- c -

• C() : protocols::fldsgn::topology::BB_Pos
• c_anchor() : protocols::sic_dock::Rose
• C_atom_id() : protocols::match::upstream::UpstreamResTypeGeometry
• c_n() : protocols::kinematic_closure::ClosureProblem
• c_n_ca() : protocols::kinematic_closure::ClosureProblem
• C_pos() : protocols::match::upstream::ProteinBackboneBuildPoint
• CA() : protocols::fldsgn::topology::BB_Pos
• CA_atom_id() : protocols::match::upstream::UpstreamResTypeGeometry
• ca_c() : protocols::kinematic_closure::ClosureProblem
• ca_c_n() : protocols::kinematic_closure::ClosureProblem
• ca_cb_orient() : protocols::fldsgn::topology::Sheet
• ca_cb_orients() : protocols::fldsgn::topology::Sheet
• CA_only() : protocols::simple_moves::AddConstraintsToCurrentConformationMover
• CA_pos() : protocols::match::upstream::ProteinBackboneBuildPoint
• CA_search_scores_and_tensors() : protocols::scoring::methods::pcs2::PcsEnergy
• CA_search_scores_and_tensors_with_svd() : protocols::scoring::methods::pcs2::PcsEnergy
• cache_fragments() : protocols::forge::components::VarLengthBuild
• cache_limit() : protocols::canonical_sampling::TrajectoryRecorder
• cache_pose() : protocols::frag_picker::VallProvider
• cache_profile() : protocols::frag_picker::VallProvider
• cache_task() : protocols::protein_interface_design::movers::RandomMutation
• cached_score() : 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 , 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
• CachingScoringMethod() : protocols::frag_picker::scores::CachingScoringMethod
• CAcstGenerator() : protocols::seeded_abinitio::CAcstGenerator
• cal_distance() : protocols::pockets::SmallMol
• cal_min_dist() : protocols::pockets::SmallMol
• calc_all_dist() : protocols::make_rot_lib::MakeRotLibMover
• 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_centroids() : protocols::make_rot_lib::MakeRotLibMover
• calc_crossing_angles() : protocols::features::helixAssembly::HelixBundleFeatures
• calc_dist() : protocols::make_rot_lib::MakeRotLibMover
• calc_dotscore() : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• calc_ElectricField() : protocols::sparta::PDB
• calc_fa_energy() : protocols::features::helixAssembly::HelixBundleFeatures
• calc_final_rotamer_probs() : protocols::make_rot_lib::MakeRotLibMover
• calc_final_rotamers() : protocols::make_rot_lib::MakeRotLibMover
• 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::Helix , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::HelixPairingSet , protocols::fldsgn::topology::HSSTriplet , protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::SheetSet , protocols::fldsgn::topology::Strand
• calc_hbond_sasaE() : protocols::analysis::InterfaceAnalyzerMover
• calc_helix_cycle() : protocols::fldsgn::topology::BetaAlphaBetaMotif
• calc_HN_S2() : protocols::sparta::PDB
• calc_inertia_tensor() : protocols::normalmode::NormalMode
• calc_inout() : protocols::fldsgn::topology::BetaAlphaBetaMotif
• calc_interaction_energy() : protocols::symmetric_docking::SymDockProtocol , protocols::ub_e2c::ubi_e2c_modeler
• calc_interface_metrics() : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• calc_interface_to_surface_fraction() : protocols::analysis::InterfaceAnalyzerMover
• calc_jacobian_cartesians() : protocols::simple_moves::BBConRotMover
• calc_Lrmsd() : protocols::ub_e2c::ubi_e2c_modeler
• calc_pc_and_com() : protocols::features::helixAssembly::HelixBundleFeatures
• calc_pep_scores() : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• calc_per_residue_and_regional_data() : protocols::analysis::InterfaceAnalyzerMover
• calc_per_residue_dG() : protocols::analysis::InterfaceAnalyzerMover
• calc_per_residue_dSASA() : protocols::analysis::InterfaceAnalyzerMover
• calc_per_residue_dSASA_general() : protocols::analysis::InterfaceAnalyzerMover
• calc_pfront_poses_filter_ranks() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• 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 , protocols::matdes::MatDesPointMutationCalculator
• calc_rms() : protocols::symmetric_docking::SymDockProtocol
• calc_rms_res() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• calc_rmsds() : protocols::farna::RNA_DeNovoProtocol
• calc_rotamer_clusters() : protocols::make_rot_lib::MakeRotLibMover
• calc_rsd_sasa() : protocols::toolbox::SelectResiduesByLayer
• calc_rsigmascore() : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• calc_running_avg() : protocols::make_rot_lib::MakeRotLibMover
• calc_sasa_bothsides() : protocols::fldsgn::topology::Sheet
• calc_sc_neighbors() : protocols::toolbox::SelectResiduesByLayer
• calc_secondary_struct() : protocols::surface_docking::FullatomRelaxMover
• calc_secondary_structure() : protocols::surface_docking::SurfaceDockingProtocol
• calc_secondary_structure_with_surface() : protocols::surface_docking::SurfaceDockingProtocol
• calc_standard_deviations() : protocols::make_rot_lib::MakeRotLibMover
• calcKineticEnergy() : protocols::cartesian::MolecularDynamics
• calcLevel1() : protocols::sparta::ANN
• calcLevel2() : protocols::sparta::ANN
• calcMetrics() : protocols::flexpep_docking::FlexPepDockingProtocol
• calcPlane() : protocols::sparta::PDB
• calcSurface() : protocols::sparta::PDB
• calcTriangles() : protocols::sparta::PDB
• calculate() : protocols::dna::DNAParameters , protocols::pack_daemon::NPDPropCalculator , protocols::protein_interface_design::ReportPSSMDifferences , protocols::protein_interface_design::ReportSequenceDifferences , protocols::scoring::Interface , protocols::scoring::InterfaceInfo , protocols::simple_filters::DdGScan , protocols::simple_moves::ddG
• calculate_all_chainbreaks() : protocols::analysis::LoopAnalyzerMover
• calculate_atom_id_domain_map() : protocols::toolbox::AllowInsert
• calculate_atom_id_map() : protocols::toolbox::AllowInsert
• calculate_axes() : protocols::docking::EllipsoidalRandomizationMover
• calculate_background_energies() : protocols::pack_daemon::PackDaemon
• calculate_ccd_angle() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• calculate_cdr_aromatic_nres() : protocols::antibody::AntibodyFeatures
• calculate_cdr_cluster() : protocols::antibody::clusters::CDRClusterSet
• calculate_cdr_contacts_nres() : protocols::antibody::AntibodyFeatures
• calculate_cdr_contacts_total() : protocols::antibody::AntibodyFeatures
• calculate_cdr_dpSASA() : protocols::antibody::AntibodyFeatures
• calculate_cdr_totals() : protocols::antibody::AntibodyFeatures
• calculate_center_xyz() : protocols::pockets::EggshellGrid
• calculate_cost_only_with_svd() : protocols::scoring::methods::pcs2::PcsDataLanthanide
• calculate_distance_matrix() : protocols::cluster::ClusterBase
• calculate_geometry() : protocols::docking::EllipsoidalRandomizationMover
• calculate_helical_parameters() : protocols::simple_filters::RepeatParameterFilter
• calculate_helical_parameters_helper() : protocols::simple_filters::RepeatParameterFilter
• calculate_highres_ref_energy() : protocols::docking::DockingEnsemble
• calculate_interface_score() : protocols::analysis::PeptideDeriverFilter
• calculate_interface_unbound_energy() : protocols::ddg::ddGMover
• calculate_iterations() : protocols::abinitio::abscript::AbscriptMover
• calculate_Jacobi_correction() : protocols::normalmode::NormalMode
• calculate_jump() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• calculate_jump_sample() : protocols::abinitio::abscript::FragmentJumpCM
• calculate_ligand_CoM() : protocols::pockets::PlaidFingerprint
• calculate_lowres_ref_energy() : protocols::docking::DockingEnsemble
• calculate_neighbor_table() : protocols::pmut_scan::PointMutScanDriver
• calculate_pcs_score() : protocols::scoring::methods::pcs::PCS_Energy , protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4
• calculate_pcs_score_on_PCS_data_center_CA() : protocols::scoring::methods::pcs2::PcsEnergy
• calculate_per_residue_interface_score() : protocols::analysis::PeptideDeriverFilter
• calculate_plane_axes() : protocols::docking::EllipsoidalRandomizationMover
• calculate_pool_diversity() : protocols::mpi_refinement::MultiObjective
• calculate_protein_CoM() : protocols::pockets::NonPlaidFingerprint
• calculate_recenter_vector() : protocols::surface_docking::SurfaceOrientMover
• calculate_residue_atomic_contacts() : protocols::antibody::AntibodyFeatures
• calculate_rmsd() : protocols::anchored_design::AnchoredDesignMover
• calculate_rotamer_set_design_targets_partition_sum() : protocols::enzdes::EnzdesFlexibleRegion
• calculate_scores_and_tensors_from_pose_and_PCS_data() : protocols::scoring::methods::pcs::PCS_Energy , protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4
• calculate_specificity() : protocols::dna::DnaInterfacePacker
• calculate_structure_diversity() : protocols::mpi_refinement::MultiObjective
• calculate_tensor_and_cost_with_svd() : protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
• calculate_tensor_only_with_svd() : protocols::scoring::methods::pcs2::PcsDataLanthanide
• calculate_total_samples() : protocols::helical_bundle::BundleGridSampler
• calculate_variations() : protocols::mpi_refinement::StructAvrgMover
• calculated() : protocols::scoring::InterfaceInfo
• calculated_atom_id_domain_map() : protocols::toolbox::AllowInsert
• calculator() : protocols::toolbox::pose_metric_calculators::MetricValueGetter
• calculator_name() : protocols::pack_daemon::NPDPropCalculatorCreator
• 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_output_observers() : protocols::jd2::Job , protocols::jd2::JobOutputter
• call_setup() : protocols::simple_moves::PackRotamersMoverLazy
• calRMSD() : protocols::pockets::SmallMol
• CamShiftEvaluator() : protocols::simple_filters::CamShiftEvaluator
• CamShiftEvaluatorCreator() : protocols::simple_filters::CamShiftEvaluatorCreator
• cancel_batch() : protocols::jd2::archive::ArchiveManager , protocols::jd2::archive::BaseArchiveManager
• cancel_batches_previous_to() : protocols::jd2::archive::BaseArchiveManager
• cancel_passports() : protocols::environment::Environment
• 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
• cap_espGrid() : protocols::pockets::ElectrostaticpotentialGrid
• cart_min() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• cart_product() : protocols::fldsgn::MatchResidues
• cartesian() : protocols::relax::RelaxProtocolBase , protocols::simple_moves::MinMover , protocols::simple_moves::SaneMinMover
• CartesianHybridize() : protocols::hybridization::CartesianHybridize
• CartesianMD() : protocols::md::CartesianMD
• CartesianNormalModeMover() : protocols::normalmode::CartesianNormalModeMover
• CartesianSampler() : protocols::hybridization::CartesianSampler
• CartesianSearchPattern() : protocols::hotspot_hashing::CartesianSearchPattern
• 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
• 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
• CB() : protocols::fldsgn::topology::BB_Pos
• CB_atom_id() : protocols::match::upstream::UpstreamResTypeGeometry
• cb_dist_cut() : protocols::simple_filters::DomainInterfaceFilter
• CB_dist_cutoff() : protocols::toolbox::task_operations::RestrictInterGroupVectorOperation , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• cb_force() : protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlacementMinimizationMover
• CBScore() : protocols::sic_dock::CBScore
• CBScoreVisitor() : protocols::sic_dock::CBScoreVisitor
• cbx() : protocols::frag_picker::VallResidue
• cby() : protocols::frag_picker::VallResidue
• cbz() : protocols::frag_picker::VallResidue
• ccd() : protocols::dna::DesignProteinBackboneAroundDNA
• ccd_close() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• ccd_closure() : protocols::simple_moves::WobbleMover
• CCD_loop_close() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• CCD_loop_close_sample_omega_recursively() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• CCDEndsGraftMover() : protocols::grafting::CCDEndsGraftMover
• CCDLoopClosureMover() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• CCDMoveWrapper() : protocols::rbsegment_relax::CCDMoveWrapper
• CCluster() : protocols::pockets::CCluster
• CClusterSet() : protocols::pockets::CClusterSet
• cdr() : protocols::antibody::CDRSetOptions , protocols::antibody::clusters::CDRCluster , protocols::antibody::design::CDRSeqDesignOptions
• cdr_cluster_enum_to_string() : protocols::antibody::clusters::CDRClusterEnumManager
• cdr_cluster_is_present() : protocols::antibody::clusters::CDRClusterEnumManager
• cdr_cluster_string_to_enum() : protocols::antibody::clusters::CDRClusterEnumManager
• cdr_definition_enum_to_string() : protocols::antibody::AntibodyEnumManager
• cdr_definition_is_present() : protocols::antibody::AntibodyEnumManager
• cdr_definition_string_to_enum() : protocols::antibody::AntibodyEnumManager
• cdr_definition_transform_present() : protocols::antibody::AntibodyInfo
• CDR_H3_filter() : protocols::antibody_legacy::CDRH3Modeler
• cdr_landmark_enum_to_string() : protocols::antibody::AntibodyEnumManager
• cdr_landmark_is_present() : protocols::antibody::AntibodyEnumManager
• cdr_landmark_string_to_enum() : protocols::antibody::AntibodyEnumManager
• cdr_name_enum_to_string() : protocols::antibody::AntibodyEnumManager
• cdr_name_is_present() : protocols::antibody::AntibodyEnumManager
• cdr_name_string_to_enum() : protocols::antibody::AntibodyEnumManager
• cdr_overhang() : protocols::antibody::design::AntibodyDesignModeler
• CDRCluster() : protocols::antibody::clusters::CDRCluster
• CDRClusterEnumManager() : protocols::antibody::clusters::CDRClusterEnumManager
• CDRClusterFeatures() : protocols::antibody::clusters::CDRClusterFeatures
• CDRClusterFeaturesCreator() : protocols::antibody::clusters::CDRClusterFeaturesCreator
• CDRClusterMatcher() : protocols::antibody::clusters::CDRClusterMatcher
• CDRClusterSet() : protocols::antibody::clusters::CDRClusterSet
• CDRGraftDesignOptions() : protocols::antibody::design::CDRGraftDesignOptions
• CDRGraftDesignOptionsParser() : protocols::antibody::design::CDRGraftDesignOptionsParser
• CDRH3Modeler() : protocols::antibody_legacy::CDRH3Modeler
• CDRPose() : protocols::antibody::CDRPose
• CDRSeqDesignOptions() : protocols::antibody::design::CDRSeqDesignOptions
• CDRSeqDesignOptionsParser() : protocols::antibody::design::CDRSeqDesignOptionsParser
• CDRSetOptions() : protocols::antibody::CDRSetOptions
• CDRSetOptionsParser() : protocols::antibody::CDRSetOptionsParser
• CDRsMinPackMin() : protocols::antibody::CDRsMinPackMin
• cell_index() : protocols::canonical_sampling::BiasEnergy::Histogram< T >
• cen_score() : protocols::abinitio::IterativeBase
• cen_score_patch() : protocols::abinitio::IterativeBase
• cen_scorefxn() : protocols::comparative_modeling::LoopRelaxMover , protocols::grafting::AnchoredGraftMover
• Cend_orient() : protocols::fldsgn::topology::SS_Base
• Cend_pos() : protocols::fldsgn::topology::SS_Base
• cenfilter() : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
• center() : protocols::membrane::geometry::EmbeddingDef , protocols::scoring::Interface
• center_all() : protocols::toolbox::DecoySetEvaluation
• center_of_mass() : protocols::hybridization::FoldTreeHybridize , protocols::loops::Loops , protocols::simple_moves::Tumble
• center_structure() : protocols::toolbox::DecoySetEvaluation
• central_residue() : protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator
• central_residues() : protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator
• centroid_axis() : protocols::rigid::RigidBodyTransMover
• centroid_bin_max() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• centroid_bin_min() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• centroid_bin_size() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• 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_output() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• centroid_score_diff_cut() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• centroid_scorefunction() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• centroid_scorefxn() : protocols::abinitio::Protocol
• centroid_screen() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• centroid_stage() : protocols::loop_modeling::LoopModeler
• centroid_weights() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• CentroidDistanceScreener() : protocols::stepwise::screener::CentroidDistanceScreener
• 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() : protocols::antibody::clusters::CDRCluster , protocols::antibody::PDBLandmark , protocols::frags::VallData , protocols::ligand_docking::StartFrom , protocols::loops::ResidueIndexDescription , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::simple_filters::AngleToVector , protocols::simple_moves::ExtendedPoseMover , protocols::toolbox::task_operations::PreventChainFromRepackingOperation , protocols::toolbox::task_operations::RestrictChainToRepackingOperation , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation , protocols::toolbox::task_operations::SelectResiduesWithinChainOperation
• chain1() : protocols::simple_filters::AlaScan
• chain2() : protocols::simple_filters::AlaScan
