ArchiveBase
• count_trial() : protocols::moves::TrialCounter , protocols::canonical_sampling::MultiTemperatureTrialCounter
• CountPair1B() : core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >
• CountPairAll() : core::scoring::etable::count_pair::CountPairAll
• CountPairData_1_1() : core::scoring::etable::etrie::CountPairData_1_1
• CountPairDataGeneric() : core::scoring::etable::etrie::CountPairDataGeneric
• CountPairFunction() : core::scoring::etable::count_pair::CountPairFunction
• CountPairGeneric() : core::scoring::etable::count_pair::CountPairGeneric
• CountPairIntraRes() : core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior >
• CountPairIntraResC3() : core::scoring::etable::count_pair::CountPairIntraResC3
• CountPairIntraResC4() : core::scoring::etable::count_pair::CountPairIntraResC4
• CountPairNone() : core::scoring::etable::count_pair::CountPairNone
• counts() : protocols::frag_picker::ContactCounts
• CountViolFunc() : core::scoring::constraints::CountViolFunc
• covalent_connections() : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• CovalentCompliance() : protocols::noesy_assign::CovalentCompliance
• CovalentConnectionReplaceInfo() : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• cp_data() : core::scoring::trie::RotamerDescriptorAtom< AT, CPDAT > , core::scoring::trie::TrieNode< AT, CPDATA >
• cp_function() : core::scoring::orbitals::OrbitalsAssigned
• cp_weighting_during_minimization() : core::conformation::symmetry::SymmetryInfo
• CPDataCorrespondence() : core::scoring::trie::CPDataCorrespondence
• cprev_n_bond_length_params() : core::scoring::methods::ResidueCartBondedParameters
• crankshaft_alpha_gamma() : protocols::swa::monte_carlo::RNA_TorsionMover
• cranny_packer() : protocols::vip::VIP_Mover
• create() : protocols::outputter::SilentFileOutputter , protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver , protocols::toolbox::DummyClass , core::fragment::DownJumpSRFD , protocols::outputter::PDBOutputter , protocols::inputter::SilentFileInputter , protocols::moves::Mover , protocols::inputter::Inputter , core::fragment::SingleResidueFragData , core::pose::datacache::LengthEventCollector , core::fragment::IndependentBBTorsionSRFD , core::fragment::BBTorsionAndAnglesSRFD , core::pose::datacache::SpecialSegmentsObserver , core::fragment::BBTorsionSRFD , core::fragment::UpJumpSRFD , core::fragment::SecstructSRFD , core::pose::datacache::CacheableObserver , protocols::forge::build::BuildManager , protocols::inputter::FastaInputter , protocols::inputter::PDBInputter , protocols::outputter::Outputter , protocols::outputter::ResFileOutputter , protocols::simple_moves::O2M_MutateMover , protocols::outputter::FormatStringOutputter
• create_adduct_combinations() : core::chemical::ResidueTypeSet
• create_and_attach_task_factory() : protocols::docking::DockTaskFactory
• create_annealer() : core::pack::annealer::AnnealerFactory
• create_atom_tree() : protocols::protein_interface_design::movers::SetAtomTree
• create_atom_type_from_database() : core::chemical::AtomTypeSet
• create_background_edge() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• create_background_node() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• create_bb_moves() : protocols::abinitio::KinematicAbinitio , protocols::abinitio::JumpingFoldConstraints
• create_bump_grid_for_bb() : protocols::match::BumpGrid
• create_collcheck_ordering() : protocols::toolbox::match_enzdes_util::LigandConformer
• create_comm() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• create_comparer() : protocols::rotamer_recovery::RRComparerChiDiffCreator , protocols::rotamer_recovery::RRComparerCreator , protocols::rotamer_recovery::RRComparerAutomorphicRMSDCreator , protocols::rotamer_recovery::RRComparerRotBinsCreator
• create_consensus_design_task() : protocols::simple_moves::ConsensusDesignMover
• create_constraint() : protocols::noesy_assign::PeakAssignment , core::scoring::constraints::MultiConstraintCreator , core::scoring::constraints::AngleConstraintCreator , protocols::constraints_additional::BindingSiteConstraintCreator , core::scoring::constraints::DihedralPairConstraintCreator , core::pack::dunbrack::DunbrackConstraintCreator , core::scoring::constraints::KofNConstraintCreator , core::scoring::constraints::SiteConstraintResiduesCreator , core::scoring::constraints::CoordinateConstraintCreator , core::scoring::constraints::LocalCoordinateConstraintCreator , core::scoring::constraints::AtomPairConstraintCreator , protocols::constraints_additional::NamedAtomPairConstraintCreator , core::scoring::constraints::ConstraintCreator , core::scoring::constraints::SequenceProfileConstraintCreator , core::scoring::constraints::DihedralConstraintCreator , core::scoring::constraints::BigBinConstraintCreator , core::scoring::constraints::AmbiguousConstraintCreator , core::scoring::constraints::AmbiguousNMRDistanceConstraintCreator , core::scoring::constraints::AmbiguousNMRConstraintCreator , core::scoring::constraints::SiteConstraintCreator , core::scoring::constraints::FabConstraintCreator , protocols::constraints_additional::SequenceCoupling1BDConstraintCreator , protocols::constraints_additional::SequenceCouplingConstraintCreator , protocols::pockets::PocketConstraintCreator
• create_constraints() : protocols::cluster::ClusterBase
• create_context_graph() : core::scoring::ContextGraphFactory
• create_count_pair_function() : core::scoring::etable::count_pair::CountPairFactory
• create_count_pair_function_and_invoke() : core::scoring::etable::count_pair::CountPairFactory
• create_db() : protocols::loophash::LoopHashLibrary
• create_dense_pdig_from_rot_to_pack() : protocols::pack_daemon::DoubleDenseIGRepacker , protocols::pack_daemon::DenseIGRepacker
• create_directed_dependency() : protocols::forge::build::BuildManager , protocols::forge::components::BDR , protocols::fldsgn::BluePrintBDR
• create_dist_constraints() : protocols::toolbox::DecoySetEvaluation
• create_dist_constraints_median() : protocols::toolbox::DecoySetEvaluation
• create_ds_builder() : protocols::match::Matcher
• create_empty_map() : protocols::frag_picker::scores::FragmentScoreManager
• create_energy_method() : core::scoring::hackaro::HackAroEnergyCreator , core::scoring::methods::CenPairEnergyCreator , core::scoring::methods::DipolarCouplingEnergyCreator , core::scoring::methods::ChainbreakEnergyCreator , core::scoring::methods::ChemicalShiftAnisotropyEnergyCreator , core::scoring::hackelec::HackElecEnergyAroAroCreator , core::scoring::methods::CartesianBondedEnergyCreator , core::scoring::hackelec::HackElecEnergyCreator , core::scoring::hackelec::RNAHackElecEnergyCreator , core::scoring::etable::EtableEnergyCreator , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergyCreator , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergyCreator , core::scoring::dna::DNATorsionEnergyCreator , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergyCreator , core::scoring::electron_density::FastDensEnergyCreator , core::scoring::electron_density::ElecDensCenEnergyCreator , core::pack::interaction_graph::SurfaceEnergyCreator , core::scoring::disulfides::FullatomDisulfideEnergyCreator , core::scoring::carbon_hbonds::CarbonHBondEnergyCreator , core::scoring::constraints::ConstraintsEnergyCreator , core::pack::dunbrack::DunbrackEnergyCreator , core::scoring::interface::DDPscoreCreator , core::scoring::rna::RNA_DataBackboneEnergyCreator , core::scoring::rna::RNA_FullAtomStackingEnergyCreator , core::scoring::methods::SecondaryStructureEnergyCreator , core::scoring::methods::DistanceChainbreakEnergyCreator , core::scoring::methods::DNA_BaseEnergyCreator , core::scoring::methods::pHEnergyCreator , core::scoring::electron_density::ElecDensAllAtomCenEnergyCreator , core::pack::interaction_graph::HPatchEnergyCreator , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergyCreator , core::scoring::disulfides::CentroidDisulfideEnergyCreator , core::scoring::disulfides::DisulfideMatchingEnergyCreator , core::scoring::dna::DNAChiEnergyCreator , core::scoring::electron_density::ElecDensEnergyCreator , core::scoring::electron_density::PattersonCorrEnergyCreator , core::scoring::etable::CoarseEtableEnergyCreator , core::scoring::geometric_solvation::GeometricSolEnergyCreator , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebodyCreator , core::scoring::geometric_solvation::OccludedHbondSolEnergyCreator , core::scoring::hackelec::HackElecEnergyAroAllCreator , core::scoring::hbonds::HBondEnergyCreator , core::scoring::methods::BurialEnergyCreator , core::scoring::methods::CenHBEnergyCreator , core::scoring::methods::ContactOrderEnergyCreator , core::scoring::methods::CustomAtomPairEnergyCreator , core::scoring::methods::dfire::DFIRE_EnergyCreator , core::scoring::methods::DirectReadoutEnergyCreator , core::scoring::methods::EnvEnergyCreator , core::scoring::methods::Fa_MbenvEnergyCreator , core::scoring::methods::GaussianOverlapEnergyCreator , core::scoring::methods::LK_BallEnergyCreator , core::scoring::methods::HybridVDW_EnergyCreator , core::scoring::methods::LK_CosThetaEnergyCreator , core::scoring::methods::LK_hackCreator , core::scoring::methods::MembraneCenPairEnergyCreator , core::scoring::methods::MembraneLipoCreator , core::scoring::methods::MMBondLengthEnergyCreator , core::scoring::methods::MMLJEnergyIntraCreator , core::scoring::methods::OmegaTetherEnergyCreator , core::scoring::methods::MembraneEnvPenaltiesCreator , core::scoring::methods::P_AA_EnergyCreator , core::scoring::methods::P_AA_pp_EnergyCreator , core::scoring::methods::PairEnergyCreator , core::scoring::methods::ProClosureEnergyCreator , core::scoring::methods::RamachandranEnergyCreator , core::scoring::methods::ReferenceEnergyNoncanonicalCreator , core::scoring::methods::RMS_EnergyCreator , core::scoring::methods::NMerPSSMEnergyCreator , core::scoring::methods::SA_EnergyCreator , core::scoring::methods::SmoothCenPairEnergyCreator , core::scoring::methods::UnfoldedStateEnergyCreator , core::scoring::methods::WaterAdductHBondEnergyCreator , core::scoring::methods::YHHPlanarityEnergyCreator , core::scoring::packing::SurfEnergyCreator , core::scoring::packing::SurfVolEnergyCreator , core::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergyCreator , core::scoring::rna::RNA_BulgeEnergyCreator , core::scoring::rna::RNA_LJ_BaseEnergyCreator , core::scoring::rna::RNA_PairwiseLowResolutionEnergyCreator , core::scoring::rna::RNA_TorsionEnergyCreator , core::scoring::saxs::SAXSEnergyCreator , core::scoring::saxs::SAXSEnergyCreatorCEN , core::scoring::saxs::SAXSEnergyCreatorFA , core::scoring::methods::ResidualDipolarCouplingEnergyCreator , protocols::fldsgn::potentials::AACompositionEnergyCreator , protocols::scoring::methods::InterchainPairEnergyCreator , protocols::scoring::methods::pcs2::PcsEnergyCreator , protocols::scoring::methods::saxs::PDDFEnergy , core::scoring::methods::EnergyMethodCreator , core::scoring::rna::RNA_Mg_EnergyCreator , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegmentsCreator , core::scoring::methods::SuckerEnergyCreator , protocols::scoring::methods::saxs::PDDFEnergyCreator , protocols::scoring::methods::SpecialRotamerEnergyCreator , core::scoring::sym_e::symECreator , protocols::scoring::methods::pcs::PseudocontactShiftEnergyCreator , protocols::scoring::methods::InterchainEnvEnergyCreator , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergyCreator , protocols::scoring::methods::EnsembleEnergyCreator , core::scoring::orbitals::OrbitalsScoreCreator , core::scoring::rna::RNA_SugarCloseEnergyCreator , core::scoring::saxs::SAXSEnergy , core::scoring::rna::RNA_VDW_EnergyCreator , core::scoring::saxs::FastSAXSEnergyCreator , core::scoring::methods::RamachandranEnergy2BCreator , core::scoring::rna::RG_Energy_RNACreator , core::scoring::rna::RNA_FullAtomVDW_BasePhosphateCreator , core::scoring::methods::WaterAdductIntraEnergyCreator , core::scoring::packing::HolesEnergyCreator , core::scoring::nv::NVscoreCreator , core::scoring::methods::SequenceDependentRefEnergyCreator , core::scoring::methods::VDW_EnergyCreator , core::scoring::methods::SymmetricLigandEnergyCreator , core::scoring::methods::SmoothEnvEnergyCreator , core::scoring::methods::ReferenceEnergyCreator , core::scoring::methods::RG_Energy_FastCreator , core::scoring::methods::ResidualDipolarCouplingEnergy_RohlCreator , core::scoring::methods::EnvSmoothEnergyCreator , core::scoring::methods::PackStatEnergyCreator , core::scoring::methods::PoissonBoltzmannEnergyCreator , core::scoring::methods::PeptideBondEnergyCreator , core::scoring::methods::MMLJEnergyInterCreator , core::scoring::methods::NMerRefEnergyCreator , core::scoring::methods::MMTorsionEnergyCreator , core::scoring::methods::MembraneCbetaEnergyCreator , core::scoring::methods::MMBondAngleEnergyCreator , core::scoring::methods::MembraneEnvSmoothEnergyCreator , core::scoring::methods::MembraneEnvEnergyCreator , core::scoring::methods::Fa_MbsolvEnergyCreator , core::scoring::methods::LinearChainbreakEnergyCreator , core::scoring::methods::GenBornEnergyCreator
• create_ensemble() : protocols::simple_moves::ShakeStructureMover
• create_enzdes_movemap() : protocols::enzdes::EnzdesBaseProtocol
• create_enzdes_pack_task() : protocols::enzdes::EnzdesBaseProtocol
• create_evaluator() : protocols::match::output::ProcessorFactory
• create_exgs() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• create_fa_and_cen_constraint() : protocols::noesy_assign::CrossPeak
• create_fa_dunbrack_libraries() : core::pack::dunbrack::RotamerLibrary
• create_fa_dunbrack_libraries_02_from_ASCII() : core::pack::dunbrack::RotamerLibrary
• create_fa_dunbrack_libraries_02_from_binary() : core::pack::dunbrack::RotamerLibrary
• create_fa_dunbrack_libraries_10_from_ASCII() : core::pack::dunbrack::RotamerLibrary
• create_fa_dunbrack_libraries_10_from_binary() : core::pack::dunbrack::RotamerLibrary
• create_fa_dunbrack_libraries_from_ASCII() : core::pack::dunbrack::RotamerLibrary
• create_fa_dunbrack_libraries_from_binary() : core::pack::dunbrack::RotamerLibrary
• create_fallback_configuration() : protocols::loops::LoopsFileFallbackConfigurationCreator
• create_faster_ig_from_rot_to_pack() : protocols::pack_daemon::FASTER_IG_Repacker
• create_features_reporter() : protocols::features::ProteinResidueConformationFeaturesCreator , protocols::features::HBondParameterFeaturesCreator , protocols::features::ProtocolFeaturesCreator , protocols::features::BetaTurnDetectionFeaturesCreator , protocols::features::JobDataFeaturesCreator , protocols::features::AtomTypesFeaturesCreator , protocols::features::BatchFeaturesCreator , protocols::features::FeaturesReporterCreator , protocols::features::helixAssembly::ConcurrencyTestCreator , protocols::features::OrbitalsFeaturesCreator , protocols::features::PoseConformationFeaturesCreator , protocols::features::ProteinBackboneAtomAtomPairFeaturesCreator , protocols::features::ProteinBackboneTorsionAngleFeaturesCreator , protocols::features::SaltBridgeFeaturesCreator , protocols::features::ResidueBurialFeaturesCreator , protocols::features::ResidueFeaturesCreator , protocols::features::ResidueScoresFeaturesCreator , protocols::features::RotamerBoltzmannWeightFeaturesCreator , protocols::features::RotamerFeaturesCreator , protocols::features::RotamerRecoveryFeaturesCreator , protocols::features::ScoreFunctionFeaturesCreator , protocols::features::strand_assembly::StrandBundleFeaturesCreator , protocols::features::StructureScoresFeaturesCreator , protocols::features::StructureFeaturesCreator , protocols::features::UnrecognizedAtomFeaturesCreator , protocols::features::ScoreTypeFeaturesCreator , protocols::features::SecondaryStructureSegmentFeaturesCreator , protocols::features::SmotifFeaturesCreator , protocols::features::ProteinBondGeometryFeaturesCreator , protocols::features::ResidueSecondaryStructureFeaturesCreator , protocols::features::ResidueTotalScoresFeaturesCreator , protocols::features::ResidueTypesFeaturesCreator , protocols::features::ResidueConformationFeaturesCreator , protocols::features::ResidueGridScoresFeaturesCreator , protocols::features::ProteinRMSDFeaturesCreator , protocols::features::RadiusOfGyrationFeaturesCreator , protocols::features::ChargeChargeFeaturesCreator , protocols::features::PairFeaturesCreator , protocols::features::PdbDataFeaturesCreator , protocols::features::PoseCommentsFeaturesCreator , protocols::features::helixAssembly::HelixBundleFeaturesCreator , protocols::features::LoopAnchorFeaturesCreator , protocols::features::GeometricSolvationFeaturesCreator , protocols::features::HBondFeaturesCreator , protocols::features::AtomAtomPairFeaturesCreator , protocols::features::AtomInResidueAtomInResiduePairFeaturesCreator