• chain_boundaries() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• chain_break_screening_general() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker
• chain_cut() : protocols::simple_moves::CutChainMover
• chain_endings() : protocols::environment::ProtectedConformation
• chain_id() : protocols::simple_moves::CutChainMover
• chain_letters() : protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator
• chain_num() : protocols::simple_moves::PSSM2BfactorMover , protocols::toolbox::task_operations::SeqprofConsensusOperation
• chain_numbers() : protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator
• chain_order() : protocols::simple_moves::SwitchChainOrderMover
• chain_pair_pose_prepared() : protocols::analysis::PeptideDeriverBasicStreamOutputter , protocols::analysis::PeptideDeriverMarkdownStreamOutputter , protocols::analysis::PeptideDeriverOutputter , protocols::analysis::PeptideDeriverOutputterContainer , protocols::analysis::PeptideDeriverPoseOutputter
• chainbreak_bias() : protocols::rigid::RigidBodyMotionMover
• chainbreak_weight() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• ChainbreakDistFunc() : core::scoring::constraints::ChainbreakDistFunc
• chainbreaks() : protocols::idealize::IdealizeMover
• chainbreakweights() : protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops
• ChainExistsFilter() : protocols::ligand_docking::ChainExistsFilter
• chains() : protocols::ligand_docking::InterfaceScoreCalculator
• chains_exist_in_pose() : protocols::features::InterfaceFeatures
• chains_from_termini() : protocols::environment::ProtectedConformation
• ChainSplitMover() : protocols::simple_moves::ChainSplitMover
• change_chi_without_replacing_residue() : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• change_CoM_to_ligandCoM() : protocols::pockets::NonPlaidFingerprint
• change_conformer() : protocols::ligand_docking::Transform
• change_espGrid_for_darc() : protocols::pockets::ElectrostaticpotentialGrid
• change_foldtree() : protocols::protein_interface_design::movers::AddChainBreak
• change_weight() : protocols::moves::MonteCarlo
• ChangeAndResetFoldTreeMover() : protocols::simple_moves::ChangeAndResetFoldTreeMover
• ChangeFoldTreeMover() : protocols::moves::ChangeFoldTreeMover
• changing_baseline() : protocols::simple_filters::DeltaFilter
• char2ss_type() : protocols::comparative_modeling::features::SSFeature
• char_type() : protocols::rbsegment_relax::RBResidueRange
• 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
• 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::hybridization::HybridizeSetup , protocols::seeded_abinitio::SegmentHybridizer
• check_and_initialize() : protocols::hotspot_hashing::movers::PlaceProbeMover
• check_angle_in_range() : protocols::stepwise::sampler::MC_OneTorsion
• check_atom_bin_in_range() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• check_base_pair() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• check_base_pairs() : protocols::farna::RNA_StructureParameters
• check_base_stack() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• check_batch() : protocols::jd2::BatchJobInputter
• check_cdr_quality() : protocols::antibody::AntibodyInfo
• check_centroid_interaction() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• check_centroid_interaction_floating_base() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• check_chain_closable_geometry() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• check_chain_closable_geometry_strict() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• check_chainbreak_variants() : protocols::topology_broker::TopologyBroker
• check_close_chain_break() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• check_closure() : protocols::farna::RNA_LoopCloser
• check_closure_criteria() : protocols::forge::remodel::RemodelLoopMover
• check_compatibility() : protocols::stepwise::modeler::rna::sugar::SugarModeling
• 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_downstream_hit_incompatibility() : protocols::match::Matcher
• check_each_job_has_startstruct() : protocols::jd2::JD2ResourceManagerJobInputter
• check_fa_dun() : protocols::match::upstream::BuildSet
• check_features_reporter_dependencies() : protocols::features::ReportToDB
• check_filters() : protocols::abinitio::AbrelaxApplication , protocols::flexpep_docking::FlexPepDockingProtocol
• check_fold_tree_OK() : protocols::farna::ChunkSet , protocols::farna::RNA_ChunkLibrary
• check_for_closeness() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased , protocols::stepwise::setup::StepWiseCSA_JobDistributor
• check_for_closeness_without_working_parameters() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• check_for_graft_instruction_inconsistencies() : protocols::antibody::AntibodyDatabaseManager
• check_for_input_domain_or_from_scratch() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• check_for_parse_error() : protocols::metal_interface::ZincSiteFinder
• check_for_parser_in_go_main() : protocols::jd2::JobDistributor
• check_for_precomputed_copy_dofs_info() : protocols::simple_moves::CopyDofMover
• check_for_symmetric_peaks() : protocols::noesy_assign::PeakAssignmentResidueMap
• check_for_top_designs() : protocols::antibody::design::AntibodyGraftDesignMover
• check_for_unique_cutpoint() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• check_for_unique_cutpoint_flanked_by_bridge_res() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• check_forward_backward() : protocols::farna::RNA_JumpLibrary , protocols::farna::RNA_StructureParameters
• check_frequency() : protocols::moves::MonteCarlo
• check_hbond_score() : protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker
• 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_in_bond_angle_list() : protocols::simple_moves::ConstrainToIdealMover
• check_in_bonded_list() : protocols::simple_moves::ConstrainToIdealMover
• check_in_chain_connections() : protocols::farna::RNA_StructureParameters
• check_in_pairing_sets() : protocols::farna::RNA_StructureParameters
• check_internals() : protocols::comparative_modeling::MultiThreadingMover
• check_library_expiry_dates() : protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master
• check_line_len() : protocols::antibody::CDRSetOptionsParser , protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser
• check_loop_closed() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker
• check_loop_residues_sensible() : protocols::generalized_kinematic_closure::GeneralizedKIC
• check_loops() : protocols::abinitio::FragmentSampler
• check_matching_atom_names() : protocols::stepwise::modeler::align::StepWisePoseAligner
• check_mmt() : protocols::simple_moves::TorsionDOFMover
• check_moved() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• check_moving_res_in_chain() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• check_moving_sugar() : protocols::stepwise::screener::SugarInstantiator
• 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_nonideal_mintype() : protocols::relax::FastRelax
• check_num_requested_atoms() : protocols::features::ProteinResidueConformationFeatures
• check_other_partition_for_contact() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• check_overlap() : protocols::hybridization::InsertChunkMover , protocols::kinematic_closure::ClosureSolution , protocols::kinematic_closure::solution_pickers::FilteredSolutions
• check_pairing_intersect() : protocols::jumping::SheetBuilder
• check_path() : protocols::antibody::AntibodyNumberingParser , protocols::antibody::CDRSetOptionsParser , protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser
• check_pdb_for_mem() : protocols::membrane::AddMembraneMover , protocols::membrane::symmetry::SymmetricAddMembraneMover
• check_phosphate_contacts_donor() : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• check_pose() : protocols::sparta::Sparta
• check_pose_tree_compatibility() : protocols::toolbox::match_enzdes_util::InvrotTree , protocols::toolbox::match_enzdes_util::TheozymeInvrotTree
• check_rama() : protocols::kinematic_closure::ClosureSolution , protocols::kinematic_closure::solution_pickers::FilteredSolutions , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::simple_moves::BackboneMover
• check_rama_scores() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• check_range() : protocols::canonical_sampling::BiasEnergy::Histogram< T > , protocols::membrane::geometry::EmbeddingDef
• check_relevant_residues() : protocols::features::FeaturesReporter
• check_relevant_residues_range() : protocols::features::FeaturesReporter
• check_res_map() : protocols::farna::RNA_ChunkLibrary
• check_resource_loader_type() : protocols::jd2::JD2ResourceManager
• check_rmsd() : protocols::ligand_docking::Transform
• check_same_chain() : protocols::stepwise::monte_carlo::mover::AddMover
• check_score_filter() : protocols::farna::RNA_DeNovoProtocol
• check_screen() : protocols::stepwise::legacy::screener::ProteinAtrRepScreener , protocols::stepwise::legacy::screener::RNA_AtrRepScreener , protocols::stepwise::legacy::screener::SimplePoseSelection , protocols::stepwise::legacy::screener::SimpleRMSD_Screener , protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker , protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker , protocols::stepwise::screener::AnchorSugarScreener , protocols::stepwise::screener::BaseCentroidScreener , protocols::stepwise::screener::CentroidDistanceScreener , protocols::stepwise::screener::IntegrationTestBreaker , protocols::stepwise::screener::NativeRMSD_Screener , protocols::stepwise::screener::O2PrimeScreener , protocols::stepwise::screener::PackScreener , protocols::stepwise::screener::PartitionContactScreener , protocols::stepwise::screener::PhosphateScreener , protocols::stepwise::screener::PoseSelectionScreener , protocols::stepwise::screener::ProteinCCD_ClosureScreener , protocols::stepwise::screener::ResidueContactScreener , protocols::stepwise::screener::RNA_ChainClosableGeometryResidueBasedScreener , protocols::stepwise::screener::RNA_ChainClosableGeometryScreener , protocols::stepwise::screener::RNA_ChainClosableGeometryStubBasedScreener , protocols::stepwise::screener::RNA_ChainClosureScreener , protocols::stepwise::screener::SampleApplier , protocols::stepwise::screener::Scorer , protocols::stepwise::screener::StepWiseScreener , protocols::stepwise::screener::StubDistanceScreener , protocols::stepwise::screener::SugarInstantiator , protocols::stepwise::screener::TagDefinition , protocols::stepwise::screener::VDW_BinScreener
• check_screen_and_kick_out_displaced_model() : protocols::stepwise::modeler::align::StepWiseClusterer
• check_sequence() : protocols::noesy_assign::FragsToAtomDist , protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• check_sheet_pairings() : protocols::jumping::SheetBuilder
• check_ss() : protocols::simple_moves::ClassicFragmentMover
• check_ss_lengths() : protocols::frags::TorsionFragmentMover
• check_state() : protocols::forge::remodel::RemodelDesignMover
• check_status() : protocols::frag_picker::quota::ABEGO_SS_Map
• check_strand_too_closeness() : protocols::features::strand_assembly::StrandBundleFeatures
• check_superimpose_res() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• check_sw_by_dis() : protocols::features::strand_assembly::StrandBundleFeatures
• check_tag() : protocols::cluster::GatherPosesMover
• check_tail_residues_sensible() : protocols::generalized_kinematic_closure::GeneralizedKIC
• check_temp_consistency() : protocols::canonical_sampling::TemperingBase
• check_that_terminal_res_are_unstacked() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• check_two_pairings() : protocols::jumping::SheetBuilder
• check_value() : protocols::match::downstream::AtomGeometrySecMatchRPE
• check_VDW_screen_bin_is_setup() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• check_working_parameters() : protocols::stepwise::modeler::StepWiseConnectionSampler
• 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 , protocols::simple_filters::ReportFilter
• checkpoint_write() : protocols::jd2::BOINCJobDistributor , protocols::jobdist::BaseJobDistributor , protocols::simple_filters::ReportFilter
• checkpoint_write_interval() : protocols::genetic_algorithm::GeneticAlgorithmBase
• checkpointed_cycle_block() : protocols::abinitio::FragmentSampler
• CheckPointer() : protocols::checkpoint::CheckPointer
• checkpointing_file() : protocols::simple_filters::ReportFilter
• ChemicalShiftEvaluator() : protocols::sparta::ChemicalShiftEvaluator
• ChemicalShiftEvaluatorCreator() : protocols::sparta::ChemicalShiftEvaluatorCreator
• chemshift_column() : protocols::abinitio::IterativeBase
• chemshift_compliance() : protocols::noesy_assign::PeakAssignment
• chi() : protocols::dna::DNABase , protocols::dna::DnaInterfaceMinMover , protocols::optimize_weights::PNatRotOptERotamerData , protocols::simple_moves::symmetry::SetupNCSMover , protocols::simple_moves::TaskAwareMinMover
• chi2max() : protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation
• chi2min() : protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation
• chi_dev() : protocols::comparative_modeling::Align_RotamerEvaluator
• chi_matches_coords() : protocols::simple_moves::MinimalRotamer
• chi_sample() : protocols::match::upstream::FullChiSampleSet
• chi_samples() : protocols::match::upstream::FullChiSampleSet
• chi_xx() : protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• chi_xy() : protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• chi_xz() : protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• chi_yy() : protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• chi_yz() : protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• ChiAngleNormalization() : protocols::qsar::scoring_grid::ChiAngleNormalization
• chinum() : protocols::simple_moves::sidechain_moves::SetChiMover
• ChiralMover() : protocols::simple_moves::chiral::ChiralMover
• chis_from_pose() : protocols::toolbox::pose_metric_calculators::RotamerRecovery
• 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::stepwise::legacy::modeler::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_fragment() : protocols::simple_moves::ClassicFragmentMover , protocols::simple_moves::SmoothFragmentMover , protocols::simple_moves::SmoothSymmetricFragmentMover
• choose_least_perturb_solution() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• choose_n_best() : protocols::enzdes::PackRotamersMoverPartGreedy
• choose_next_pairing() : protocols::jumping::SheetBuilder
• choose_origin_with_lowest_eggshell_ruggedness() : protocols::pockets::NonPlaidFingerprint
• choose_random() : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser , protocols::stepwise::monte_carlo::SWA_MoveSelector
• choose_window_length() : protocols::simple_moves::ClassicFragmentMover
• choose_window_start() : protocols::simple_moves::ClassicFragmentMover
• Chunk() : protocols::nonlocal::Chunk
• chunk_coverage() : protocols::farna::RNA_ChunkLibrary
• chunk_key() : protocols::frag_picker::VallChunk
• chunk_set() : protocols::farna::RNA_ChunkLibrary
• ChunkSet() : protocols::farna::ChunkSet
• ChunkTrialMover() : protocols::hybridization::ChunkTrialMover
• CircularPermutation() : protocols::fldsgn::CircularPermutation
• claim_accepted() : protocols::topology_broker::TopologyClaimer
• claim_backbone() : protocols::environment::claims::TorsionClaim
• claim_sidechain() : protocols::environment::claims::TorsionClaim
• claimer() : protocols::topology_broker::TopologyBroker
• claimer_builds_own_fold_tree() : protocols::topology_broker::MembraneTopologyClaimer , protocols::topology_broker::TMHTopologySamplerClaimer , protocols::topology_broker::TopologyClaimer
• ClaimerMessage() : protocols::topology_broker::ClaimerMessage
• ClaimStrength() : protocols::environment::claims::ClaimStrength
• clash_check() : protocols::scoring::ImplicitFastClashCheck
• clash_check_test() : protocols::scoring::ImplicitFastClashCheck
• clash_check_trimer() : protocols::scoring::ImplicitFastClashCheck
• clash_count() : protocols::scoring::ImplicitFastClashCheck
• clash_dist() : protocols::matdes::ClashCheckFilter
• ClashCheckFilter() : protocols::matdes::ClashCheckFilter
• ClashCountCalculator() : protocols::toolbox::pose_metric_calculators::ClashCountCalculator
• clashes() : protocols::sic_dock::Rose
• clashes_naive() : protocols::sic_dock::Rose
• ClashWithTargetFilter() : protocols::protein_interface_design::filters::ClashWithTargetFilter
• class_name() : protocols::environment::claims::EnvLabelSelector
• 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
• clean_jumps() : protocols::abinitio::TemplateJumpSetup , protocols::jumping::BaseJumpSetup , protocols::jumping::JumpSelector , protocols::jumping::JumpSetup , protocols::jumping::ResiduePairJumpSetup , protocols::jumping::SheetBuilder
• clean_pose_store() : protocols::cluster::ClusterBase
• 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
• cleanup() : protocols::simple_moves::GreenPacker
• cleanup_after_job_completion() : protocols::jd2::JD2ResourceManagerJobInputter
• cleanup_pose() : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• cleanup_reqs() : protocols::wum2::EndPoint
• clear() : protocols::abinitio::AbrelaxMover , protocols::analysis::PeptideDeriverOutputterContainer , protocols::antibody::clusters::CDRClusterSet , 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::Cluster , protocols::cluster::GatherPosesMover , protocols::dna::DnaChains , protocols::environment::ProtectedConformation , 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::forge::remodel::RemodelAccumulator , protocols::frag_picker::BoundedCollector< 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::frags::FragLib , protocols::frags::SingleResidueTorsionFragmentLibrary , protocols::frags::TorsionFragmentLibrary , protocols::hotspot_hashing::HotspotStubSet , protocols::jd2::JD2ResourceManager , protocols::jumping::JumpSetup , protocols::jumping::ResiduePairJumpSetup , protocols::kinematic_closure::perturbers::PerturberSet , protocols::loop_modeling::utilities::LoopMoverGroup , protocols::loops::Loops , protocols::match::Bool3DGrid , protocols::match::downstream::ActiveSiteGrid , protocols::moves::CompositionMover , protocols::moves::MoverContainer , protocols::moves::MoverStatistics , protocols::moves::PDBDumpMover , protocols::mpi_refinement::Scheduler , protocols::pack_daemon::TopEntitySet , protocols::pockets::CClusterSet , protocols::pockets::PClusterSet , protocols::pockets::PocketGrid , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::qsar::qsarMap , protocols::rosetta_scripts::ParsedProtocol , 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::wum2::WUQueue , protocols::wum::SilentStructStore , protocols::wum::WorkUnitQueue
• 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::toolbox::match_enzdes_util::EnzCstTemplateRes
• clear_at_inds() : protocols::match::downstream::AtomGeometrySecMatchRPE
• clear_blacklist() : protocols::wum::WorkUnitBase
• clear_buffers() : protocols::analysis::PeptideDeriverMarkdownStreamOutputter
• clear_cached_data() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• clear_cdr_set_exclude_options() : protocols::antibody::CDRSetOptionsParser
• clear_cdr_set_include_options() : protocols::antibody::CDRSetOptionsParser
• clear_channel_from_garbage_collector() : protocols::jd2::MpiFileBuffer
• clear_checkpoints() : protocols::abinitio::MembraneAbinitio , protocols::checkpoint::CheckPointer
• clear_children() : protocols::loop_modeling::LoopMover
• clear_combine_history() : protocols::simple_moves::CombinePoseMover
• clear_connected_resonances() : protocols::noesy_assign::Resonance
• 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_dependencies() : protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager
• clear_design_taskset() : protocols::flxbb::FlxbbDesign
• clear_downstream_orientation_atoms() : protocols::match::MatcherTask
• clear_edges() : protocols::toolbox::ResidueNetwork
• clear_energies() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• clear_evaluators() : protocols::jd2::JobOutputter
• clear_external_geom_samplers() : protocols::match::downstream::ClassicMatchAlgorithm
• clear_filters() : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::match::output::MatchProcessor
• clear_fragments() : protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelLoopMover , protocols::loops::loop_mover::LoopMover
• clear_hash_map() : protocols::match::HitHasher
• 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_lib() : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• clear_match_data() : protocols::match::output::CloudPDBWriter
• clear_movers() : protocols::loop_modeling::LoopProtocol
• clear_movers_and_refiners() : protocols::loop_modeling::LoopProtocol
• clear_movesets() : protocols::rbsegment_relax::RBSegmentRelax
• clear_overall_prob_set() : protocols::antibody::design::ResidueProbDesignOperation
• clear_parents() : protocols::genetic_algorithm::GeneticAlgorithmBase
• clear_perturbers() : protocols::kinematic_closure::KicMover
• clear_poses() : protocols::moves::MonteCarlo
• clear_positions() : protocols::antibody::design::ConservativeDesignOperation
• clear_prob_set() : protocols::antibody::design::ResidueProbDesignOperation
• clear_rcgs() : protocols::forge::components::VarLengthBuild
• clear_refiners() : protocols::loop_modeling::LoopProtocol
• clear_reset_filters() : protocols::filters::CombinedFilter , protocols::filters::CompoundFilter
• clear_rnl_pose() : protocols::enzdes::EnzdesScorefileFilter
• clear_rotamer() : protocols::stepwise::sampler::MC_Comb , protocols::stepwise::sampler::rna::RNA_MC_MultiSuite , protocols::stepwise::sampler::rna::RNA_MC_Suite , protocols::stepwise::sampler::StepWiseSamplerAny , protocols::stepwise::sampler::StepWiseSamplerComb , protocols::stepwise::sampler::StepWiseSamplerSizedAny , protocols::stepwise::sampler::StepWiseSamplerSizedComb
• 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_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_torsion_string_stack() : protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber , protocols::loops::loop_closure::kinematic_closure::KinematicPerturber
• clear_torsions_using() : protocols::normalmode::NormalMode
• clear_user_provided_movers() : protocols::forge::components::VarLengthBuild
• ClearConstraintsMover() : protocols::simple_moves::ClearConstraintsMover
• clearSmallPockets() : protocols::pockets::PocketGrid
• client() : protocols::environment::ScriptCM
• ClientMover() : protocols::environment::ClientMover
• clone() : core::scoring::constraints::ChainbreakDistFunc , protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::abinitio::abscript::AbscriptMover , protocols::abinitio::abscript::ConstraintPreparer , protocols::abinitio::abscript::FragmentJumpCM , protocols::abinitio::abscript::JumpSampleData , protocols::abinitio::abscript::RigidChunkCM , protocols::abinitio::abscript::StructPerturberCM , protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::DomainAssembly , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::JumpingFoldConstraintsWrapper , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio , protocols::analysis::InterfaceAnalyzerMover , protocols::analysis::PeptideDeriverFilter , protocols::anchored_design::AnchoredDesignMover , protocols::anchored_design::AnchorMoversData , protocols::antibody::AntibodyModelerProtocol , protocols::antibody::CDRSetOptions , protocols::antibody::clusters::BasicCDRClusterSet , protocols::antibody::clusters::CDRCluster , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::CDRGraftDesignOptions , protocols::antibody::design::CDRSeqDesignOptions , protocols::antibody::design::ConservativeDesignOperation , protocols::antibody::design::ResidueProbDesignOperation , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::H3PerturbCCD , protocols::antibody::H3RefineCCD , protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , protocols::antibody::RefineOneCDRLoop , protocols::antibody::SnugDock , protocols::antibody::SnugDockProtocol , protocols::antibody_legacy::AntibodyModeler , protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover , protocols::canonical_sampling::BiasedMonteCarlo , protocols::canonical_sampling::DbTrajectoryRecorder , protocols::canonical_sampling::FixedTemperatureController , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::PDBTrajectoryRecorder , protocols::canonical_sampling::ProgressBarObserver , protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TrialCounterObserver , protocols::cluster::AssignToClustersMover , protocols::cluster::ClusterPhilStyle , protocols::cluster::ClusterPhilStyle_Loop , protocols::cluster::ClusterPhilStyle_PoseReporter , protocols::cluster::EnsembleConstraints_Simple , 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::comparative_modeling::ThreadingMover , protocols::constraints_additional::AmbiguousMultiConstraint , protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::COMCoordinateConstraint , protocols::constraints_additional::MaxSeqSepConstraintSet , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::contact_map::ContactMap , protocols::cryst::FitBfactorsMover , protocols::cryst::LoadDensityMapMover , protocols::cryst::RecomputeDensityMapMover , protocols::cryst::SetCrystWeightMover , protocols::cryst::SetRefinementOptionsMover , protocols::cryst::TagPoseWithRefinementStatsMover , protocols::cryst::UpdateSolventMover , protocols::cyclic_peptide::CreateAngleConstraint , protocols::cyclic_peptide::CreateDistanceConstraint , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::cyclic_peptide::DeclareBond , protocols::cyclic_peptide::PeptideStubMover , protocols::denovo_design::filters::ExposedHydrophobicsFilter , 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::DockingHighResFilter , protocols::docking::DockingHighResLegacy , protocols::docking::DockingInitialPerturbation , protocols::docking::DockingLowRes , protocols::docking::DockingLowResEnsemble , protocols::docking::DockingLowResFilter , protocols::docking::DockingProtocol , protocols::docking::DockMCMCycle , protocols::docking::DockMCMProtocol , protocols::docking::DockSetupMover , protocols::docking::EllipsoidalRandomizationMover , protocols::docking::membrane::MPDockingMover , protocols::docking::membrane::MPDockingSetupMover , protocols::docking::TemperedDocking , protocols::electron_density::BfactorFittingMover , protocols::electron_density::DensityMorphingMover , protocols::electron_density::ReportFSC , protocols::electron_density::ScaleMapIntensities , protocols::electron_density::SetupForDensityScoringMover , protocols::environment::AutoCutData , protocols::environment::claims::CutBiasClaim , protocols::environment::claims::EnvClaim , protocols::environment::claims::JumpClaim , protocols::environment::claims::TorsionClaim , protocols::environment::claims::VirtResClaim , protocols::environment::claims::XYZClaim , protocols::environment::CoMTrackerCM , protocols::environment::EnvMover , protocols::environment::ProtectedConformation , protocols::environment::ScriptCM , protocols::enzdes::AddLigandMotifRotamers , protocols::enzdes::AddOrRemoveMatchCsts , protocols::enzdes::AddRigidBodyLigandConfs , protocols::enzdes::BackboneSampler , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::DiffAtomSasaFilter , protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::EnzScoreFilter , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::enzdes::PredesignPerturbMover , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::enzdes::RemoveLigandFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::enzdes::ResidueConformerFilter , protocols::enzdes::SetCatalyticResPackBehavior , protocols::enzdes::UpdateEnzdesHeaderMover , protocols::farna::MultipleDomainMover , protocols::farna::RNA_DeNovoProtocol , protocols::farna::RNA_FragmentMover , protocols::farna::RNA_LoopCloser , protocols::farna::RNA_Minimizer , protocols::farna::RNA_SecStructInfo , protocols::features::ReportToDB , protocols::features::TrajectoryReportToDB , protocols::filters::CalculatorFilter , protocols::filters::CombinedFilter , protocols::filters::CompoundFilter , protocols::filters::ContingentFilter , protocols::filters::FalseFilter , protocols::filters::Filter , protocols::filters::IfThenFilter , protocols::filters::MoveBeforeFilter , protocols::filters::ReplicateFilter , protocols::filters::StochasticFilter , protocols::filters::TimeFilter , protocols::filters::TrueFilter , 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::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , 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::CombinedTaskOperation , protocols::flxbb::FilterStructs , protocols::flxbb::FilterStructs_Packstat , protocols::flxbb::FilterStructs_TotalCharge , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::flxbb::LayerDesignOperation , protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager , protocols::forge::build::ConnectRight , protocols::forge::build::CountFromLeft , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::RelativeConnectRight , protocols::forge::build::RelativeSequencePosition , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::constraints::ConstraintFileRCG , 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::RemodelGlobalFrame , 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::frags::TorsionFragment , protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber , protocols::genetic_algorithm::Entity , protocols::genetic_algorithm::EntityElement , protocols::grafting::AnchoredGraftMover , protocols::grafting::CCDEndsGraftMover , protocols::grafting::simple_movers::DeleteRegionMover , protocols::grafting::simple_movers::InsertPoseIntoPoseMover , protocols::grafting::simple_movers::KeepRegionMover , protocols::grafting::simple_movers::ReplaceRegionMover , protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::BundleGridSamplerHelper , protocols::helical_bundle::FitSimpleHelix , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::parameters::BundleParametersSet , protocols::helical_bundle::PerturbBundle , protocols::helical_bundle::PerturbBundleHelix , protocols::helical_bundle::PerturbBundleOptions , protocols::hotspot_hashing::AddSearchPatternRotSetOp , protocols::hotspot_hashing::movers::PlaceSurfaceProbe , protocols::hotspot_hashing::SearchPatternRotSetOp , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::hybridization::CartesianHybridize , protocols::hybridization::CartesianSampler , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup , protocols::hybridization::HybridizeSetupMover , protocols::hybridization::MRMover , protocols::hybridization::TemplateHistory , protocols::idealize::IdealizeMover , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::ligand_docking::AddHydrogens , protocols::ligand_docking::AtomCountFilter , protocols::ligand_docking::ChainExistsFilter , protocols::ligand_docking::CompleteConnectionsFilter , protocols::ligand_docking::CompoundTranslate , protocols::ligand_docking::ComputeLigandRDF , 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::ligand_docking::WriteLigandMolFile , protocols::loop_build::LoopmodelWrapper , protocols::loop_build::LoopMover_SlidingWindow , protocols::loop_modeling::LoopModeler , protocols::loophash::FastGapMover , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashLibrary , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashRelaxProtocol , protocols::loophash::Mover_LoopHashRefine , protocols::loophash::WorkUnit_LoopHash , protocols::LoopRebuild , protocols::loops::FoldTreeFromLoops , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::RamaCheck1B , protocols::loops::loop_closure::ccd::RamaCheck2B , protocols::loops::loop_closure::ccd::RamaCheckBase , 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::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::matdes::BuildingBlockInterfaceOperation , protocols::matdes::ClashCheckFilter , protocols::matdes::ExtractSubposeMover , protocols::matdes::GetRBDOFValues , protocols::matdes::InterfacePackingFilter , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SchemePlaceMotifsMover , protocols::matdes::SymDofMover , protocols::matdes::SymUnsatHbondFilter , protocols::md::CartesianMD , protocols::medal::MedalExchangeMover , protocols::medal::MedalMover , protocols::membrane::AddMembraneMover , protocols::membrane::FlipMover , protocols::membrane::MembranePositionFromTopologyMover , protocols::membrane::RotationMover , protocols::membrane::SetMembraneCenterMover , protocols::membrane::SetMembraneNormalMover , protocols::membrane::SetMembranePositionMover , protocols::membrane::symmetry::SymmetricAddMembraneMover , protocols::membrane::TransformIntoMembraneMover , protocols::membrane::TranslationMover , protocols::membrane::TranslationRotationMover , protocols::membrane::visualize::VisualizeEmbeddingMover , protocols::membrane::visualize::VisualizeMembraneMover , protocols::motif_grafting::movers::MotifGraftMover , protocols::motifs::BuildPosition , protocols::motifs::Motif , protocols::motifs::MotifDnaPacker , protocols::motifs::MotifHit , protocols::moves::CycleMover , protocols::moves::CyclicMover , protocols::moves::DsspMover , protocols::moves::FilterReporterMover , protocols::moves::IfMover , protocols::moves::IteratedConvergenceMover , protocols::moves::MonteCarlo , protocols::moves::MonteCarloUtil , protocols::moves::Mover , protocols::moves::NullMover , protocols::moves::PyMolMover , protocols::moves::RampingMover , protocols::moves::RandomMover , protocols::moves::RepeatMover , protocols::moves::SequenceMover , protocols::moves::StructureRestrictor , protocols::moves::TrialMover , protocols::mpi_refinement::WorkUnit_bbGauss , protocols::mpi_refinement::WorkUnit_CombinePose , protocols::mpi_refinement::WorkUnit_FragInsert , protocols::mpi_refinement::WorkUnit_KicCloser , protocols::mpi_refinement::WorkUnit_LoopHash , protocols::mpi_refinement::WorkUnit_MD , protocols::mpi_refinement::WorkUnit_NormalMode , protocols::mpi_refinement::WorkUnit_PartialAbinitio , protocols::mpi_refinement::WorkUnit_RamaPerturber , protocols::mpi_refinement::WorkUnit_Relax , protocols::multistate_design::MultiStateEntity< T > , protocols::multistate_design::PosType , protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopCreatorMover , protocols::ncbb::oop::OopDockDesignProtocol , protocols::noesy_assign::FloatingResonance , protocols::noesy_assign::LabelResonance , protocols::noesy_assign::ProtonResonance , protocols::noesy_assign::Resonance , protocols::nonlocal::HelixRotate , protocols::nonlocal::SheetTranslate , protocols::nonlocal::SingleFragmentMover , protocols::normalmode::CartesianNormalModeMover , protocols::normalmode::NormalModeMinimizer , protocols::normalmode::TorsionNormalModeMover , 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::ClashWithTargetFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::filters::FNatFilter , protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::InterfaceHolesFilter , protocols::protein_interface_design::filters::IRmsdFilter , protocols::protein_interface_design::filters::LRmsdFilter , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::filters::RmsdSimpleFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::filters::SSamountFilter , 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::DockWithHotspotMover , 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::PatchdockTransform , 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::SubroutineMover , protocols::protein_interface_design::movers::TaskAwareCsts , protocols::protein_interface_design::movers::TopologyBrokerMover , 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::GaussianRBSegmentMover , protocols::rbsegment_relax::HelicalGaussianMover , protocols::rbsegment_relax::IdealizeHelicesMover , protocols::rbsegment_relax::MakeStarTopologyMover , protocols::rbsegment_relax::OptimizeThreadingMover , protocols::rbsegment_relax::SequenceShiftMover , protocols::rbsegment_relax::StrandTwistingMover , protocols::relax::AtomCoordinateCstMover , protocols::relax::CentroidRelax , protocols::relax::ClassicRelax , protocols::relax::FastRelax , protocols::relax::membrane::MPFastRelaxMover , protocols::relax::MiniRelax , protocols::relax::WorkUnit_BatchRelax , protocols::relax::WorkUnit_BatchRelax_and_PostRescore , protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::rigid::RigidBodyTransMover , protocols::rigid::RollMover , protocols::rigid::UniformRigidBodyCM , protocols::rigid::UniformRigidBodyMover , protocols::rosetta_scripts::AdditionalOutputWrapper , protocols::rosetta_scripts::MultipleOutputWrapper , protocols::rosetta_scripts::MultiplePoseMover , 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::pcs2::PcsDataCenterManager , protocols::scoring::methods::pcs2::PcsEnergy , protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcs::PCS_Energy , protocols::scoring::methods::pcsTs1::PCS_data_Ts1 , protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_Ts2 , protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_Ts3 , protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_Ts4 , protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4 , 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::SeedFoldTree , protocols::seeded_abinitio::SeedSetupMover , protocols::seeded_abinitio::SegmentHybridizer , protocols::seeded_abinitio::SwapSegment , protocols::simple_filters::AbinitioBaseFilter , protocols::simple_filters::AlaScan , protocols::simple_filters::AngleToVector , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::AveragePathLengthFilter , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::COFilter , protocols::simple_filters::ConservedPosMutationFilter , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::DdgFilter , protocols::simple_filters::DdGScan , protocols::simple_filters::DeltaFilter , protocols::simple_filters::DisulfideEntropyFilter , protocols::simple_filters::DomainInterfaceFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ExpiryFilter , protocols::simple_filters::FileExistFilter , protocols::simple_filters::FileRemoveFilter , protocols::simple_filters::GeometryFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterfaceBindingEnergyDensityFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::MotifScoreFilter , protocols::simple_filters::MultipleSigmoids , protocols::simple_filters::MutationsFilter , protocols::simple_filters::NeighborTypeFilter , protocols::simple_filters::NetChargeFilter , protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::NMerSVMEnergyFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::Operator , protocols::simple_filters::PackerNeighborGraphFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::PDDFScoreFilter , protocols::simple_filters::PoseComment , protocols::simple_filters::PoseInfoFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::RepeatParameterFilter , 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::SavePoseConstraintToFileFilter , protocols::simple_filters::SaveResfileToDiskFilter , 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::SSMotifFinder , protocols::simple_filters::StemFinder , protocols::simple_filters::SymmetricMotifFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_filters::TerminusDistanceFilter , protocols::simple_filters::TotalSasaFilter , protocols::simple_moves::AddChainMover , protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::simple_moves::AddJobPairData , protocols::simple_moves::AlignChainMover , protocols::simple_moves::BBG8T3AMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::bin_transitions::InitializeByBins , protocols::simple_moves::bin_transitions::PerturbByBins , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::ChainGroupDiscriminator , protocols::simple_moves::ChainSplitMover , protocols::simple_moves::ChangeAndResetFoldTreeMover , protocols::simple_moves::ClassicFragmentMover , protocols::simple_moves::ClearConstraintsMover , protocols::simple_moves::ConsensusDesignMover , protocols::simple_moves::ConstrainToIdealMover , protocols::simple_moves::ConstraintSetMover , protocols::simple_moves::ContingentAcceptMover , protocols::simple_moves::CoupledMover , 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::FavorSymmetricSequence , protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::ForceDisulfidesMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::GroupDiscriminator , 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::MissingDensityToJumpMover , protocols::simple_moves::ModifyVariantTypeMover , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloReset , protocols::simple_moves::MonteCarloTest , protocols::simple_moves::MSDMover , protocols::simple_moves::MutateResidue , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::PDBReloadMover , protocols::simple_moves::PeptideStapleMover , protocols::simple_moves::PSSM2BfactorMover , protocols::simple_moves::RandomOmegaFlipMover , protocols::simple_moves::RandomTorsionMover , protocols::simple_moves::RepackSidechainsMover , protocols::simple_moves::RepeatPropagationMover , protocols::simple_moves::ReportEffectivePKA , protocols::simple_moves::ResetBaselineMover , protocols::simple_moves::ResidueTypeConstraintMover , protocols::simple_moves::ReturnSidechainMover , protocols::simple_moves::RingConformationMover , 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::ShearMover , protocols::simple_moves::ShortBackrubMover , 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::SmallMover , protocols::simple_moves::SuperimposeMover , protocols::simple_moves::SwitchChainOrderMover , protocols::simple_moves::SwitchResidueTypeSetMover , protocols::simple_moves::symmetry::DetectSymmetry , protocols::simple_moves::symmetry::ExtractAsymmetricPoseMover , protocols::simple_moves::symmetry::ExtractAsymmetricUnitMover , protocols::simple_moves::symmetry::NCSResMapping , protocols::simple_moves::symmetry::SetupForSymmetryMover , protocols::simple_moves::symmetry::SetupNCSMover , protocols::simple_moves::symmetry::SymMinMover , protocols::simple_moves::symmetry::SymPackRotamersMover , protocols::simple_moves::symmetry::TaskAwareSymMinMover , protocols::simple_moves::TaskAwareMinMover , protocols::simple_moves::Tumble , protocols::simple_moves::UserDefinedGroupDiscriminator , protocols::simple_moves::VirtualRootMover , protocols::star::StarAbinitio , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::modeler::options::StepWiseModelerOptions , protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler , protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions , protocols::stepwise::options::StepWiseBasicOptions , protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::SurfaceDockingProtocol , protocols::surface_docking::SurfaceParameters , protocols::symmetric_docking::membrane::MPSymDockMover , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::symmetric_docking::SymDockProtocol , protocols::symmetric_docking::SymRestrictTaskForDocking , protocols::toolbox::AllowInsert , protocols::toolbox::DummyClass , 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::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::rotamer_set_operations::AddGood2BPairEnergyRotamers , protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO , protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO , protocols::toolbox::SF_Replica , protocols::toolbox::task_operations::AlignedThreadOperation , protocols::toolbox::task_operations::CrystalContactsOperation , protocols::toolbox::task_operations::DatabaseThread , protocols::toolbox::task_operations::DesignAroundOperation , protocols::toolbox::task_operations::DockingNoRepack1 , protocols::toolbox::task_operations::DockingNoRepack2 , protocols::toolbox::task_operations::DsspDesignOperation , protocols::toolbox::task_operations::ImportUnboundRotamersOperation , protocols::toolbox::task_operations::InteractingRotamerExplosion , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::LinkResidues , 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::RestrictConservedLowDdgOperation , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::toolbox::task_operations::RestrictIdentitiesOperation , 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::RestrictToInterface , protocols::toolbox::task_operations::RestrictToInterfaceOperation , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation , protocols::toolbox::task_operations::RestrictToLoops , protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors , protocols::toolbox::task_operations::RestrictToMoveMapChiOperation , protocols::toolbox::task_operations::RestrictToNeighborhoodOperation , protocols::toolbox::task_operations::RestrictToTerminiOperation , protocols::toolbox::task_operations::RetrieveStoredTaskOperation , protocols::toolbox::task_operations::SelectByDeltaScoreOperation , protocols::toolbox::task_operations::SelectByDensityFitOperation , protocols::toolbox::task_operations::SelectBySASAOperation , protocols::toolbox::task_operations::SelectResiduesWithinChainOperation , protocols::toolbox::task_operations::SeqprofConsensusOperation , protocols::toolbox::task_operations::SetIGTypeOperation , protocols::toolbox::task_operations::STMStoredTask , protocols::toolbox::task_operations::StoreCombinedStoredTasksMover , protocols::toolbox::task_operations::StoreCompoundTaskMover , protocols::toolbox::task_operations::StoreTaskMover , protocols::toolbox::task_operations::ThreadSequenceOperation , protocols::topology_broker::AsymFoldandDockClaimer , protocols::topology_broker::BasicJumpClaimer , protocols::topology_broker::claims::BBClaim , protocols::topology_broker::claims::CutClaim , protocols::topology_broker::claims::DofClaim , protocols::topology_broker::claims::JumpClaim , protocols::topology_broker::claims::LegacyRootClaim , protocols::topology_broker::claims::SequenceClaim , protocols::topology_broker::claims::SymmetryClaim , protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::CutBiasClaimer , protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::DisulfJumpClaimer , protocols::topology_broker::FibrilModelingClaimer , protocols::topology_broker::FoldandDockClaimer , protocols::topology_broker::FragmentClaimer , protocols::topology_broker::FragmentJumpClaimer , protocols::topology_broker::MembraneTopologyClaimer , protocols::topology_broker::MetalloClaimer , protocols::topology_broker::PcsEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4 , protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::SequenceClaimer , protocols::topology_broker::StartStructClaimer , protocols::topology_broker::SymmetryClaimer , protocols::topology_broker::TemplateFragmentClaimer , protocols::topology_broker::TemplateJumpClaimer , protocols::topology_broker::TMHTopologySamplerClaimer , protocols::topology_broker::TopologyClaimer , protocols::ub_e2c::ubi_e2c_modeler , protocols::wum::DatabaseEntryWorkUnit , protocols::wum::WorkUnit_MoverWrapper , protocols::wum::WorkUnit_SilentStructStore , protocols::wum::WorkUnit_Wait , protocols::wum::WorkUnitBase
• clone_modeler() : protocols::stepwise::modeler::StepWiseModeler
• clone_sampler() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• clone_scorefxn() : protocols::farna::RNA_Minimizer
• closable() : protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• close() : protocols::dna::DnaNeighbor , protocols::jd2::SingleFileBuffer
• close_all_loops() : protocols::farna::MultipleDomainMover
• close_at_all_cutpoints() : protocols::coarse_rna::CoarseRNA_LoopCloser
• close_at_cutpoint() : protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• close_bond() : protocols::generalized_kinematic_closure::GeneralizedKIC
• close_chainbreaks() : protocols::stepwise::modeler::StepWiseMinimizer
• close_channel() : protocols::jd2::MpiFileBuffer
• close_file() : protocols::jd2::MpiFileBuffer
• close_gaps() : protocols::loophash::LoopHashSampler
• close_loop_in_single_direction() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• close_loops() : protocols::abinitio::AbrelaxApplication
• close_loops_carefully() : protocols::farna::RNA_LoopCloser
• close_one_loop_stem() : protocols::antibody_legacy::CloseOneMover
• close_the_loop() : protocols::coarse_rna::CoarseRNA_LoopCloser
• close_with_idealization() : protocols::abinitio::AbrelaxMover
• closed_loop() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• CloseFold() : protocols::seeded_abinitio::CloseFold
• CloseOneCDRLoop() : protocols::antibody::CloseOneCDRLoop
• CloseOneMover() : protocols::antibody_legacy::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
• ClosureProblem() : protocols::kinematic_closure::ClosureProblem
• ClosureSolution() : protocols::kinematic_closure::ClosureSolution
• CloudPDBWriter() : protocols::match::output::CloudPDBWriter
• cluster() : protocols::abinitio::IterativeBase , protocols::antibody::clusters::CDRCluster , protocols::cluster::APCluster
• Cluster() : protocols::cluster::Cluster
• cluster() : protocols::comparative_modeling::AlignmentClustering , protocols::hotspot_hashing::HotspotStubSet , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased , protocols::toolbox::ClusterBase , protocols::toolbox::KCluster
• cluster_by_all_atom_rmsd() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• cluster_KeyFeatures() : protocols::pockets::GenPharmacophore
• cluster_loop() : protocols::forge::remodel::RemodelAccumulator
• Cluster_Member() : protocols::stepwise::legacy::modeler::rna::Cluster_Member
• cluster_pose() : protocols::forge::remodel::RemodelAccumulator
• cluster_pose_list() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection
• cluster_rmsd() : protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::options::StepWiseBasicOptions
• cluster_switch() : protocols::forge::remodel::RemodelAccumulator
• cluster_with_auto_tune() : protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• ClusterBase() : protocols::cluster::ClusterBase , protocols::toolbox::ClusterBase
• clusterCPockets() : protocols::pockets::PocketGrid
• clustered_best_poses() : protocols::forge::remodel::RemodelAccumulator
• clustered_pose_list() : protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• clustered_top_poses() : protocols::forge::remodel::RemodelAccumulator
• Clusterer() : protocols::mpi_refinement::Clusterer
• clusterlist() : protocols::toolbox::ClusterBase
• ClusterOptions() : protocols::toolbox::ClusterOptions
• ClusterPhilStyle() : protocols::cluster::ClusterPhilStyle , protocols::toolbox::ClusterPhilStyle
• ClusterPhilStyle_Loop() : protocols::cluster::ClusterPhilStyle_Loop
• ClusterPhilStyle_PoseReporter() : protocols::cluster::ClusterPhilStyle_PoseReporter
• clusterPockets() : protocols::pockets::PocketGrid
• ClusterPoseSelector() : protocols::pose_selectors::ClusterPoseSelector
• 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
• CoarseRNA_DeNovoProtocol() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• CoarseRNA_Fragments() : protocols::coarse_rna::CoarseRNA_Fragments
• CoarseRNA_LoopCloser() : protocols::coarse_rna::CoarseRNA_LoopCloser