• create_filter() : protocols::filters::ContingentFilterCreator , protocols::simple_filters::EnergyPerResidueFilterCreator , protocols::simple_filters::InterfaceSasaFilterCreator , protocols::simple_filters::InterfaceBindingEnergyDensityFilterCreator , protocols::filters::CalculatorFilterCreator , protocols::simple_filters::HolesFilterCreator , protocols::simple_filters::AtomicDistanceFilterCreator , protocols::simple_filters::NMerPSSMEnergyFilterCreator , protocols::simple_filters::RotamerBoltzmannWeightFilterCreator , protocols::protein_interface_design::filters::DisulfideFilterCreator , protocols::simple_filters::PoseInfoFilterCreator , protocols::simple_filters::ResidueCountFilterCreator , protocols::protein_interface_design::filters::DesignableResiduesFilterCreator , protocols::ligand_docking::HBondAcceptorFilterCreator , protocols::protein_interface_design::filters::RmsdFilterCreator , protocols::protein_interface_design::filters::InterfaceHolesFilterCreator , protocols::protein_interface_design::filters::StubScoreFilterCreator , protocols::simple_filters::ResiduesInInterfaceFilterCreator , protocols::protein_interface_design::filters::StubScoreLoopsFilterCreator , protocols::simple_filters::FileExistFilterCreator , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilterCreator , protocols::simple_filters::ConservedPosMutationFilterCreator , protocols::protein_interface_design::filters::BindingStrainFilterCreator , protocols::enzdes::EnzScoreFilterCreator , protocols::simple_filters::DdgFilterCreator , protocols::simple_filters::ConstraintScoreCutoffFilterCreator , protocols::simple_filters::ResidueBurialFilterCreator , protocols::simple_filters::ExpiryFilterCreator , protocols::simple_filters::ResidueSetChainEnergyFilterCreator , protocols::simple_filters::ResidueDistanceFilterCreator , protocols::protein_interface_design::filters::FilterScanFilterCreator , protocols::simple_filters::SymmetricMotifFilterCreator , protocols::simple_filters::RangeFilterCreator , protocols::simple_filters::RelativePoseFilterCreator , protocols::simple_filters::AlaScanFilterCreator , protocols::fldsgn::filters::HelixPairingFilterCreator , protocols::simple_filters::ScoreTypeFilterCreator , protocols::simple_filters::ShapeComplementarityFilterCreator , protocols::simple_filters::TerminusDistanceFilterCreator , protocols::simple_filters::NonSequentialNeighborsFilterCreator , protocols::fldsgn::filters::HelixKinkFilterCreator , protocols::simple_filters::PackStatFilterCreator , protocols::enzdes::LigDSasaFilterCreator , protocols::enzdes::DiffAtomSasaFilterCreator , protocols::enzdes::LigInterfaceEnergyFilterCreator , protocols::enzdes::EnzdesScorefileFilterCreator , protocols::filters::MoveBeforeFilterCreator , protocols::fldsgn::filters::FragQualFilterCreator , protocols::fldsgn::filters::InterlockingAromaFilterCreator , protocols::fldsgn::filters::SheetTopologyFilterCreator , protocols::protein_interface_design::filters::BoltzmannFilterCreator , protocols::ligand_docking::MolecularMassFilterCreator , protocols::protein_interface_design::filters::AtomicContactCountFilterCreator , protocols::protein_interface_design::filters::AverageDegreeFilterCreator , protocols::protein_interface_design::filters::HbondsToResidueFilterCreator , protocols::protein_interface_design::filters::TorsionCreator , protocols::simple_filters::AtomicContactFilterCreator , protocols::simple_filters::DeltaFilterCreator , protocols::protein_interface_design::filters::RelativeSegmentFilterCreator , protocols::simple_filters::BuriedUnsatHbondFilterCreator , protocols::simple_filters::NeighborTypeFilterCreator , protocols::simple_filters::ReportFilterCreator , protocols::protein_interface_design::filters::SequenceRecoveryFilterCreator , protocols::simple_filters::ScoreCutoffFilterCreator , protocols::filters::FalseFilterCreator , protocols::enzdes::RepackWithoutLigandFilterCreator , protocols::filters::CombinedFilterCreator , protocols::simple_filters::SigmoidFilterCreator , protocols::enzdes::LigBurialFilterCreator , protocols::filters::CompoundFilterCreator , protocols::filters::StochasticFilterCreator , protocols::filters::TimeFilterCreator , protocols::filters::IfThenFilterCreator , protocols::fldsgn::filters::CoreDunbrackFilterCreator , protocols::simple_filters::SidechainRmsdFilterCreator , protocols::filters::ReplicateFilterCreator , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilterCreator , protocols::filters::TrueFilterCreator , protocols::filters::FilterCreator , protocols::fldsgn::filters::HSSTripletFilterCreator , protocols::fldsgn::filters::SecondaryStructureFilterCreator , protocols::ligand_docking::ChainExistsFilterCreator , protocols::fldsgn::filters::NcontactsFilterCreator , protocols::ligand_docking::CompleteConnectionsFilterCreator , protocols::ligand_docking::HeavyAtomFilterCreator , protocols::simple_filters::FileRemoveFilterCreator , protocols::ligand_docking::AtomCountFilterCreator , protocols::ligand_docking::MolarMassFilterCreator , protocols::simple_filters::OperatorFilterCreator , protocols::ligand_docking::HBondDonorFilterCreator , protocols::simple_filters::ResidueIEFilterCreator
• create_filters() : protocols::match::output::ProcessorFactory
• create_flexbb_interaction_graph() : protocols::flexpack::interaction_graph::FlexbbIGFactory
• create_fold_tree_with_cutpoints() : protocols::ligand_docking::MinimizeBackbone
• create_fold_tree_with_ligand_jumps_from_attach_pts() : protocols::ligand_docking::MinimizeBackbone
• create_fragment_and_rigid_mover() : protocols::medal::MedalMover
• create_fragment_mover() : protocols::medal::MedalMover
• create_fragment_movers() : protocols::forge::remodel::RemodelLoopMover
• create_fragments() : protocols::seeded_abinitio::PlaceFragments
• create_fresh_packer_neighbor_graph() : protocols::simple_moves::GreenPacker
• create_fresh_rotamers() : protocols::simple_moves::GreenPacker
• create_fresh_task() : protocols::simple_moves::GreenPacker
• create_grid() : protocols::qsar::scoring_grid::RepGridCreator , protocols::qsar::scoring_grid::ChargeGridCreator , protocols::qsar::scoring_grid::GridCreator , protocols::qsar::scoring_grid::HbdGridCreator , protocols::qsar::scoring_grid::VdwGridCreator , protocols::qsar::scoring_grid::AtrGridCreator , protocols::qsar::scoring_grid::VdwGridCreator , protocols::qsar::scoring_grid::SolvationMetaGridCreator , protocols::qsar::scoring_grid::SolvationGridCreator , protocols::qsar::scoring_grid::HbdGridCreator , protocols::qsar::scoring_grid::HbaGridCreator , protocols::qsar::scoring_grid::SolvationMetaGridCreator , protocols::qsar::scoring_grid::ClassicGridCreator , protocols::qsar::scoring_grid::RepGridCreator , protocols::qsar::scoring_grid::HbaGridCreator , protocols::qsar::scoring_grid::GridCreator , protocols::qsar::scoring_grid::ClassicGridCreator , protocols::qsar::scoring_grid::ChargeGridCreator
• create_grid_for_bb() : protocols::match::Bool3DGrid
• create_grid_for_sphere() : protocols::match::Bool3DGrid
• create_grouper() : protocols::match::output::ProcessorFactory