• 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 , protocols::abinitio::IterativeCentroid
• collect_claims() : protocols::environment::EnvClaimBroker
• 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_elements() : protocols::environment::EnvClaimBroker
• collect_fragment_atom_ids() : protocols::electron_density::DensityMorphingMover
• 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
• com() : protocols::features::helixAssembly::HelicalFragment
• CoM() : protocols::pockets::FingerprintBase
• combine() : protocols::noesy_assign::Resonance
• combine_exclude_file() : protocols::abinitio::abscript::ConstraintPreparer
• combine_exclude_res() : protocols::abinitio::abscript::ConstraintPreparer
• combine_long_loop_mode() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• combine_ratio() : protocols::abinitio::abscript::ConstraintPreparer , protocols::topology_broker::ConstraintClaimer
• Combine_Tags_Info() : protocols::stepwise::modeler::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
• CombinePoseMover() : protocols::simple_moves::CombinePoseMover
• COMCoordinateConstraint() : protocols::constraints_additional::COMCoordinateConstraint
• comment_exists() : protocols::simple_filters::PoseComment
• comment_name() : protocols::simple_filters::PoseComment
• comment_value() : protocols::simple_filters::PoseComment
• commit_alt_bb_substitution() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• commit_considered_backbone_move() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• commit_considered_substitution() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• compact_bbindex() : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• Comparator() : protocols::environment::Comparator
• compare() : protocols::loophash::BackboneSegment
• compare_input_pose_geometry_to_reference() : protocols::simple_moves::GreenPacker
• compare_SizeRealPairs() : protocols::enzdes::EnzdesFlexibleRegion
• compare_to_native() : protocols::enzdes::DesignVsNativeComparison
• compare_to_ref() : protocols::matdes::SymUnsatHbondFilter
• CompareByScoreCombination() : protocols::frag_picker::CompareByScoreCombination
• compareCoverage() : protocols::pockets::ComparisonGrid
• CompareScoreComponent() : protocols::frag_picker::CompareScoreComponent
• CompareTags() : protocols::jd2::CompareTags
• CompareTotalScore() : protocols::frag_picker::CompareTotalScore
• ComparisonGrid() : protocols::pockets::ComparisonGrid
• compatibility_check() : protocols::forge::build::BuildManager
• compatible() : protocols::abinitio::AlternativePairings , protocols::abinitio::PairingStatEntry , 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_restype() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• compatible_with() : protocols::forge::build::BuildInstruction
• compatible_with_current_format() : protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::PeakFileFormat_Base
• complete() : protocols::genetic_algorithm::GeneticAlgorithmBase
• complete_deltaE_prediction_for_bbmove() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• complete_partial_state_assignment() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• CompleteConnectionsFilter() : protocols::ligand_docking::CompleteConnectionsFilter
• completed() : protocols::jd2::Job
• CompletionMessage() : protocols::jd2::archive::MPIArchiveJobDistributor::CompletionMessage
• component() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• ComposeSearchPatterns() : protocols::hotspot_hashing::ComposeSearchPatterns
• CompositeFragmentSelector() : protocols::frag_picker::CompositeFragmentSelector
• CompositionMover() : protocols::moves::CompositionMover
• CompoundDesignableTask() : protocols::toolbox::task_operations::StoreCompoundTaskMover
• CompoundFilter() : protocols::filters::CompoundFilter
• CompoundPackableTask() : protocols::toolbox::task_operations::StoreCompoundTaskMover
• CompoundTranslate() : protocols::ligand_docking::CompoundTranslate
• compute() : protocols::abinitio::PairingStatistics , protocols::denovo_design::filters::ExposedHydrophobicsFilter , protocols::enzdes::DiffAtomSasaFilter , protocols::enzdes::EnzScoreFilter , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::filters::CalculatorFilter , protocols::filters::CombinedFilter , protocols::filters::CompoundFilter , protocols::filters::IfThenFilter , protocols::filters::ReplicateFilter , protocols::filters::TimeFilter , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::fldsgn::MatchResidues , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::jumping::SameStrand , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::InterfacePackingFilter , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymUnsatHbondFilter , 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::ClashWithTargetFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::FNatFilter , protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::InterfaceHolesFilter , protocols::protein_interface_design::filters::IRmsdFilter , protocols::protein_interface_design::filters::LRmsdFilter , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::filters::RmsdSimpleFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::filters::SSamountFilter , protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::filters::Torsion , protocols::simple_filters::AngleToVector , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::AveragePathLengthFilter , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::DdgFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::DisulfideEntropyFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ExpiryFilter , protocols::simple_filters::FileExistFilter , protocols::simple_filters::FileRemoveFilter , protocols::simple_filters::GeometryFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterfaceBindingEnergyDensityFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::MotifScoreFilter , protocols::simple_filters::MultipleSigmoids , protocols::simple_filters::MutationsFilter , protocols::simple_filters::NeighborTypeFilter , protocols::simple_filters::NetChargeFilter , protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::NMerSVMEnergyFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::Operator , protocols::simple_filters::PackStatFilter , protocols::simple_filters::PoseComment , protocols::simple_filters::PoseInfoFilter , 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::RotamerBoltzmannWeight , protocols::simple_filters::SavePoseConstraintToFileFilter , protocols::simple_filters::ScoreTypeFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SidechainRmsdFilter , protocols::simple_filters::Sigmoid , protocols::simple_filters::SymmetricMotifFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_filters::TerminusDistanceFilter , protocols::simple_filters::TotalSasaFilter , protocols::toolbox::ClusterPhilStyle , protocols::toolbox::SelectResiduesByLayer
• 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_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_chi() : protocols::scoring::methods::saxs::PDDFEnergy
• compute_closure_metrics() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• compute_comb() : protocols::fldsgn::MatchResidues
• compute_cores() : protocols::abinitio::IterativeBase
• compute_d2() : protocols::simple_filters::SymmetricMotifFilter
• compute_designable_neighbors() : protocols::enzdes::PackRotamersMoverPartGreedy
• compute_distance_matrix() : protocols::toolbox::DecoySetEvaluation
• compute_energies() : protocols::features::StructureScoresFeatures , protocols::simple_moves::GreenPacker
• compute_energy_for_assignment() : protocols::pack_daemon::DaemonSet , protocols::pack_daemon::PackDaemon
• compute_entropy_reduction() : protocols::simple_filters::RotamerBoltzmannWeight
• compute_fragment_bias() : protocols::hybridization::CartesianSampler
• 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
• 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_jump() : protocols::simple_filters::SSMotifFinder
• compute_L1() : protocols::scoring::methods::saxs::PDDFEnergy
• compute_ligand_natoms() : protocols::pockets::PlaidFingerprint
• compute_ligand_natoms_with_hydrogens() : protocols::pockets::PlaidFingerprint
• compute_ligand_nconformers() : protocols::pockets::PlaidFingerprint
• compute_ligand_resnum() : protocols::pockets::PlaidFingerprint
• 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_number_cavities() : protocols::vip::VIP_Mover
• compute_one_body_energies_for_otf_ig() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• compute_onebody_interactions_with_background() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• 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_proposal_density() : protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• compute_rama_score() : protocols::loops::loop_closure::ccd::RamaCheck1B , protocols::loops::loop_closure::ccd::RamaCheck2B , protocols::loops::loop_closure::ccd::RamaCheckBase
• compute_rdf() : protocols::ligand_docking::ComputeLigandRDF
• compute_reference_intragroup_rpes() : protocols::simple_moves::GreenPacker
• compute_residual() : protocols::simple_filters::DisulfideEntropyFilter
• compute_residue() : protocols::simple_filters::NMerPSSMEnergyFilter
• compute_rmsd() : protocols::comparative_modeling::LoopRelaxMover
• compute_rotamer_energies_for_assigned_pdbs() : protocols::optimize_weights::IterativeOptEDriver
• 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_size() : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• compute_sr_one_body_energies_for_flexsets() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• compute_state_energies() : protocols::pack_daemon::MPIMultistateFitnessFunction , protocols::pack_daemon::MultistateFitnessFunction
• compute_swap_trim_CSPs() : protocols::ub_e2c::ubi_e2c_modeler
• compute_tempered_rotamer_probabilities() : protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover
• compute_total_score() : protocols::scoring::ResidualDipolarCouplingRigidSegments
• compute_transform_and_write_to_db() : protocols::features::LoopAnchorFeatures
• compute_trim_CSPs() : protocols::ub_e2c::ubi_e2c_modeler
• computeAllBoltz() : protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• computeBoltzSum() : protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• computeBoltzWeight() : protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• computeGradient() : protocols::viewer::triangleIterator
• computeGunnTuples() : protocols::frag_picker::scores::GunnCostScore
• ComputeLigandRDF() : protocols::ligand_docking::ComputeLigandRDF
• ComputeTotalDistCst() : protocols::abinitio::ComputeTotalDistCst
• CoMTrackerCM() : protocols::environment::CoMTrackerCM
• ConcurrencyTest() : protocols::features::helixAssembly::ConcurrencyTest
• ConcurrencyTestCreator() : protocols::features::helixAssembly::ConcurrencyTestCreator
• conf_size() : protocols::docking::DockingEnsemble
• configure() : protocols::abinitio::abscript::RigidChunkCM
• configure_new_scorefunction() : protocols::optimize_weights::IterativeOptEDriver
• confirm_sequence() : protocols::forge::remodel::RemodelMover
• conformationEvent() : protocols::moves::PyMolObserver
• ConformationViewer() : protocols::viewer::ConformationViewer
• ConformerSwitchMover() : protocols::docking::ConformerSwitchMover
• connect() : protocols::pockets::SmallMol
• connected() : protocols::pockets::SmallMol
• connected_components() : protocols::match::HitNeighborFinder
• connected_resonance_ids() : protocols::noesy_assign::Resonance
• connected_resonances() : protocols::noesy_assign::Resonance
• connections() : protocols::farna::RNA_StructureParameters
• connectivity_index() : protocols::toolbox::ResidueNetwork
• ConnectRight() : protocols::forge::build::ConnectRight
• ConsensusDesignMover() : protocols::simple_moves::ConsensusDesignMover
• conservation_cutoff_aligned_segments() : protocols::toolbox::task_operations::SeqprofConsensusOperation
• conservation_cutoff_protein_interface_design() : protocols::toolbox::task_operations::SeqprofConsensusOperation
• ConservativeDesignOperation() : protocols::antibody::design::ConservativeDesignOperation
• ConservedPosMutationFilter() : protocols::simple_filters::ConservedPosMutationFilter
• 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() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• consolidate_matches() : protocols::match::MatcherTask
• const_full_to_sub() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• const_state() : protocols::wum2::WorkUnit_ElScripts
• const_states() : protocols::multistate_design::MultiStateFitnessFunction
• const_sub_to_full() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• ConstAbinitioMoverWeight() : protocols::topology_broker::weights::ConstAbinitioMoverWeight
• ConstantScoreBase() : protocols::qsar::scoring_grid::ConstantScoreBase
• 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
• constrain_to_antigen_chains() : protocols::antibody::constraints::ParatopeSiteConstraintMover
• constrain_to_epitope_residues() : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover
• constrain_to_paratope_cdrs() : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover
• constrain_to_paratope_residues() : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover
• constrained_lig_atoms() : protocols::enzdes::EnzdesConstraintReporter
• constrained_nonligand_atoms() : protocols::enzdes::EnzdesConstraintReporter
• constraint_energy() : protocols::enzdes::LigInterfaceEnergyFilter
• constraint_file() : protocols::simple_moves::ConstraintSetMover
• constraint_set() : protocols::simple_moves::ConstraintSetMover
• ConstraintClaimer() : protocols::topology_broker::ConstraintClaimer
• 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
• ConstraintFileRCG() : protocols::forge::constraints::ConstraintFileRCG
• ConstraintFragmentSampler() : protocols::abinitio::ConstraintFragmentSampler
• ConstrainToIdealMover() : protocols::simple_moves::ConstrainToIdealMover
• ConstraintPreparer() : protocols::abinitio::abscript::ConstraintPreparer
• constraints() : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::Template , protocols::hotspot_hashing::HotspotStubSet
• constraints_only() : protocols::idealize::IdealizeMover
• ConstraintScoreCutoffFilter() : protocols::simple_filters::ConstraintScoreCutoffFilter
• ConstraintSetMover() : protocols::simple_moves::ConstraintSetMover
• ConstraintSetScore() : protocols::sic_dock::ConstraintSetScore
• construct_and_dump_outpose() : protocols::enzdes::PoseFoundResiduesCombination
• ConstScore() : protocols::frag_picker::scores::ConstScore
• Contact() : protocols::contact_map::Contact
• contact() : protocols::dna::DnaNeighbor
• Contact() : protocols::frag_picker::Contact
• contact_buried_problematic_res() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• contact_dist() : protocols::matdes::InterfacePackingFilter
• contact_distance() : protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::NcontactsCalculator
• contact_list() : protocols::scoring::Interface
• contact_order() : protocols::abinitio::PairingStatEntry
• ContactCounts() : protocols::frag_picker::ContactCounts
• ContactMap() : protocols::contact_map::ContactMap
• ContactMapEvaluator() : protocols::simple_filters::ContactMapEvaluator
• ContactMapEvaluatorCreator() : protocols::simple_filters::ContactMapEvaluatorCreator
• ContactPartner() : protocols::contact_map::ContactPartner
• contacts() : protocols::sic_dock::Rose
• contacts_naive() : protocols::sic_dock::Rose
• contains() : protocols::dna::DnaChains , protocols::forge::build::Interval
• contains_catalytic_res() : protocols::enzdes::EnzdesFlexibleRegion
• contains_position() : protocols::toolbox::match_enzdes_util::EnzConstraintIO , protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache , protocols::toolbox::match_enzdes_util::EnzdesCstCache , protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• contents_in_pose_store() : protocols::forge::remodel::RemodelAccumulator
• ContingentAcceptMover() : protocols::simple_moves::ContingentAcceptMover
• ContingentFilter() : protocols::filters::ContingentFilter
• continue_slide() : protocols::simple_moves::symmetry::SymmetrySlider
• control_grid_param() : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• controlling_chi_for_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• converged() : protocols::optimize_weights::IterativeOptEDriver
• convert_cart_to_spherical_and_round() : protocols::pockets::NonPlaidFingerprint
• convert_GeomSampleInfo_to_FuncOP() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• convert_matrix_to_xyz() : protocols::hybridization::TMalign
• convert_scores_to_probabilities() : protocols::toolbox::task_operations::SeqprofConsensusOperation
• convert_silent_file_to_pose_data_list() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• convert_spherical_list_to_cartesian_list() : protocols::pockets::NonPlaidFingerprint
• convert_to_centroid() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• convert_to_rotation_matrix() : protocols::stepwise::sampler::rigid_body::EulerAngles