• create_hotspot_after_pose() : protocols::hotspot_hashing::HotspotStubSet
• create_hts_for_chi() : protocols::match::upstream::FullChiSampleSet
• create_inner_cycle() : protocols::loops::loop_mover::refine::LoopRefineInnerCycleFactory
• create_interaction_graph() : core::pack::interaction_graph::InteractionGraphFactory
• create_intrares_count_pair_function() : core::scoring::etable::count_pair::CountPairFactory
• create_job_distributor() : protocols::jd2::JobDistributorFactory
• create_job_inputter() : protocols::jd2::JobDistributorFactory
• create_job_outputter() : protocols::jd2::JobDistributorFactory
• create_JobInputter() : protocols::comparative_modeling::ThreadingJobInputterCreator , protocols::jd2::JD2ResourceManagerJobInputterCreator , protocols::enzdes::EnzdesJobInputterCreator , protocols::jd2::JobInputterCreator , protocols::jd2::SilentFileJobInputterCreator , protocols::features::DatabaseJobInputterCreator , protocols::jd2::PDBJobInputterCreator , protocols::jd2::LazySilentFileJobInputterCreator , protocols::protein_interface_design::ParserJobInputterCreator , protocols::comparative_modeling::GenericJobInputterCreator , protocols::jd2::PoseInputStreamJobInputterCreator , protocols::jd2::AtomTreeDiffJobInputterCreator
• create_JobOutputter() : protocols::jd2::PDBJobOutputterCreator , protocols::jd2::JobOutputterCreator , protocols::jd2::AtomTreeDiffJobOutputterCreator , protocols::jd2::ScoreOnlyJobOutputterCreator , protocols::enzdes::EnzdesJobOutputterCreator , protocols::jd2::SilentFileJobOutputterCreator , protocols::jd2::NoOutputJobOutputterCreator , protocols::features::DatabaseJobOutputterCreator
• create_jump_def() : protocols::abinitio::Templates
• create_jump_fragments() : protocols::jumping::DisulfPairingLibrary , protocols::jumping::PairingLibrary , protocols::jumping::BasePairingLibrary
• create_jump_moves() : protocols::abinitio::KinematicAbinitio , protocols::abinitio::JumpingFoldConstraints
• create_jump_sample() : protocols::jumping::JumpSelector , protocols::jumping::SheetBuilder , protocols::abinitio::FixTemplateJumpSetup , protocols::jumping::BaseJumpSetup , protocols::abinitio::TemplateJumpSetup , protocols::jumping::ResiduePairJumpSetup , protocols::jumping::JumpsFromAllPairings , protocols::jumping::JumpSetup
• create_key() : protocols::frag_picker::VallChunk
• create_large_cluster_centers_member_list() : protocols::swa::rna::StepWiseRNA_Clusterer
• create_loader() : protocols::ligand_docking::InterfaceBuilderLoaderCreator , protocols::jd2::parser::FragSetLoaderCreator , protocols::jd2::parser::MonteCarloLoaderCreator , protocols::ligand_docking::LigandAreaLoaderCreator , protocols::ligand_docking::MoveMapBuilderLoaderCreator , protocols::jd2::parser::TaskOperationLoaderCreator , protocols::loops::loops_definers::LoopsDefinerLoaderCreator , protocols::jd2::parser::DataLoaderCreator , protocols::jd2::parser::ScoreFunctionLoaderCreator , protocols::qsar::scoring_grid::ScoringGridLoaderCreator
• create_loop_mover() : protocols::loops::LoopMoverFactory
• create_loophash_WUs() : protocols::loophash::MPI_LoopHashRefine_Master
• create_loops_definer() : protocols::loops::loops_definers::LoopsDefinerFactory , protocols::loops::loops_definers::LoopsDatabaseDefinerCreator , protocols::loops::loops_definers::LoopsFileDefinerCreator , protocols::loops::loops_definers::LoopsDefinerCreator , protocols::loops::loops_definers::LoopsExplicitDefinerCreator
• create_map_helix_pairings() : protocols::fldsgn::topology::HelixPairingSet
• create_mover() : protocols::seeded_abinitio::GrowPeptidesCreator , protocols::simple_moves::GenericMonteCarloMoverCreator , protocols::simple_moves::MutateResidueCreator , protocols::simple_moves::MinPackMoverCreator , protocols::simple_moves::ConstraintSetMoverCreator , protocols::simple_moves::FavorSequenceProfileCreator , protocols::seeded_abinitio::SeedFoldTreeCreator , protocols::protein_interface_design::movers::FavorNativeResiduePreCycleCreator , protocols::hybridization::CartesianSamplerCreator , protocols::simple_moves::ddGCreator , protocols::simple_moves::CutChainMoverCreator , protocols::simple_moves::AddConstraintsToCurrentConformationMoverCreator , protocols::protein_interface_design::movers::RepackMinimizeCreator , protocols::simple_moves::ShearMoverCreator , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMoverCreator , protocols::simple_moves::symmetry::SetupForSymmetryMoverCreator , protocols::protein_interface_design::movers::SpliceCreator , protocols::protein_interface_design::movers::SpinMoverCreator , protocols::protein_interface_design::movers::PlaceSimultaneouslyMoverCreator , protocols::seeded_abinitio::DefineMovableLoopsCreator , protocols::protein_interface_design::movers::VLBCreator , protocols::protein_interface_design::movers::ShoveResidueMoverCreator , protocols::protein_interface_design::movers::PlaceStubMoverCreator , protocols::protein_interface_design::movers::SetupHotspotConstraintsMoverCreator , protocols::rotamer_recovery::RotamerRecoveryMoverCreator , protocols::seeded_abinitio::CloseFoldCreator , protocols::seeded_abinitio::CAcstGeneratorCreator , protocols::rigid::RigidBodyPerturbNoCenterMoverCreator , protocols::qsar::RenderGridsToKinemageCreator , protocols::rosetta_scripts::ParsedProtocolCreator , protocols::rigid::RollMoverCreator , protocols::qsar::scoring_grid::GridInitMoverCreator , protocols::relax::ClassicRelaxCreator , protocols::protein_interface_design::movers::TaskAwareCstsCreator , protocols::protein_interface_design::movers::SetAtomTreeCreator , protocols::seeded_abinitio::SegmentHybridizerCreator , protocols::protein_interface_design::movers::SetTemperatureFactorCreator , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMoverCreator , protocols::simple_moves::ClearConstraintsMoverCreator , protocols::protein_interface_design::movers::RandomMutationCreator , protocols::simple_moves::DumpPdbCreator , protocols::motifs::MotifDnaPackerCreator , protocols::simple_moves::MakePolyXMoverCreator , protocols::simple_moves::MembraneTopologyCreator , protocols::simple_moves::LoadUnboundRotMoverCreator , protocols::simple_moves::ModifyVariantTypeMoverCreator , protocols::simple_moves::PackRotamersMoverCreator , protocols::simple_moves::symmetry::ExtractAsymmetricPoseMoverCreator , protocols::protein_interface_design::movers::PlaceOnLoopCreator , protocols::protein_interface_design::movers::DisulfideMoverCreator , protocols::simple_moves::SetTorsionCreator , protocols::enzdes::AddOrRemoveMatchCstsCreator , protocols::simple_moves::SequenceProfileMoverCreator , protocols::protein_interface_design::movers::PeptideStapleDesignMoverCreator , protocols::loops::loop_mover::refine::LoopMover_Refine_CCDCreator , protocols::simple_moves::sidechain_moves::SetChiMoverCreator , protocols::protein_interface_design::movers::LoopOverCreator , protocols::simple_moves::SaneMinMoverCreator , protocols::canonical_sampling::MetropolisHastingsMoverCreator , protocols::moves::RampingMoverCreator , protocols::idealize::IdealizeMoverCreator , protocols::simple_moves::SwitchChainOrderMoverCreator , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMoverCreator , protocols::protein_interface_design::movers::BackrubDDMoverCreator , protocols::loophash::LoopHashDiversifierCreator , protocols::simple_moves::symmetry::SymRotamerTrialsMoverCreator , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMoverCreator , protocols::seeded_abinitio::CoordinateCstCreator , protocols::simple_moves::ForceDisulfidesMoverCreator , protocols::nonlocal::SingleFragmentMoverCreator , protocols::pb_potential::SetupPoissonBoltzmannPotentialCreator , protocols::ligand_docking::TranslateCreator , protocols::protein_interface_design::movers::TryRotamersCreator , protocols::relax::FastRelaxCreator , protocols::loops::loop_mover::refine::LoopMover_Refine_KICCreator , protocols::protein_interface_design::movers::DesignMinimizeHbondsCreator , protocols::protein_interface_design::movers::DockAndRetrieveSidechainsCreator , protocols::moves::IfMoverCreator , protocols::loops::loop_mover::refine::RepackTrialCreator , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_MovesCreator , protocols::ligand_docking::InterfaceScoreCalculatorCreator , protocols::dna::DnaInterfacePackerCreator , protocols::forge::remodel::RemodelLoopMoverCreator , protocols::loops::FoldTreeFromLoopsCreator , protocols::docking::ConformerSwitchMoverCreator , protocols::flxbb::InterlockAromaCreator , protocols::ligand_docking::RotateCreator , protocols::enzdes::BackboneSamplerCreator , protocols::ligand_docking::SlideTogetherCreator , protocols::flexpep_docking::FlexPepDockingProtocolCreator , protocols::ligand_docking::FinalMinimizerCreator , protocols::ligand_docking::RandomConformersCreator , protocols::fldsgn::potentials::SetAACompositionPotentialCreator , protocols::loops::loop_mover::refine::LoopMover_Refine_BackrubCreator , protocols::canonical_sampling::PDBTrajectoryRecorderCreator , protocols::hotspot_hashing::movers::PlaceSurfaceProbeCreator , protocols::forge::constraints::InvrotTreeCstGeneratorCreator , protocols::forge::constraints::RemoveCstsCreator , protocols::forge::constraints::NtoCCstGeneratorCreator , protocols::flxbb::FlxbbDesignCreator , protocols::simple_moves::PDBReloadMoverCreator , protocols::fldsgn::CircularPermutationCreator , protocols::enzdes::PackRotamersMoverPartGreedyCreator , protocols::features::ReportToDBCreator , protocols::fldsgn::SheetCstGeneratorCreator , protocols::fldsgn::BluePrintBDRCreator , protocols::enzdes::EnzRepackMinimizeCreator , protocols::canonical_sampling::SilentTrajectoryRecorderCreator , protocols::docking::DockSetupMoverCreator , protocols::canonical_sampling::MetricRecorderCreator , protocols::docking::TemperedDockingCreator , protocols::dna::SeparateDnaFromNonDnaCreator , protocols::design_opt::ParetoOptMutationMoverCreator , protocols::docking::DockingInitialPerturbationCreator , protocols::comparative_modeling::LoopRelaxMoverCreator , protocols::design_opt::GreedyOptMutationMoverCreator , protocols::canonical_sampling::SimulatedTemperingCreator , protocols::canonical_sampling::SidechainMetropolisHastingsMoverCreator , protocols::backrub::BackrubSidechainMoverCreator , protocols::electron_density::SetupForDensityScoringMoverCreator , protocols::analysis::InterfaceAnalyzerMoverCreator , protocols::backrub::BackrubMoverCreator , protocols::dna::DnaInterfaceMultiStateDesignCreator , protocols::forge::constraints::ConstraintFileCstGeneratorCreator , protocols::canonical_sampling::ParallelTemperingCreator , protocols::abinitio::DomainAssemblyCreator , protocols::enzdes::PredesignPerturbMoverCreator , protocols::dna::DnaInterfaceMinMoverCreator , protocols::dna::DesignProteinBackboneAroundDNACreator , protocols::contact_map::ContactMapCreator , protocols::simple_moves::ConsensusDesignMoverCreator , protocols::simple_moves::MonteCarloRecoverCreator , protocols::simple_moves::SuperimposeMoverCreator , protocols::rosetta_scripts::SavePoseMoverCreator , protocols::seeded_abinitio::SwapSegmentCreator , protocols::simple_moves::SmallMoverCreator , protocols::protein_interface_design::movers::MapHotspotCreator , protocols::simple_moves::MonteCarloTestCreator , protocols::protein_interface_design::movers::PlacementAuctionMoverCreator , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMoverCreator , protocols::ligand_docking::StartFromCreator , protocols::simple_moves::SwitchResidueTypeSetMoverCreator , protocols::protein_interface_design::movers::InterfaceRecapitulationMoverCreator , protocols::simple_moves::RotamerTrialsMoverCreator , protocols::moves::DsspMoverCreator , protocols::simple_moves::sidechain_moves::SidechainMCMoverCreator , protocols::simple_moves::symmetry::SymPackRotamersMoverCreator , protocols::simple_moves::symmetry::SymMinMoverCreator , protocols::loops::loop_mover::perturb::LoopMover_Perturb_KICCreator , protocols::docking::DockingProtocolCreator , protocols::ligand_docking::AddHydrogensCreator , protocols::ligand_docking::MinimizeBackboneCreator , protocols::ligand_docking::GrowLigandCreator , protocols::ligand_docking::LigandDesignCreator , protocols::fldsgn::potentials::SetSecStructEnergiesCreator , protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCDCreator , protocols::ligand_docking::HighResDockerCreator , protocols::forge::remodel::ResidueVicinityCstGeneratorCreator , protocols::forge::remodel::RemodelMoverCreator , protocols::ligand_docking::RotatesCreator , protocols::seeded_abinitio::SeedSetupMoverCreator , protocols::protein_interface_design::movers::AddChainBreakCreator , protocols::canonical_sampling::HamiltonianExchangeCreator , protocols::canonical_sampling::TrialCounterObserverCreator , protocols::protein_interface_design::movers::BuildAlaPoseCreator , protocols::fldsgn::MatchResiduesMoverCreator , protocols::forge::constraints::InverseRotamersCstGeneratorCreator , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCDCreator , protocols::simple_moves::ScoreMoverCreator , protocols::ligand_docking::TransformCreator , protocols::loop_build::LoopMover_SlidingWindowCreator , protocols::simple_moves::LoadPDBMoverCreator , protocols::simple_moves::MinMoverCreator , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainerCreator , protocols::simple_moves::RotamerTrialsMinMoverCreator , protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycleCreator , protocols::protein_interface_design::movers::LoopFinderCreator , protocols::match::MatcherMoverCreator , protocols::moves::RandomMoverCreator , protocols::protein_interface_design::movers::BestHotspotCstMoverCreator , protocols::protein_interface_design::movers::SubroutineMoverCreator , protocols::ligand_docking::CompoundTranslateCreator , protocols::moves::IteratedConvergenceMoverCreator , protocols::moves::MoverCreator , protocols::simple_moves::symmetry::ExtractAsymmetricUnitMoverCreator , protocols::simple_moves::ExtendedPoseMoverCreator , protocols::protein_interface_design::movers::SaveAndRetrieveSidechainsCreator , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspotsCreator , protocols::protein_interface_design::movers::LoopRemodelCreator , protocols::protein_interface_design::movers::HotspotHasherMoverCreator , protocols::simple_moves::symmetry::DetectSymmetryMoverCreator , protocols::simple_moves::TaskAwareMinMoverCreator , protocols::protein_interface_design::movers::PlacementMinimizationMoverCreator , protocols::protein_interface_design::movers::PrepackMoverCreator , protocols::simple_moves::RepackSidechainsMoverCreator , protocols::qsar::qsarCreator , protocols::loops::loop_mover::refine::ShearMinCCDTrialCreator , protocols::loops::loop_mover::refine::SmallMinCCDTrialCreator , protocols::simple_moves::sidechain_moves::SidechainMoverCreator , protocols::protein_interface_design::movers::LoopMoverFromCommandLineCreator , protocols::loophash::LoopHashMoverWrapperCreator , protocols::protein_interface_design::movers::LoopLengthChangeCreator , protocols::hybridization::HybridizeProtocolCreator , protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMoverCreator , protocols::simple_moves::symmetry::SetupNCSMoverCreator
• create_new_block() : core::graph::ArrayPool< T >
• create_new_bump_grid_for_bb() : protocols::match::BumpGrid
• create_new_edge() : core::scoring::MinimizationGraph , core::scoring::TwelveANeighborGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::graph::Graph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DensePDInteractionGraph , core::graph::Graph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::FASTERInteractionGraph , core::scoring::constraints::ConstraintGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , core::scoring::constraints::ConstraintGraph , core::pack::interaction_graph::LazyInteractionGraph , core::scoring::TwelveANeighborGraph , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::scoring::EnergyGraph , core::pack::interaction_graph::InteractionGraphBase , core::scoring::MinimizationGraph , core::scoring::EnergyGraph , core::scoring::TenANeighborGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , core::scoring::TenANeighborGraph
• create_new_node() : core::scoring::TwelveANeighborGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::scoring::TenANeighborGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::scoring::MinimizationGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::graph::Graph , core::scoring::constraints::ConstraintGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::InteractionGraphBase , core::scoring::EnergyGraph
• create_new_random_topol() : protocols::jumping::RandomSheetBuilder , protocols::jumping::SheetBuilder
• create_options() : core::scoring::electron_density::ElectronDensityOptionsCreator , core::conformation::symmetry::SymmDataOptionsCreator , core::chemical::ResidueLoaderOptionsCreator , core::io::silent::SilentFileOptionsCreator , protocols::loops::LoopsFileOptionsCreator , core::import_pose::ImportPoseOptionsCreator
• create_output_upstream_pose() : protocols::match::output::PDBWriter
• create_output_writer() : protocols::match::output::ProcessorFactory
• create_packer_data() : protocols::multistate_design::PackingState
• create_packer_task() : core::pack::task::TaskFactory
• create_parameters_for_restype() : core::scoring::methods::IdealParametersDatabase
• create_parser() : protocols::jd2::JobDistributorFactory
• create_partitioned_search_pattern() : protocols::hotspot_hashing::movers::PlaceSurfaceProbe , protocols::hotspot_hashing::movers::PlaceProbeMover
• create_pddf() : protocols::scoring::methods::saxs::PDDFEnergy
• create_per_loop_fragment_movers() : protocols::forge::remodel::RemodelLoopMover
• create_pose_reference() : protocols::simple_moves::ConstrainToIdealMover
• create_position_data() : protocols::optimize_weights::OptEPositionDataFactory
• create_processor() : protocols::match::output::ProcessorFactory
• create_protocol() : protocols::rotamer_recovery::RRProtocolPackRotamersCreator , protocols::rotamer_recovery::RRProtocolReferenceStructureCreator , protocols::rotamer_recovery::RRProtocolMinPackCreator , protocols::rotamer_recovery::RRProtocolMoverCreator , protocols::rotamer_recovery::RRProtocolRotamerTrialsCreator , protocols::rotamer_recovery::RRProtocolRTMinCreator , protocols::rotamer_recovery::RRProtocolCreator
• create_ptask() : protocols::enzdes::EnzRepackMinimize
• create_random_rotation() : protocols::ligand_docking::Rotate
• create_random_rotations() : protocols::ligand_docking::Rotate
• create_reference_packer_neighbor_graph() : protocols::simple_moves::GreenPacker
• create_reference_packer_task() : protocols::simple_moves::GreenPacker
• create_reference_rotamers() : protocols::simple_moves::GreenPacker
• create_refinement_packing_task() : protocols::hotspot_hashing::movers::PlaceProbeMover
• create_refinement_pattern() : protocols::hotspot_hashing::movers::PlaceProbeMover , protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• create_reporter() : protocols::rotamer_recovery::RRReporterSimpleCreator , protocols::rotamer_recovery::RRReporterSQLiteCreator , protocols::rotamer_recovery::RRReporterHumanCreator , protocols::rotamer_recovery::RRReporterCreator
• create_res_filter() : core::pack::task::operation::AllResFilterCreator , core::pack::task::operation::ResidueName3IsntCreator , core::pack::task::operation::ResidueName3IsCreator , core::pack::task::operation::ResFilterCreator , core::pack::task::operation::ResidueTypeFilterCreator , core::pack::task::operation::ResidueHasPropertyCreator , core::pack::task::operation::ChainIsCreator , core::pack::task::operation::ChainIsntCreator , core::pack::task::operation::ResiduePDBIndexIsCreator , core::pack::task::operation::ResidueIndexIsntCreator , core::pack::task::operation::AnyResFilterCreator , core::pack::task::operation::ResidueIndexIsCreator , core::pack::task::operation::NoResFilterCreator , core::pack::task::operation::ResidueLacksPropertyCreator , protocols::toolbox::task_operations::ProteinCoreFilterCreator , core::pack::task::operation::ResiduePDBIndexIsntCreator
• create_res_level_task_operation() : core::pack::task::operation::PreventRepackingRLTCreator , core::pack::task::operation::DisallowIfNonnativeRLTCreator , core::pack::task::operation::RestrictToRepackingRLTCreator , core::pack::task::operation::AddBehaviorRLTCreator , core::pack::task::operation::ResLvlTaskOperationCreator , core::pack::task::operation::RestrictAbsentCanonicalAASRLTCreator
• create_residue() : core::conformation::Residue , core::conformation::ResidueFactory
• create_residue_from_resname_() : protocols::simple_moves::HelicalPeptideLengthMover
• create_resource() : core::scoring::electron_density::ElectronDensityLoader , protocols::loops::LoopsFileLoader , core::io::silent::SilentFileLoader , core::conformation::symmetry::SymmDataLoader , core::import_pose::PoseFromPDBLoader , core::chemical::ResidueLoader
• create_resource_from_fallback() : protocols::jd2::JD2ResourceManager
• create_resource_loader() : core::conformation::symmetry::SymmDataLoaderCreator , core::io::silent::SilentFileLoaderCreator , core::chemical::ResidueLoaderCreator , core::scoring::electron_density::ElectronDensityLoaderCreator , core::import_pose::PoseFromPDBLoaderCreator , protocols::loops::LoopsFileLoaderCreator
• create_resource_manager() : protocols::jd2::JD2ResourceManagerCreator
• create_rigid_body_movers() : protocols::ligand_docking::HighResDocker
• create_rotamer() : core::conformation::Residue
• create_rotamer_set() : core::pack::rotamer_set::RotamerSetFactory , protocols::protein_interface_design::movers::MapHotspot , core::pack::rotamer_set::symmetry::SymmetricRotamerSetFactory
• create_rotamer_string() : protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler
• create_rotamer_subsets_from_rot_to_pack() : protocols::pack_daemon::RotamerSubsetRepacker
• create_rotamer_trie() : core::scoring::methods::MMLJEnergyInter , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::MMLJEnergyInter , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hackelec::HackElecEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::hackelec::HackElecEnergy
• create_rotamer_trie_1() : core::scoring::etable::BaseEtableEnergy< Derived >
• create_rotamer_trie_2() : core::scoring::etable::BaseEtableEnergy< Derived >
• create_rotameric_dunlib() : core::pack::dunbrack::RotamerLibrary
• create_rotamers_from_chisets() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
• create_rules() : core::coarse::RuleSet
• create_sample_vector() : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• create_scalar_and_vector_expression_variable_expressions() : protocols::pack_daemon::DynamicAggregateFunction
• create_score_function() : core::scoring::ScoreFunctionFactory
• create_scores() : protocols::frag_picker::scores::FragmentScoreManager
• create_scoring_method() : protocols::frag_picker::scores::FragmentScoreManager
• create_search_pattern() : protocols::hotspot_hashing::movers::PlaceSurfaceProbe , protocols::hotspot_hashing::movers::PlaceProbeMover
• create_SecMatchResiduePairEvaluatorOP() : protocols::match::downstream::SecMatchEvaluatorFactory
• create_semaphore() : protocols::boinc::Boinc
• create_semi_rotameric_dunlib() : core::pack::dunbrack::RotamerLibrary
• create_sequence() : core::sequence::SequenceCouplingCreator , core::sequence::CompositeSequenceCreator , core::sequence::SequenceProfileCreator , core::sequence::SimpleSequenceCreator , core::sequence::ChemicalShiftSequenceCreator , core::sequence::SequenceCreator
• create_sequence_profile_constraints() : protocols::simple_moves::ConsensusDesignMover
• create_silent_file_and_tag_list() : protocols::swa::rna::StepWiseRNA_Clusterer
• create_silent_struct() : core::io::silent::ScoreFileSilentStructCreator , core::io::silent::SilentStructCreator , core::io::silent::ProteinSilentStruct_SinglePrecCreator , core::io::silent::ProteinSilentStructCreator , core::io::silent::BinaryProteinSilentStructCreator , core::io::silent::RNA_SilentStructCreator , core::io::silent::BinaryRNASilentStructCreator , core::import_pose::PDBSilentStructCreator
• create_SilentStructOP() : core::io::silent::SilentFileData
• create_sliced_pose() : protocols::swa::rna::SlicedPoseJobParameters
• create_small_mover() : protocols::medal::MedalMover
• create_srdl() : core::pack::dunbrack::RotamerLibrary
• create_state_variable_expressions() : protocols::pack_daemon::DynamicAggregateFunction
• create_sub_to_full_map() : protocols::swa::StepWiseJobParameters , protocols::swa::rna::StepWiseRNA_JobParameters
• create_subpose() : protocols::simple_moves::CutChainMover
• create_symm_data() : core::conformation::symmetry::SymmDataFactory
• create_tag() : protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler
• create_tags_map() : protocols::swa::rna::StepWiseRNA_Clusterer
• create_task_and_apply_taskoperations() : core::pack::task::TaskFactory
• create_task_for_hotspot_packing() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• create_task_operation() : protocols::toolbox::task_operations::SetIGTypeOperationCreator , protocols::enzdes::DetectProteinLigandInterfaceOperationCreator , core::pack::task::operation::ReplicateTaskCreator , core::pack::task::operation::AppendRotamerSetCreator , protocols::toolbox::task_operations::RestrictResiduesToRepackingOperationCreator , protocols::toolbox::task_operations::ProteinInterfaceDesignOperationCreator , protocols::toolbox::task_operations::RestrictToNeighborhoodOperationCreator , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperationCreator , protocols::toolbox::task_operations::RestrictToCDRH3LoopCreator , core::pack::task::operation::ExtraRotamersCreator , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperationCreator , protocols::toolbox::task_operations::RestrictConservedLowDdgOperationCreator , core::pack::task::operation::ReadResfileCreator , protocols::toolbox::task_operations::ThreadSequenceOperationCreator , core::pack::task::operation::AppendRotamerCreator , core::pack::task::operation::IncludeCurrentCreator , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperationCreator , core::pack::task::operation::AppendResidueRotamerSetCreator , protocols::toolbox::task_operations::LimitAromaChi2OperationCreator , core::pack::task::operation::OptCysHGCreator , core::pack::task::operation::TaskOperationCreator , protocols::enzdes::AddLigandMotifRotamersOperationCreator , protocols::toolbox::task_operations::RestrictInterGroupVectorOperationCreator , core::pack::task::operation::InitializeExtraRotsFromCommandlineCreator , protocols::enzdes::SetCatalyticResPackBehaviorCreator , protocols::toolbox::task_operations::RestrictToLoopsAndNeighborsCreator , protocols::toolbox::task_operations::RestrictChainToRepackingOperationCreator , core::pack::task::operation::ExtraChiCutoffCreator , protocols::toolbox::task_operations::JointSequenceOperationCreator , core::pack::task::operation::ReadResfileAndObeyLengthEventsCreator , protocols::toolbox::task_operations::ModifyAnnealerCreator , core::pack::task::operation::DisallowIfNonnativeCreator , protocols::toolbox::task_operations::RestrictToInterfaceOperationCreator , core::pack::task::operation::PreserveCBetaCreator , protocols::toolbox::task_operations::SeqprofConsensusOperationCreator , core::pack::task::operation::NoRepackDisulfidesCreator , protocols::forge::remodel::RemodelRotamerLinksCreator , protocols::toolbox::task_operations::RestrictToInterfaceCreator , core::pack::task::operation::RestrictAbsentCanonicalAASCreator , protocols::enzdes::AddRigidBodyLigandConfsCreator , core::pack::task::operation::RestrictYSDesignCreator , protocols::toolbox::task_operations::RestrictNonSurfaceToRepackingOperationCreator , protocols::dna::RestrictDesignToProteinDNAInterfaceCreator , protocols::toolbox::task_operations::RestrictByCalculatorsOperationCreator , protocols::flxbb::LayerDesignOperationCreator , protocols::toolbox::task_operations::SelectBySASAOperationCreator , protocols::toolbox::task_operations::DesignAroundOperationCreator , core::pack::task::operation::RestrictToRepackingCreator , protocols::enzdes::ProteinLigandInterfaceUpweighterOperationCreator , core::pack::task::operation::OptHCreator , core::pack::task::operation::SetRotamerCouplingsCreator , core::pack::task::operation::PreventRepackingCreator , core::pack::task::operation::InitializeFromCommandlineCreator , protocols::toolbox::task_operations::ReadResfileFromDBCreator , core::pack::task::operation::RestrictResidueToRepackingCreator , core::pack::task::operation::SetRotamerLinksCreator , core::pack::task::operation::OperateOnCertainResiduesCreator , protocols::toolbox::task_operations::PreventResiduesFromRepackingOperationCreator , protocols::dna::WatsonCrickRotamerCouplingsCreator , protocols::toolbox::task_operations::PreventChainFromRepackingOperationCreator , core::pack::task::operation::RotamerExplosionCreator , protocols::toolbox::task_operations::RestrictToTerminiOperationCreator , core::pack::task::operation::ExtraRotamersGenericCreator , protocols::toolbox::task_operations::RestrictNativeResiduesOperationCreator
• create_torsion_value_string() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler
• create_torsions() : protocols::rna::RNA_suite_list
• create_unique_id() : protocols::wum2::WorkUnit , protocols::wum::WorkUnitBase
• create_unweighted_scorefunction() : protocols::optimize_weights::IterativeOptEDriver
• create_variable_vector_expressions() : protocols::pack_daemon::DynamicAggregateFunction
• create_VDW_rep_screen_pose() : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• create_VDW_screen_bin() : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• create_vertices() : core::graph::UpperEdgeGraph< V, E >
• create_weighted_scorefunction() : protocols::optimize_weights::IterativeOptEDriver
• create_work_units_from_query() : protocols::wum::DatabaseQueryWorkUnitManager< T >
• create_working_data() : core::io::pdb::FileData
• create_xyz_constraints_median() : protocols::toolbox::DecoySetEvaluation
• createAngleList() : protocols::cartesian::MolecularDynamics
• createBondList() : protocols::cartesian::MolecularDynamics
• createCartesianArray() : protocols::cartesian::MolecularDynamics
• createCartesianDerivatives() : protocols::cartesian::MolecularDynamics
• createConstraints() : protocols::cluster::EnsembleConstraints , protocols::cluster::EnsembleConstraints_Simple
• createDihedral() : protocols::cartesian::MolecularDynamics
• createDihedralList() : protocols::cartesian::MolecularDynamics
• createFileData() : core::io::pdb::PDB_DReader
• createPDBData() : core::io::pdb::PDB_DReader
• createPDBData_vector() : core::io::pdb::PDB_DReader
• createPDBString() : core::io::pdb::PDB_DReader
• createRecords() : core::io::pdb::PDB_DReader
• creates_undefined_backbone() : protocols::forge::build::BuildInstruction , protocols::forge::build::GrowLeft , protocols::forge::build::SegmentRebuild , protocols::forge::build::GrowRight , protocols::forge::build::SegmentSwap , protocols::forge::build::ConnectRight , protocols::forge::build::SegmentInsert , protocols::forge::build::Bridge
• cross_angle() : protocols::fldsgn::topology::HelixPairing
• cross_over() : core::optimization::GA_Minimizer , protocols::fldsgn::topology::BetaAlphaBetaMotif
• cross_product_helper() : core::chemical::orbitals::AssignOrbitals
• crossover() : protocols::genetic_algorithm::EntityRandomizer , core::scoring::etable::etrie::TrieCountPairGeneric
• CrossPeak() : protocols::noesy_assign::CrossPeak
• crosspeak() : protocols::noesy_assign::PeakAssignment
• CrossPeak() : protocols::noesy_assign::CrossPeak
• CrossPeak3D() : protocols::noesy_assign::CrossPeak3D
• CrossPeak4D() : protocols::noesy_assign::CrossPeak4D
• CrossPeakInfo() : protocols::noesy_assign::CrossPeakInfo
• CrossPeakList() : protocols::noesy_assign::CrossPeakList
• crosspeaks() : protocols::noesy_assign::NoesyModule
• CS2ndShift() : protocols::frag_picker::CS2ndShift
• CSA() : core::scoring::CSA
• csa_from_pose() : core::scoring::methods::ChemicalShiftAnisotropyEnergy
• CSAcomputed() : core::scoring::CSA
• CSAerr() : core::scoring::CSA
• CSAval() : core::scoring::CSA
• CSD_TorsionEnergy() : core::scoring::methods::CSD_TorsionEnergy
• CSDAtomType() : core::chemical::CSDAtomType
• CSDAtomTypeSet() : core::chemical::CSDAtomTypeSet
• CSP_fraction() : protocols::ub_e2c::ubi_e2c_modeler
• CSScore() : protocols::frag_picker::scores::CSScore
• cst_block() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters , protocols::toolbox::match_enzdes_util::CstResInteractions
• cst_cache() : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• cst_cleanup() : protocols::protein_interface_design::movers::PlaceStubMover
• cst_interactions() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• cst_io() : protocols::match::output::OutputWriter
• cst_max_seq_sep() : core::scoring::methods::EnergyMethodOptions
• cst_minimize() : protocols::enzdes::EnzdesBaseProtocol
• cst_type() : protocols::protein_interface_design::movers::TaskAwareCsts
• CSTalosIO() : protocols::frag_picker::CSTalosIO
• cstAtoms() : protocols::jumping::ResiduePairJump , protocols::jumping::ResiduePairJumpSingle
• cstAtoms_defined() : protocols::jumping::ResiduePairJumpSingle , protocols::jumping::ResiduePairJump
• CstEnergyContainer() : core::scoring::constraints::CstEnergyContainer
• cstfile() : protocols::enzdes::AddOrRemoveMatchCsts
• cstfile_name() : protocols::match::MatcherTask , protocols::match::output::PDBWriter
• cstInfoMap_defined() : protocols::jumping::ResiduePairJump
• CstMinimizationData() : core::scoring::constraints::CstMinimizationData
• CstResInteractions() : protocols::toolbox::match_enzdes_util::CstResInteractions
• CstResNeighbConstIterator() : core::scoring::constraints::CstResNeighbConstIterator
• CstResNeighbIterator() : core::scoring::constraints::CstResNeighbIterator
• CtabBase() : core::chemical::sdf::CtabBase
• ctabV2000Parser() : core::chemical::sdf::ctabV2000Parser
• ctabV3000Parser() : core::chemical::sdf::ctabV3000Parser
• ctor() : protocols::loops::loop_closure::kinematic_closure::KinematicWrapper
• cubic_interpolation() : core::optimization::LineMinimizationAlgorithm
• cull_mutatable_residues() : protocols::vip::VIP_Mover
• cull_violators() : protocols::abinitio::Template
• cumulate_jobs() : protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::TrajectoryRecorder
• cumulate_replicas() : protocols::canonical_sampling::TrajectoryRecorder , protocols::canonical_sampling::MetricRecorder
• cumulative_peak_volume() : protocols::noesy_assign::CrossPeak
• cur_energy() : protocols::flexpack::interaction_graph::FlexbbEdge
• curr_bb() : protocols::flexpack::interaction_graph::FlexbbNode
• curr_sc_centroid() : core::pack::interaction_graph::SimpleNode
• curr_sc_radius() : core::pack::interaction_graph::SimpleNode
• curr_state_energy() : core::pack::interaction_graph::SymmMinimalistEdge
• curr_state_exp_hphobes() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• curr_state_hphobes() : core::pack::interaction_graph::HPatchNode< V, E, G >
• curr_state_inv_dots() : core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• curr_state_one_body_energy() : protocols::flexpack::interaction_graph::FlexbbNode
• curr_state_rotamer() : core::pack::interaction_graph::HPatchNode< V, E, G >
• curr_state_total_energy() : protocols::flexpack::interaction_graph::FlexbbNode
• curr_state_two_body_energies() : protocols::flexpack::interaction_graph::FlexbbNode
• current_acceptance_ratio() : protocols::jd2::archive::ArchiveBase
• current_base_state() : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• current_batch_id() : protocols::jd2::JobDistributor
• current_binary_format_version_id_02() : core::pack::dunbrack::RotamerLibrary
• current_binary_format_version_id_10() : core::pack::dunbrack::RotamerLibrary
• current_cycle_number() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• current_dna_design_string() : protocols::dna::DnaInterfacePacker
• current_generation() : protocols::genetic_algorithm::GeneticAlgorithm
• current_generation_complete() : protocols::genetic_algorithm::GeneticAlgorithm
• current_job() : protocols::jd2::JobDistributor , protocols::jobdist::BaseJobDistributor
• current_job_finished() : protocols::jd2::JobDistributor , protocols::jd2::FileSystemJobDistributor
• current_job_id() : protocols::jd2::JobDistributor
• current_kinematics() : protocols::abinitio::KinematicTaskControl
• current_mem() : protocols::wum2::WUQueue , protocols::wum2::EndPoint
• current_nstruct() : protocols::jobdist::BaseJobDistributor
• current_one_body_energy() : core::pack::interaction_graph::SimpleNode
• current_output_name() : protocols::jd2::JobDistributor
• current_pose() : protocols::topology_broker::TopologyBroker
• current_pucker_state() : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• current_rot_index() : core::pack::annealer::SimAnnealerBase
• current_rotamer_coords() : core::pack::rotamer_set::ContinuousRotamerSet
• current_score() : protocols::simple_moves::GenericMonteCarloMover
• current_scorefxn() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• current_size() : protocols::frag_picker::quota::SecondaryStructurePool , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaPool
• current_state() : protocols::flexpack::interaction_graph::FlexbbNode
• current_state_info() : protocols::flexpack::interaction_graph::FlexbbNode
• current_tag() : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• current_temp() : protocols::canonical_sampling::TemperingBase
• current_trial() : protocols::flxbb::FilterStructs
• current_working_sequence() : protocols::dna::DnaInterfacePacker
• CustomAtomPairEnergy() : core::scoring::methods::CustomAtomPairEnergy
• CustomScoreSelector() : protocols::frag_picker::CustomScoreSelector
• cut() : protocols::loops::Loop
• cut_bond_neighbor() : core::conformation::Residue , core::chemical::ResidueType
• cut_edge() : core::kinematics::FoldTree
• cut_random_edge() : core::kinematics::FoldTree
• cut_secondarystruc() : protocols::protein_interface_design::movers::Splice
• cut_site() : protocols::protein_interface_design::movers::ResidueBBDofs
• CutBiasClaimer() : protocols::topology_broker::CutBiasClaimer
• CutChainMover() : protocols::simple_moves::CutChainMover
• CutClaim() : protocols::topology_broker::CutClaim
• cutoff() : protocols::simple_filters::PDDFScoreFilter , protocols::simple_filters::SAXSScoreFilter , protocols::simple_filters::PDDFScoreFilter , protocols::simple_filters::ScoreCutoffFilter , core::scoring::CenHBPotential , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_moves::FragmentCost
• cutoff_distance() : protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors
• cutoff_lower() : core::scoring::constraints::FadeFunc
• cutoff_upper() : core::scoring::constraints::FadeFunc
• cutpoint() : core::kinematics::FoldTree
• cutpoint_by_jump() : core::kinematics::FoldTree
• cutpoint_closed_list() : protocols::swa::rna::StepWiseRNA_JobParameters
• cutpoint_map() : core::kinematics::FoldTree
• cutpoint_res() : protocols::loops::LoopFromFileData
• cutpoint_separation() : protocols::antibody::CDRH3Modeler
• cutpoints() : core::kinematics::FoldTree , protocols::star::Extender
• cutpoints_in_full_pose() : protocols::swa::monte_carlo::SubToFullInfo
• cutpoints_separation() : protocols::antibody::CDRH3Modeler
• cutpos_list() : protocols::coarse_rna::CoarseRNA_LoopCloser
• cuts() : protocols::jumping::JumpSample
• CycleMover() : protocols::moves::CycleMover
• cycles() : protocols::moves::IteratedConvergenceMover
• CyclicMover() : protocols::moves::CyclicMover