• convert_to_torsion_crd() : protocols::normalmode::NormalMode
• 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
• coord() : protocols::match::downstream::TargetRotamerCoords
• coord2key() : protocols::canonical_sampling::HamiltonianExchange
• coord_dev() : protocols::simple_moves::AddConstraintsToCurrentConformationMover
• coord_sdev() : protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots
• CoordConstraintClaimer() : protocols::topology_broker::CoordConstraintClaimer
• coordinate_cacher() : protocols::match::output::PDBWriter
• 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
• 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
• coords() : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::ligand_docking::StartFrom , protocols::toolbox::DecoySetEvaluation , protocols::toolbox::KClusterData
• coordTransformFromThreePoints() : protocols::rbsegment_relax::RBSegmentMover
• copy() : protocols::docking::DockSetupMover , protocols::docking::TemperedDocking , protocols::toolbox::task_operations::RestrictToLoops
• copy_all_o2prime_torsions() : protocols::stepwise::modeler::rna::o2prime::O2PrimePacker
• copy_alternate_to_current() : protocols::flexpack::interaction_graph::FlexbbEdge , protocols::flexpack::interaction_graph::FlexbbNode
• copy_CCD_torsions() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker
• copy_CCD_torsions_general() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker
• copy_comments() : protocols::simple_filters::RelativePoseFilter
• copy_coord() : protocols::toolbox::KMedoid
• copy_coordinates() : protocols::frag_picker::DiversifyCrmsdByClustering , protocols::frag_picker::DiversifyCrmsdSelector
• copy_coords() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• copy_data() : protocols::canonical_sampling::BiasEnergy::Histogram< T > , protocols::docking::EllipsoidalRandomizationMover , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::RamaCheck1B , protocols::loops::loop_closure::ccd::RamaCheck2B , protocols::loops::loop_closure::ccd::RamaCheckBase , protocols::match::output::MatchScoreWriter , protocols::simple_moves::RingConformationMover , protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::SurfaceDockingProtocol
• copy_dna_chains() : protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::RestrictDesignToProteinDNAInterface
• copy_dofs_rotamer() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList
• copy_fragments() : protocols::frags::FragLib , protocols::frags::SingleResidueTorsionFragmentLibrary , protocols::frags::TorsionFragmentLibrary
• copy_from_ref() : protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• copy_hit() : protocols::match::downstream_hit , protocols::match::upstream_hit
• copy_interface() : protocols::dna::RestrictDesignToProteinDNAInterface
• copy_native_packertask_logic() : protocols::optimize_weights::IterativeOptEDriver
• copy_native_structure() : protocols::abinitio::AbrelaxApplication
• copy_next_pose_segment() : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• copy_pdbinfo() : protocols::grafting::GraftMoverBase
• copy_phi_psi_omega() : protocols::simple_moves::RepeatPropagationMover
• copy_phosphates() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• copy_rna_chi() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• copy_sidechains() : protocols::comparative_modeling::LoopRelaxMover
• copy_stretch() : protocols::simple_filters::RelativePoseFilter
• copy_structure() : protocols::abinitio::AbrelaxApplication
• copy_targeted_dna() : protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::RestrictDesignToProteinDNAInterface
• copy_to_centroid() : protocols::metal_interface::ZincHeterodimerMover
• copy_without_output() : protocols::jd2::Job
• CopyDofMover() : protocols::simple_moves::CopyDofMover
• CopyDofStepWiseSampler() : protocols::stepwise::sampler::copy_dofs::CopyDofStepWiseSampler
• copying_side_chains() : protocols::seeded_abinitio::SwapSegment
• core() : protocols::abinitio::IterativeBase
• CoreDunbrackFilter() : protocols::fldsgn::filters::CoreDunbrackFilter
• corners() : protocols::match::Bool3DGrid
• correct_jump_atoms_for_fragments() : protocols::jumping::JumpSample
• CorrectionVisitor() : protocols::sic_dock::CorrectionVisitor
• correctly_copy_HO2prime_positions() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• correspondence() : protocols::pack_daemon::PackDaemon
• corresponding_res_block() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• could_be_accepted() : protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaPool , protocols::frag_picker::quota::SecondaryStructurePool
• could_not_create_resource_error_message() : protocols::loops::LoopsFileFallbackConfiguration , protocols::surface_docking::SurfaceVectorFallbackConfiguration
• count() : protocols::stepwise::screener::StepWiseScreener
• count_accepted() : protocols::canonical_sampling::MultiTemperatureTrialCounter , protocols::moves::TrialCounter
• count_assignments() : protocols::noesy_assign::CrossPeakList
• count_bb_atoms() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• count_bb_atoms_in_residue() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• count_candidates() : protocols::frag_picker::BoundedCollector< StrictWeakOrdering > , protocols::frag_picker::CandidatesCollector , protocols::frag_picker::GrabAllCollector , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaCollector , protocols::frag_picker::quota::QuotaPool , protocols::frag_picker::quota::SecondaryStructurePool
• count_children() : protocols::loop_modeling::LoopMover
• count_clashes_between_two_poses() : protocols::motif_grafting::movers::MotifGraftMover
• count_components() : protocols::frag_picker::scores::FragmentScoreManager
• count_data() : protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• count_dynamic_memory() : protocols::flexpack::interaction_graph::FlexbbEdge , protocols::flexpack::interaction_graph::FlexbbInteractionGraph , protocols::flexpack::interaction_graph::FlexbbNode , protocols::flexpack::interaction_graph::MinimalistFlexbbEdge , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbNode , protocols::flexpack::interaction_graph::OTFFlexbbEdge , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flexpack::interaction_graph::OTFFlexbbNode
• count_energy_drop() : protocols::canonical_sampling::MultiTemperatureTrialCounter , protocols::moves::TrialCounter
• count_energy_to_node_in_my_fragtotalE() : protocols::flexpack::interaction_graph::FlexbbNode
• count_file_reads() : protocols::pack_daemon::DynamicAggregateFunction
• count_inserted() : 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_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_static_memory() : protocols::flexpack::interaction_graph::MinimalistFlexbbEdge , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• count_structure() : protocols::jd2::archive::ArchiveBase
• count_trial() : protocols::canonical_sampling::MultiTemperatureTrialCounter , protocols::moves::TrialCounter
• counts() : protocols::frag_picker::ContactCounts
• CoupledMover() : protocols::simple_moves::CoupledMover
• covalent_connections() : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• CovalentCompliance() : protocols::noesy_assign::CovalentCompliance
• CovalentConnectionReplaceInfo() : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• crankshaft_alpha_gamma() : protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• cranny_packer() : protocols::vip::VIP_Mover
• create() : protocols::forge::build::BuildManager , protocols::inputter::FastaInputter , protocols::inputter::Inputter , protocols::inputter::PDBInputter , protocols::inputter::SilentFileInputter , protocols::moves::Mover , protocols::outputter::FormatStringOutputter , protocols::outputter::Outputter , protocols::outputter::PDBOutputter , protocols::outputter::ResFileOutputter , protocols::outputter::SilentFileOutputter , protocols::simple_moves::O2M_MutateMover , protocols::toolbox::DummyClass , protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• create_and_attach_task_factory() : protocols::docking::DockTaskFactory
• create_atom_tree() : protocols::protein_interface_design::movers::SetAtomTree
• create_bb_moves() : protocols::abinitio::KinematicAbinitio
• 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::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• create_comparer() : protocols::rotamer_recovery::RRComparerAutomorphicRMSDCreator , protocols::rotamer_recovery::RRComparerChiDiffCreator , protocols::rotamer_recovery::RRComparerCreator , protocols::rotamer_recovery::RRComparerElecDensDiffCreator , protocols::rotamer_recovery::RRComparerRotBinsCreator
• create_consensus_design_task() : protocols::simple_moves::ConsensusDesignMover
• create_constraint() : protocols::constraints_additional::BindingSiteConstraintCreator , protocols::constraints_additional::NamedAtomPairConstraintCreator , protocols::constraints_additional::SequenceCoupling1BDConstraintCreator , protocols::constraints_additional::SequenceCouplingConstraintCreator , protocols::noesy_assign::PeakAssignment , protocols::pockets::PocketConstraintCreator
• create_constraints() : protocols::cluster::ClusterBase
• create_coordinate_constraints() : protocols::stepwise::modeler::align::StepWisePoseAligner
• create_data() : protocols::abinitio::abscript::JumpSampleDataCreator , protocols::environment::AutoCutDataCreator
• create_db() : protocols::loophash::LoopHashLibrary
• create_dense_pdig_from_rot_to_pack() : protocols::pack_daemon::DenseIGRepacker , protocols::pack_daemon::DoubleDenseIGRepacker
• create_directed_dependency() : protocols::fldsgn::BluePrintBDR , protocols::forge::build::BuildManager , protocols::forge::components::BDR
• create_dist_constraints() : protocols::toolbox::DecoySetEvaluation
• create_dist_constraints_median() : protocols::toolbox::DecoySetEvaluation
• create_ds_builder() : protocols::match::Matcher
• create_embedding_virtual() : protocols::membrane::visualize::VisualizeEmbeddingMover
• create_empty_map() : protocols::frag_picker::scores::FragmentScoreManager
• create_energy_method() : protocols::fldsgn::potentials::AACompositionEnergyCreator , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergyCreator , protocols::scoring::methods::EnsembleEnergyCreator , protocols::scoring::methods::InterchainEnvEnergyCreator , protocols::scoring::methods::InterchainPairEnergyCreator , protocols::scoring::methods::pcs2::PcsEnergyCreator , protocols::scoring::methods::pcs::PseudocontactShiftEnergyCreator , protocols::scoring::methods::pcsTs1::PseudocontactShiftEnergyCreator_Ts1 , protocols::scoring::methods::pcsTs2::PseudocontactShiftEnergyCreator_Ts2 , protocols::scoring::methods::pcsTs3::PseudocontactShiftEnergyCreator_Ts3 , protocols::scoring::methods::pcsTs4::PseudocontactShiftEnergyCreator_Ts4 , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegmentsCreator , protocols::scoring::methods::saxs::PDDFEnergy , protocols::scoring::methods::saxs::PDDFEnergyCreator , protocols::scoring::methods::SpecialRotamerEnergyCreator
• 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_fallback_configuration() : protocols::loops::LoopsFileFallbackConfigurationCreator , protocols::surface_docking::SurfaceVectorFallbackConfigurationCreator
• create_faster_ig_from_rot_to_pack() : protocols::pack_daemon::FASTER_IG_Repacker
• create_features_reporter() : protocols::antibody::AntibodyFeaturesCreator , protocols::antibody::clusters::CDRClusterFeaturesCreator , protocols::features::AtomAtomPairFeaturesCreator , protocols::features::AtomInResidueAtomInResiduePairFeaturesCreator , protocols::features::AtomTypesFeaturesCreator , protocols::features::BetaTurnDetectionFeaturesCreator , protocols::features::ChargeChargeFeaturesCreator , protocols::features::DdGFeaturesCreator , protocols::features::FeaturesReporterCreator , protocols::features::GeometricSolvationFeaturesCreator , protocols::features::HBondFeaturesCreator , protocols::features::HBondParameterFeaturesCreator , protocols::features::helixAssembly::ConcurrencyTestCreator , protocols::features::helixAssembly::HelixBundleFeaturesCreator , protocols::features::HelixCapFeaturesCreator , protocols::features::InterfaceFeaturesCreator , protocols::features::JobDataFeaturesCreator , protocols::features::LoopAnchorFeaturesCreator , protocols::features::OrbitalsFeaturesCreator , protocols::features::PairFeaturesCreator , protocols::features::PdbDataFeaturesCreator , protocols::features::PoseCommentsFeaturesCreator , protocols::features::PoseConformationFeaturesCreator , protocols::features::ProteinBackboneAtomAtomPairFeaturesCreator , protocols::features::ProteinBackboneTorsionAngleFeaturesCreator , protocols::features::ProteinBondGeometryFeaturesCreator , protocols::features::ProteinResidueConformationFeaturesCreator , protocols::features::ProteinRMSDFeaturesCreator , protocols::features::ProteinRMSDNoSuperpositionFeaturesCreator , protocols::features::RadiusOfGyrationFeaturesCreator , protocols::features::ResidueBurialFeaturesCreator , protocols::features::ResidueConformationFeaturesCreator , protocols::features::ResidueFeaturesCreator , protocols::features::ResidueGridScoresFeaturesCreator , protocols::features::ResidueScoresFeaturesCreator , protocols::features::ResidueSecondaryStructureFeaturesCreator , protocols::features::ResidueTotalScoresFeaturesCreator , protocols::features::ResidueTypesFeaturesCreator , protocols::features::RotamerBoltzmannWeightFeaturesCreator , protocols::features::RotamerFeaturesCreator , protocols::features::RotamerRecoveryFeaturesCreator , protocols::features::RuntimeFeaturesCreator , protocols::features::SaltBridgeFeaturesCreator , protocols::features::ScoreFunctionFeaturesCreator , protocols::features::ScoreTypeFeaturesCreator , protocols::features::ScreeningFeaturesCreator , protocols::features::SecondaryStructureSegmentFeaturesCreator , protocols::features::SmotifFeaturesCreator , protocols::features::strand_assembly::SandwichFeaturesCreator , protocols::features::strand_assembly::StrandBundleFeaturesCreator , protocols::features::StructureFeaturesCreator , protocols::features::StructureScoresFeaturesCreator , protocols::features::TaskOperationFeaturesCreator , protocols::features::TotalScoreFeaturesCreator , protocols::features::TrajectoryMapFeaturesCreator , protocols::features::UnrecognizedAtomFeaturesCreator , protocols::features::WaterFeaturesCreator
• create_filter() : protocols::analysis::PeptideDeriverFilterCreator , protocols::denovo_design::filters::ExposedHydrophobicsFilterCreator , protocols::enzdes::DiffAtomSasaFilterCreator , protocols::enzdes::EnzdesScorefileFilterCreator , protocols::enzdes::EnzScoreFilterCreator , protocols::enzdes::LigBurialFilterCreator , protocols::enzdes::LigDSasaFilterCreator , protocols::enzdes::LigInterfaceEnergyFilterCreator , protocols::enzdes::RemoveLigandFilterCreator , protocols::enzdes::RepackWithoutLigandFilterCreator , protocols::enzdes::ResidueConformerFilterCreator , protocols::filters::CalculatorFilterCreator , protocols::filters::CombinedFilterCreator , protocols::filters::CompoundFilterCreator , protocols::filters::ContingentFilterCreator , protocols::filters::FalseFilterCreator , protocols::filters::FilterCreator , protocols::filters::IfThenFilterCreator , protocols::filters::MoveBeforeFilterCreator , protocols::filters::ReplicateFilterCreator , protocols::filters::StochasticFilterCreator , protocols::filters::TimeFilterCreator , protocols::filters::TrueFilterCreator , protocols::fldsgn::filters::CoreDunbrackFilterCreator , protocols::fldsgn::filters::FragQualFilterCreator , protocols::fldsgn::filters::HelixKinkFilterCreator , protocols::fldsgn::filters::HelixPairingFilterCreator , protocols::fldsgn::filters::HSSTripletFilterCreator , protocols::fldsgn::filters::InterlockingAromaFilterCreator , protocols::fldsgn::filters::NcontactsFilterCreator , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilterCreator , protocols::fldsgn::filters::SecondaryStructureCountFilterCreator , protocols::fldsgn::filters::SecondaryStructureFilterCreator , protocols::fldsgn::filters::SecondaryStructureHasResidueFilterCreator , protocols::fldsgn::filters::SheetTopologyFilterCreator , protocols::indexed_structure_store::filters::FragmentLookupFilterCreator , protocols::ligand_docking::AtomCountFilterCreator , protocols::ligand_docking::ChainExistsFilterCreator , protocols::ligand_docking::CompleteConnectionsFilterCreator , protocols::ligand_docking::HBondAcceptorFilterCreator , protocols::ligand_docking::HBondDonorFilterCreator , protocols::ligand_docking::HeavyAtomFilterCreator , protocols::ligand_docking::MolarMassFilterCreator , protocols::ligand_docking::MolecularMassFilterCreator , protocols::matdes::ClashCheckFilterCreator , protocols::matdes::GetRBDOFValuesCreator , protocols::matdes::InterfacePackingFilterCreator , protocols::matdes::OligomericAverageDegreeFilterCreator , protocols::matdes::SymUnsatHbondFilterCreator , protocols::protein_interface_design::filters::AtomicContactCountFilterCreator , protocols::protein_interface_design::filters::AverageDegreeFilterCreator , protocols::protein_interface_design::filters::BindingStrainFilterCreator , protocols::protein_interface_design::filters::BoltzmannFilterCreator , protocols::protein_interface_design::filters::ClashWithTargetFilterCreator , protocols::protein_interface_design::filters::DesignableResiduesFilterCreator , protocols::protein_interface_design::filters::DisulfideFilterCreator , protocols::protein_interface_design::filters::FilterScanFilterCreator , protocols::protein_interface_design::filters::FNatFilterCreator , protocols::protein_interface_design::filters::HbondsToAtomFilterCreator , protocols::protein_interface_design::filters::HbondsToResidueFilterCreator , protocols::protein_interface_design::filters::InterfaceHolesFilterCreator , protocols::protein_interface_design::filters::IRmsdFilterCreator , protocols::protein_interface_design::filters::LRmsdFilterCreator , protocols::protein_interface_design::filters::RelativeSegmentFilterCreator , protocols::protein_interface_design::filters::RmsdFilterCreator , protocols::protein_interface_design::filters::RmsdSimpleFilterCreator , protocols::protein_interface_design::filters::SequenceRecoveryFilterCreator , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilterCreator , protocols::protein_interface_design::filters::SSamountFilterCreator , protocols::protein_interface_design::filters::StubScoreFilterCreator , protocols::protein_interface_design::filters::StubScoreLoopsFilterCreator , protocols::protein_interface_design::filters::TorsionCreator , protocols::simple_filters::AlaScanFilterCreator , protocols::simple_filters::AngleToVectorFilterCreator , protocols::simple_filters::AtomicContactFilterCreator , protocols::simple_filters::AtomicDistanceFilterCreator , protocols::simple_filters::AveragePathLengthFilterCreator , protocols::simple_filters::BuriedUnsatHbondFilterCreator , protocols::simple_filters::ConservedPosMutationFilterCreator , protocols::simple_filters::ConstraintScoreCutoffFilterCreator , protocols::simple_filters::DdgFilterCreator , protocols::simple_filters::DdGScanCreator , protocols::simple_filters::DeltaFilterCreator , protocols::simple_filters::DisulfideEntropyFilterCreator , protocols::simple_filters::EnergyPerResidueFilterCreator , protocols::simple_filters::ExpiryFilterCreator , protocols::simple_filters::FileExistFilterCreator , protocols::simple_filters::FileRemoveFilterCreator , protocols::simple_filters::GeometryFilterCreator , protocols::simple_filters::HolesFilterCreator , protocols::simple_filters::InterfaceBindingEnergyDensityFilterCreator , protocols::simple_filters::InterfaceSasaFilterCreator , protocols::simple_filters::InterRepeatContactFilterCreator , protocols::simple_filters::IntraRepeatContactFilterCreator , protocols::simple_filters::MotifScoreFilterCreator , protocols::simple_filters::MultipleSigmoidsFilterCreator , protocols::simple_filters::MutationsFilterCreator , protocols::simple_filters::NeighborTypeFilterCreator , protocols::simple_filters::NetChargeFilterCreator , protocols::simple_filters::NMerPSSMEnergyFilterCreator , protocols::simple_filters::NMerSVMEnergyFilterCreator , protocols::simple_filters::NonSequentialNeighborsFilterCreator , protocols::simple_filters::OperatorFilterCreator , protocols::simple_filters::PackStatFilterCreator , protocols::simple_filters::PoseCommentFilterCreator , protocols::simple_filters::PoseInfoFilterCreator , protocols::simple_filters::RangeFilterCreator , protocols::simple_filters::RelativePoseFilterCreator , protocols::simple_filters::RepeatParameterFilterCreator , protocols::simple_filters::ReportFilterCreator , protocols::simple_filters::ResidueBurialFilterCreator , protocols::simple_filters::ResidueCountFilterCreator , protocols::simple_filters::ResidueDistanceFilterCreator , protocols::simple_filters::ResidueIEFilterCreator , protocols::simple_filters::ResidueSetChainEnergyFilterCreator , protocols::simple_filters::ResiduesInInterfaceFilterCreator , protocols::simple_filters::RotamerBoltzmannWeightFilterCreator , protocols::simple_filters::SavePoseConstraintToFileFilterCreator , protocols::simple_filters::SaveResfileToDiskFilterCreator , protocols::simple_filters::ScoreCutoffFilterCreator , protocols::simple_filters::ScoreTypeFilterCreator , protocols::simple_filters::ShapeComplementarityFilterCreator , protocols::simple_filters::SidechainRmsdFilterCreator , protocols::simple_filters::SigmoidFilterCreator , protocols::simple_filters::SSMotifFinderFilterCreator , protocols::simple_filters::StemFinderFilterCreator , protocols::simple_filters::SymmetricMotifFilterCreator , protocols::simple_filters::TaskAwareSASAFilterCreator , protocols::simple_filters::TaskAwareScoreTypeFilterCreator , protocols::simple_filters::TerminusDistanceFilterCreator , protocols::simple_filters::TotalSasaFilterCreator
• create_filters() : protocols::match::output::ProcessorFactory
• create_flexbb_interaction_graph() : protocols::flexpack::interaction_graph::FlexbbIGFactory
• create_float_constraint() : protocols::noesy_assign::PeakAssignment
• 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_fragment_movers_limit_size() : protocols::forge::remodel::RemodelLoopMover
• create_fresh_packer_neighbor_graph() : protocols::simple_moves::GreenPacker
• create_fresh_rotamers() : protocols::simple_moves::GreenPacker
• create_fresh_task() : protocols::simple_moves::GreenPacker
• create_from_pose() : protocols::toolbox::ResidueNetwork
• create_grid() : protocols::qsar::scoring_grid::AtrGridCreator , protocols::qsar::scoring_grid::ChargeGridCreator , protocols::qsar::scoring_grid::ClassicGridCreator , protocols::qsar::scoring_grid::GridCreator , protocols::qsar::scoring_grid::HbaGridCreator , protocols::qsar::scoring_grid::HbdGridCreator , protocols::qsar::scoring_grid::LigandPropertyScoreCreator , protocols::qsar::scoring_grid::RepGridCreator , protocols::qsar::scoring_grid::ShapeGridCreator , protocols::qsar::scoring_grid::SolvationGridCreator , protocols::qsar::scoring_grid::SolvationMetaGridCreator , protocols::qsar::scoring_grid::VdwGridCreator
• 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_job_distributor() : protocols::jd2::JobDistributorFactory
• create_job_inputter() : protocols::jd2::JobDistributorFactory
• create_job_outputter() : protocols::jd2::JobDistributorFactory
• create_JobInputter() : protocols::comparative_modeling::GenericJobInputterCreator , protocols::comparative_modeling::ThreadingJobInputterCreator , protocols::enzdes::EnzdesJobInputterCreator , protocols::features::DatabaseJobInputterCreator , protocols::jd2::AtomTreeDiffJobInputterCreator , protocols::jd2::JD2ResourceManagerJobInputterCreator , protocols::jd2::JobInputterCreator , protocols::jd2::LazySilentFileJobInputterCreator , protocols::jd2::PDBJobInputterCreator , protocols::jd2::PoseInputStreamJobInputterCreator , protocols::jd2::ScreeningJobInputterCreator , protocols::jd2::SilentFileJobInputterCreator , protocols::make_rot_lib::MakeRotLibJobInputterCreator , protocols::protein_interface_design::ParserJobInputterCreator
• create_JobOutputter() : protocols::enzdes::EnzdesJobOutputterCreator , protocols::features::DatabaseJobOutputterCreator , protocols::jd2::AtomTreeDiffJobOutputterCreator , protocols::jd2::JobOutputterCreator , protocols::jd2::NoOutputJobOutputterCreator , protocols::jd2::PDBJobOutputterCreator , protocols::jd2::ScoreOnlyJobOutputterCreator , protocols::jd2::SilentFileJobOutputterCreator
• create_jump_def() : protocols::abinitio::Templates
• create_jump_fragments() : protocols::jumping::BasePairingLibrary , protocols::jumping::DisulfPairingLibrary , protocols::jumping::PairingLibrary
• create_jump_moves() : protocols::abinitio::KinematicAbinitio
• create_jump_sample() : protocols::abinitio::FixTemplateJumpSetup , protocols::abinitio::TemplateJumpSetup , protocols::jumping::BaseJumpSetup , protocols::jumping::JumpSelector , protocols::jumping::JumpSetup , protocols::jumping::JumpsFromAllPairings , protocols::jumping::ResiduePairJumpSetup , protocols::jumping::SheetBuilder
• create_key() : protocols::frag_picker::VallChunk
• create_large_cluster_centers_member_list() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• create_loader() : protocols::jd2::parser::DataLoaderCreator , protocols::jd2::parser::FragSetLoaderCreator , protocols::jd2::parser::MonteCarloLoaderCreator , protocols::jd2::parser::ResidueSelectorLoaderCreator , protocols::jd2::parser::ScoreFunctionLoaderCreator , protocols::jd2::parser::TaskOperationLoaderCreator , protocols::ligand_docking::InterfaceBuilderLoaderCreator , protocols::ligand_docking::LigandAreaLoaderCreator , protocols::ligand_docking::MoveMapBuilderLoaderCreator , protocols::loops::loops_definers::LoopsDefinerLoaderCreator , 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::LoopsDatabaseDefinerCreator , protocols::loops::loops_definers::LoopsDefinerCreator , protocols::loops::loops_definers::LoopsDefinerFactory , protocols::loops::loops_definers::LoopsExplicitDefinerCreator , protocols::loops::loops_definers::LoopsFileDefinerCreator
• create_map_helix_pairings() : protocols::fldsgn::topology::HelixPairingSet
• create_match_score_writer() : protocols::match::output::ProcessorFactory
• create_membrane_virtual() : protocols::membrane::visualize::VisualizeMembraneMover
• create_mover() : protocols::abinitio::abscript::AbscriptLoopCloserCMCreator , protocols::abinitio::abscript::AbscriptMoverCreator , protocols::abinitio::abscript::ConstraintPreparerCreator , protocols::abinitio::abscript::FragmentCMCreator , protocols::abinitio::abscript::FragmentJumpCMCreator , protocols::abinitio::abscript::RigidChunkCMCreator , protocols::abinitio::abscript::StructPerturberCMCreator , protocols::abinitio::DomainAssemblyCreator , protocols::analysis::InterfaceAnalyzerMoverCreator , protocols::backrub::BackrubMoverCreator , protocols::backrub::BackrubSidechainMoverCreator , protocols::canonical_sampling::DbTrajectoryRecorderCreator , protocols::canonical_sampling::HamiltonianExchangeCreator , protocols::canonical_sampling::MetricRecorderCreator , protocols::canonical_sampling::MetropolisHastingsMoverCreator , protocols::canonical_sampling::ParallelTemperingCreator , protocols::canonical_sampling::PDBTrajectoryRecorderCreator , protocols::canonical_sampling::ProgressBarObserverCreator , protocols::canonical_sampling::SidechainMetropolisHastingsMoverCreator , protocols::canonical_sampling::SilentTrajectoryRecorderCreator , protocols::canonical_sampling::SimulatedTemperingCreator , protocols::canonical_sampling::TrialCounterObserverCreator , protocols::comparative_modeling::LoopRelaxMoverCreator , protocols::contact_map::ContactMapCreator , protocols::cryst::FitBfactorsMoverCreator , protocols::cryst::LoadDensityMapMoverCreator , protocols::cryst::RecomputeDensityMapMoverCreator , protocols::cryst::SetCrystWeightMoverCreator , protocols::cryst::SetRefinementOptionsMoverCreator , protocols::cryst::TagPoseWithRefinementStatsMoverCreator , protocols::cryst::UpdateSolventMoverCreator , protocols::cyclic_peptide::CreateAngleConstraintCreator , protocols::cyclic_peptide::CreateDistanceConstraintCreator , protocols::cyclic_peptide::CreateTorsionConstraintCreator , protocols::cyclic_peptide::DeclareBondCreator , protocols::cyclic_peptide::PeptideStubMoverCreator , protocols::design_opt::GreedyOptMutationMoverCreator , protocols::design_opt::ParetoOptMutationMoverCreator , protocols::dna::DesignProteinBackboneAroundDNACreator , protocols::dna::DnaInterfaceMinMoverCreator , protocols::dna::DnaInterfaceMultiStateDesignCreator , protocols::dna::DnaInterfacePackerCreator , protocols::dna::SeparateDnaFromNonDnaCreator , protocols::docking::ConformerSwitchMoverCreator , protocols::docking::DockingInitialPerturbationCreator , protocols::docking::DockingProtocolCreator , protocols::docking::DockSetupMoverCreator , protocols::docking::membrane::MPDockingMoverCreator , protocols::docking::membrane::MPDockingSetupMoverCreator , protocols::docking::TemperedDockingCreator , protocols::electron_density::BfactorFittingMoverCreator , protocols::electron_density::DensityMorphingMoverCreator , protocols::electron_density::ReportFSCCreator , protocols::electron_density::ScaleMapIntensitiesCreator , protocols::electron_density::SetupForDensityScoringMoverCreator , protocols::environment::CoMTrackerCMCreator , protocols::environment::EnvMoverCreator , protocols::environment::ScriptCMCreator , protocols::enzdes::AddOrRemoveMatchCstsCreator , protocols::enzdes::BackboneSamplerCreator , protocols::enzdes::EnzRepackMinimizeCreator , protocols::enzdes::PackRotamersMoverPartGreedyCreator , protocols::enzdes::PredesignPerturbMoverCreator , protocols::enzdes::UpdateEnzdesHeaderMoverCreator , protocols::features::ReportToDBCreator , protocols::features::TrajectoryReportToDBCreator , protocols::fldsgn::BluePrintBDRCreator , protocols::fldsgn::CircularPermutationCreator , protocols::fldsgn::MatchResiduesMoverCreator , protocols::fldsgn::potentials::SetAACompositionPotentialCreator , protocols::fldsgn::potentials::SetSecStructEnergiesCreator , protocols::fldsgn::SheetCstGeneratorCreator , protocols::flexpep_docking::FlexPepDockingProtocolCreator , protocols::flxbb::FlxbbDesignCreator , protocols::flxbb::InterlockAromaCreator , protocols::forge::constraints::ConstraintFileCstGeneratorCreator , protocols::forge::constraints::InverseRotamersCstGeneratorCreator , protocols::forge::constraints::InvrotTreeCstGeneratorCreator , protocols::forge::constraints::NtoCCstGeneratorCreator , protocols::forge::constraints::RemoveCstsCreator , protocols::forge::remodel::RemodelMoverCreator , protocols::forge::remodel::ResidueVicinityCstGeneratorCreator , protocols::generalized_kinematic_closure::GeneralizedKICCreator , protocols::grafting::AnchoredGraftMoverCreator , protocols::grafting::CCDEndsGraftMoverCreator , protocols::grafting::simple_movers::DeleteRegionMoverCreator , protocols::grafting::simple_movers::InsertPoseIntoPoseMoverCreator , protocols::grafting::simple_movers::KeepRegionMoverCreator , protocols::grafting::simple_movers::ReplaceRegionMoverCreator , protocols::helical_bundle::BundleGridSamplerCreator , protocols::helical_bundle::FitSimpleHelixCreator , protocols::helical_bundle::MakeBundleCreator , protocols::helical_bundle::MakeBundleHelixCreator , protocols::helical_bundle::PerturbBundleCreator , protocols::helical_bundle::PerturbBundleHelixCreator , protocols::hotspot_hashing::movers::PlaceSurfaceProbeCreator , protocols::hybridization::BackboneTorsionPerturbationCreator , protocols::hybridization::BackboneTorsionSamplerCreator , protocols::hybridization::CartesianHybridizeCreator , protocols::hybridization::CartesianSamplerCreator , protocols::hybridization::FoldTreeHybridizeCreator , protocols::hybridization::HybridizeProtocolCreator , protocols::hybridization::HybridizeSetupMoverCreator , protocols::idealize::IdealizeMoverCreator , protocols::kinematic_closure::KicMoverCreator , protocols::ligand_docking::AddHydrogensCreator , protocols::ligand_docking::CompoundTranslateCreator , protocols::ligand_docking::ComputeLigandRDFCreator , protocols::ligand_docking::FinalMinimizerCreator , protocols::ligand_docking::GrowLigandCreator , protocols::ligand_docking::HighResDockerCreator , protocols::ligand_docking::InterfaceScoreCalculatorCreator , protocols::ligand_docking::LigandDesignCreator , protocols::ligand_docking::MinimizeBackboneCreator , protocols::ligand_docking::RandomConformersCreator , protocols::ligand_docking::RotateCreator , protocols::ligand_docking::RotatesCreator , protocols::ligand_docking::SlideTogetherCreator , protocols::ligand_docking::StartFromCreator , protocols::ligand_docking::TransformCreator , protocols::ligand_docking::TranslateCreator , protocols::ligand_docking::WriteLigandMolFileCreator , protocols::loop_build::LoopmodelWrapperCreator , protocols::loop_build::LoopMover_SlidingWindowCreator , protocols::loop_modeling::LoopBuilderCreator , protocols::loop_modeling::LoopModelerCreator , protocols::loop_modeling::LoopProtocolCreator , protocols::loop_modeling::refiners::MinimizationRefinerCreator , protocols::loop_modeling::refiners::RepackingRefinerCreator , protocols::loop_modeling::refiners::RotamerTrialsRefinerCreator , protocols::loop_modeling::samplers::LegacyKicSamplerCreator , protocols::loop_modeling::utilities::PrepareForCentroidCreator , protocols::loop_modeling::utilities::PrepareForFullatomCreator , protocols::loophash::LoopHashDiversifierCreator , protocols::loophash::LoopHashMoverWrapperCreator , protocols::loops::FoldTreeFromLoopsCreator , protocols::loops::loop_closure::ccd::CCDLoopClosureMoverCreator , protocols::loops::loop_mover::LoopCMCreator , protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCDCreator , protocols::loops::loop_mover::perturb::LoopMover_Perturb_KICCreator , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_MovesCreator , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCDCreator , protocols::loops::loop_mover::refine::LoopMover_Refine_BackrubCreator , protocols::loops::loop_mover::refine::LoopMover_Refine_CCDCreator , protocols::loops::loop_mover::refine::LoopMover_Refine_KICCreator , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainerCreator , protocols::loops::loop_mover::refine::RepackTrialCreator , protocols::loops::loop_mover::refine::ShearMinCCDTrialCreator , protocols::loops::loop_mover::refine::SmallMinCCDTrialCreator , protocols::match::MatcherMoverCreator , protocols::matdes::ExtractSubposeMoverCreator , protocols::matdes::MatDesGreedyOptMutationMoverCreator , protocols::matdes::SchemePlaceMotifsMoverCreator , protocols::matdes::SymDofMoverCreator , protocols::md::CartesianMDCreator , protocols::membrane::AddMembraneMoverCreator , protocols::membrane::FlipMoverCreator , protocols::membrane::MembranePositionFromTopologyMoverCreator , protocols::membrane::RotationMoverCreator , protocols::membrane::SetMembraneCenterMoverCreator , protocols::membrane::SetMembraneNormalMoverCreator , protocols::membrane::SetMembranePositionMoverCreator , protocols::membrane::symmetry::SymmetricAddMembraneMoverCreator , protocols::membrane::TransformIntoMembraneMoverCreator , protocols::membrane::TranslationMoverCreator , protocols::membrane::TranslationRotationMoverCreator , protocols::membrane::visualize::VisualizeEmbeddingMoverCreator , protocols::membrane::visualize::VisualizeMembraneMoverCreator , protocols::motif_grafting::movers::MotifGraftCreator , protocols::motifs::MotifDnaPackerCreator , protocols::moves::DsspMoverCreator , protocols::moves::IfMoverCreator , protocols::moves::IteratedConvergenceMoverCreator , protocols::moves::MoverCreator , protocols::moves::PyMolMoverCreator , protocols::moves::RampingMoverCreator , protocols::moves::RandomMoverCreator , protocols::ncbb::NcbbDockDesignProtocolCreator , protocols::ncbb::oop::OopCreatorMoverCreator , protocols::ncbb::oop::OopDockDesignProtocolCreator , protocols::nonlocal::SingleFragmentMoverCreator , protocols::normalmode::NormalModeMinimizerCreator , protocols::pb_potential::SetupPoissonBoltzmannPotentialCreator , protocols::protein_interface_design::movers::AddChainBreakCreator , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspotsCreator , protocols::protein_interface_design::movers::BackrubDDMoverCreator , protocols::protein_interface_design::movers::BestHotspotCstMoverCreator , protocols::protein_interface_design::movers::BuildAlaPoseCreator , protocols::protein_interface_design::movers::DesignMinimizeHbondsCreator , protocols::protein_interface_design::movers::DisulfideMoverCreator , protocols::protein_interface_design::movers::DockAndRetrieveSidechainsCreator , protocols::protein_interface_design::movers::DockWithHotspotMoverCreator , protocols::protein_interface_design::movers::FavorNativeResiduePreCycleCreator , protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycleCreator , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMoverCreator , protocols::protein_interface_design::movers::HotspotHasherMoverCreator , protocols::protein_interface_design::movers::InterfaceRecapitulationMoverCreator , protocols::protein_interface_design::movers::LoopFinderCreator , protocols::protein_interface_design::movers::LoopLengthChangeCreator , protocols::protein_interface_design::movers::LoopMoverFromCommandLineCreator , protocols::protein_interface_design::movers::LoopOverCreator , protocols::protein_interface_design::movers::LoopRemodelCreator , protocols::protein_interface_design::movers::MapHotspotCreator , protocols::protein_interface_design::movers::PatchdockTransformCreator , protocols::protein_interface_design::movers::PeptideStapleDesignMoverCreator , protocols::protein_interface_design::movers::PlacementAuctionMoverCreator , protocols::protein_interface_design::movers::PlacementMinimizationMoverCreator , protocols::protein_interface_design::movers::PlaceOnLoopCreator , protocols::protein_interface_design::movers::PlaceSimultaneouslyMoverCreator , protocols::protein_interface_design::movers::PlaceStubMoverCreator , protocols::protein_interface_design::movers::PrepackMoverCreator , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMoverCreator , protocols::protein_interface_design::movers::RandomMutationCreator , protocols::protein_interface_design::movers::RepackMinimizeCreator , protocols::protein_interface_design::movers::SaveAndRetrieveSidechainsCreator , protocols::protein_interface_design::movers::SetAtomTreeCreator , protocols::protein_interface_design::movers::SetTemperatureFactorCreator , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMoverCreator , protocols::protein_interface_design::movers::SetupHotspotConstraintsMoverCreator , protocols::protein_interface_design::movers::ShoveResidueMoverCreator , protocols::protein_interface_design::movers::SpinMoverCreator , protocols::protein_interface_design::movers::SubroutineMoverCreator , protocols::protein_interface_design::movers::TaskAwareCstsCreator , protocols::protein_interface_design::movers::TopologyBrokerMoverCreator , protocols::protein_interface_design::movers::TryRotamersCreator , protocols::protein_interface_design::movers::VLBCreator , protocols::qsar::qsarCreator , protocols::qsar::RenderGridsToKinemageCreator , protocols::qsar::scoring_grid::GridInitMoverCreator , protocols::rbsegment_relax::IdealizeHelicesMoverCreator , protocols::rbsegment_relax::MakeStarTopologyMoverCreator , protocols::rbsegment_relax::OptimizeThreadingMoverCreator , protocols::relax::AtomCoordinateCstMoverCreator , protocols::relax::ClassicRelaxCreator , protocols::relax::FastRelaxCreator , protocols::relax::membrane::MPFastRelaxMoverCreator , protocols::rigid::RigidBodyPerturbNoCenterMoverCreator , protocols::rigid::RigidBodyTransMoverCreator , protocols::rigid::RollMoverCreator , protocols::rigid::UniformRigidBodyCMCreator , protocols::rigid::UniformRigidBodyMoverCreator , protocols::rosetta_scripts::AdditionalOutputWrapperCreator , protocols::rosetta_scripts::MultipleOutputWrapperCreator , protocols::rosetta_scripts::MultiplePoseMoverCreator , protocols::rosetta_scripts::ParsedProtocolCreator , protocols::rosetta_scripts::SavePoseMoverCreator , protocols::rotamer_recovery::RotamerRecoveryMoverCreator , protocols::seeded_abinitio::CAcstGeneratorCreator , protocols::seeded_abinitio::CloseFoldCreator , protocols::seeded_abinitio::CoordinateCstCreator , protocols::seeded_abinitio::DefineMovableLoopsCreator , protocols::seeded_abinitio::GrowPeptidesCreator , protocols::seeded_abinitio::SeedFoldTreeCreator , protocols::seeded_abinitio::SeedSetupMoverCreator , protocols::seeded_abinitio::SegmentHybridizerCreator , protocols::seeded_abinitio::SwapSegmentCreator , protocols::simple_moves::AddChainMoverCreator , protocols::simple_moves::AddConstraintsToCurrentConformationMoverCreator , protocols::simple_moves::AddJobPairDataCreator , protocols::simple_moves::AlignChainMoverCreator , protocols::simple_moves::BBGaussianMoverCreator , protocols::simple_moves::bin_transitions::InitializeByBinsCreator , protocols::simple_moves::bin_transitions::PerturbByBinsCreator , protocols::simple_moves::BoltzmannRotamerMoverCreator , protocols::simple_moves::ChangeAndResetFoldTreeMoverCreator , protocols::simple_moves::ClearConstraintsMoverCreator , protocols::simple_moves::ConsensusDesignMoverCreator , protocols::simple_moves::ConstraintSetMoverCreator , protocols::simple_moves::ContingentAcceptMoverCreator , protocols::simple_moves::CoupledMoverCreator , protocols::simple_moves::CutChainMoverCreator , protocols::simple_moves::ddGCreator , protocols::simple_moves::DumpPdbCreator , protocols::simple_moves::ExtendedPoseMoverCreator , protocols::simple_moves::FavorSequenceProfileCreator , protocols::simple_moves::FavorSymmetricSequenceCreator , protocols::simple_moves::FindConsensusSequenceCreator , protocols::simple_moves::ForceDisulfidesMoverCreator , protocols::simple_moves::GenericMonteCarloMoverCreator , protocols::simple_moves::LoadPDBMoverCreator , protocols::simple_moves::LoadUnboundRotMoverCreator , protocols::simple_moves::MakePolyXMoverCreator , protocols::simple_moves::MembraneTopologyCreator , protocols::simple_moves::MinMoverCreator , protocols::simple_moves::MinPackMoverCreator , protocols::simple_moves::ModifyVariantTypeMoverCreator , protocols::simple_moves::MonteCarloRecoverCreator , protocols::simple_moves::MonteCarloResetCreator , protocols::simple_moves::MonteCarloTestCreator , protocols::simple_moves::MSDMoverCreator , protocols::simple_moves::MutateResidueCreator , protocols::simple_moves::PackRotamersMoverCreator , protocols::simple_moves::PDBReloadMoverCreator , protocols::simple_moves::PSSM2BfactorMoverCreator , protocols::simple_moves::RandomOmegaFlipMoverCreator , protocols::simple_moves::RandomTorsionMoverCreator , protocols::simple_moves::RepackSidechainsMoverCreator , protocols::simple_moves::RepeatPropagationMoverCreator , protocols::simple_moves::ReportEffectivePKACreator , protocols::simple_moves::ResetBaselineMoverCreator , protocols::simple_moves::ResidueTypeConstraintMoverCreator , protocols::simple_moves::RotamerTrialsMinMoverCreator , protocols::simple_moves::RotamerTrialsMoverCreator , protocols::simple_moves::SaneMinMoverCreator , protocols::simple_moves::ScoreMoverCreator , protocols::simple_moves::SequenceProfileMoverCreator , protocols::simple_moves::SetTorsionCreator , protocols::simple_moves::ShearMoverCreator , protocols::simple_moves::ShortBackrubMoverCreator , protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMoverCreator , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMoverCreator , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMoverCreator , protocols::simple_moves::sidechain_moves::SetChiMoverCreator , protocols::simple_moves::sidechain_moves::SidechainMCMoverCreator , protocols::simple_moves::sidechain_moves::SidechainMoverCreator , protocols::simple_moves::SmallMoverCreator , protocols::simple_moves::SuperimposeMoverCreator , protocols::simple_moves::SwitchChainOrderMoverCreator , protocols::simple_moves::SwitchResidueTypeSetMoverCreator , protocols::simple_moves::symmetry::DetectSymmetryMoverCreator , protocols::simple_moves::symmetry::ExtractAsymmetricPoseMoverCreator , protocols::simple_moves::symmetry::ExtractAsymmetricUnitMoverCreator , protocols::simple_moves::symmetry::SetupForSymmetryMoverCreator , protocols::simple_moves::symmetry::SetupNCSMoverCreator , protocols::simple_moves::symmetry::SymMinMoverCreator , protocols::simple_moves::symmetry::SymPackRotamersMoverCreator , protocols::simple_moves::symmetry::SymRotamerTrialsMoverCreator , protocols::simple_moves::symmetry::TaskAwareSymMinMoverCreator , protocols::simple_moves::TaskAwareMinMoverCreator , protocols::simple_moves::TumbleCreator , protocols::simple_moves::VirtualRootMoverCreator , protocols::symmetric_docking::membrane::MPSymDockMoverCreator , protocols::symmetric_docking::SymDockProtocolCreator , protocols::symmetric_docking::SymFoldandDockMoveRbJumpMoverCreator , protocols::symmetric_docking::SymFoldandDockRbTrialMoverCreator , protocols::symmetric_docking::SymFoldandDockSlideTrialMoverCreator , protocols::toolbox::task_operations::StoreCombinedStoredTasksMoverCreator , protocols::toolbox::task_operations::StoreCompoundTaskMoverCreator , protocols::toolbox::task_operations::StoreTaskMoverCreator
• create_new_bump_grid_for_bb() : protocols::match::BumpGrid
• create_new_edge() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• create_new_node() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• create_new_random_topol() : protocols::jumping::RandomSheetBuilder , protocols::jumping::SheetBuilder
• create_options() : protocols::loophash::LoopHashLibraryOptionsCreator , protocols::loops::LoopsFileOptionsCreator , protocols::membrane::io::LipoFileOptionsCreator , protocols::membrane::io::SpanFileOptionsCreator , protocols::surface_docking::SurfaceVectorOptionsCreator
• create_output_upstream_pose() : protocols::match::output::PDBWriter
• create_output_writer() : protocols::match::output::ProcessorFactory
• create_packer_data() : protocols::multistate_design::PackingState
• create_parser() : protocols::jd2::JobDistributorFactory
• create_partitioned_search_pattern() : protocols::hotspot_hashing::movers::PlaceProbeMover , protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• create_pddf() : protocols::scoring::methods::saxs::PDDFEnergy
• create_per_loop_fragment_movers() : protocols::forge::remodel::RemodelLoopMover
• create_pose_from_input_poses() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• 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::RRProtocolCreator , protocols::rotamer_recovery::RRProtocolMinPackCreator , protocols::rotamer_recovery::RRProtocolMoverCreator , protocols::rotamer_recovery::RRProtocolPackRotamersCreator , protocols::rotamer_recovery::RRProtocolReferenceStructureCreator , protocols::rotamer_recovery::RRProtocolRelaxCreator , protocols::rotamer_recovery::RRProtocolRotamerTrialsCreator , protocols::rotamer_recovery::RRProtocolRTMinCreator
• create_ptask() : protocols::enzdes::EnzRepackMinimize
• create_random_fragments() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• create_random_rotation() : protocols::ligand_docking::Rotate
• create_random_rotations() : protocols::ligand_docking::Rotate
• create_rdf_function() : protocols::ligand_docking::rdf::RDFBinaryHbondCreator , protocols::ligand_docking::rdf::RDFBinaryOrbitalFunctionCreator , protocols::ligand_docking::rdf::RDFChargeCreator , protocols::ligand_docking::rdf::RDFElecCreator , protocols::ligand_docking::rdf::RDFEtableCreator , protocols::ligand_docking::rdf::RDFFunctionCreator , protocols::ligand_docking::rdf::RDFHbondCreator , protocols::ligand_docking::rdf::RDFOrbitalFunctionCreator
• 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::pose_reporters::EnergyReporterCreator , protocols::pose_reporters::FilterReporterCreator , protocols::pose_reporters::RMSDReporterCreator , protocols::rosetta_scripts::PosePropertyReporterCreator , protocols::rotamer_recovery::RRReporterCreator , protocols::rotamer_recovery::RRReporterHumanCreator , protocols::rotamer_recovery::RRReporterSimpleCreator , protocols::rotamer_recovery::RRReporterSQLiteCreator
• create_res_filter() : protocols::toolbox::task_operations::ProteinCoreFilterCreator
• create_resource() : protocols::loophash::LoopHashLibraryLoader , protocols::loops::LoopsFileLoader , protocols::membrane::io::LipoFileLoader , protocols::membrane::io::SpanFileLoader , protocols::surface_docking::SurfaceVectorLoader
• create_resource_from_fallback() : protocols::jd2::JD2ResourceManager
• create_resource_loader() : protocols::loophash::LoopHashLibraryLoaderCreator , protocols::loops::LoopsFileLoaderCreator , protocols::membrane::io::LipoFileLoaderCreator , protocols::membrane::io::SpanFileLoaderCreator , protocols::surface_docking::SurfaceVectorLoaderCreator
• create_resource_manager() : protocols::jd2::JD2ResourceManagerCreator
• create_rigid_body_movers() : protocols::ligand_docking::HighResDocker
• create_rotamer_set() : protocols::protein_interface_design::movers::MapHotspot
• create_rotamer_subsets_from_rot_to_pack() : protocols::pack_daemon::RotamerSubsetRepacker
• create_sample_vector() : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• create_scalar_and_vector_expression_variable_expressions() : protocols::pack_daemon::DynamicAggregateFunction
• create_scores() : protocols::frag_picker::scores::FragmentScoreManager
• create_scoring_method() : protocols::frag_picker::scores::FragmentScoreManager
• create_search_pattern() : protocols::hotspot_hashing::movers::PlaceProbeMover , protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• create_SecMatchResiduePairEvaluatorOP() : protocols::match::downstream::SecMatchEvaluatorFactory
• create_selector() : protocols::pose_selectors::AndSelectorCreator , protocols::pose_selectors::ClusterPoseSelectorCreator , protocols::pose_selectors::FilterCreator , protocols::pose_selectors::OrSelectorCreator , protocols::pose_selectors::TopNByPropertyCreator , protocols::rosetta_scripts::PoseSelectorCreator
• create_semaphore() : protocols::boinc::Boinc
• create_sequence_match_fragments() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• create_sequence_profile_constraints() : protocols::simple_moves::ConsensusDesignMover
• create_silent_file_and_tag_list() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• create_singleton_instance() : protocols::evaluation::EvaluatorFactory , protocols::features::FeaturesReporterFactory , protocols::filters::FilterFactory , protocols::genetic_algorithm::EntityElementFactory , protocols::jd2::JobDistributor , protocols::jd2::JobInputterFactory , protocols::jd2::JobOutputterFactory , protocols::jd2::parser::DataLoaderFactory , protocols::jumping::StandardDisulfPairingLibrary , protocols::jumping::StandardPairingLibrary , protocols::ligand_docking::DistributionMap , protocols::loops::loop_mover::refine::LoopRefineInnerCycleFactory , protocols::loops::LoopMoverFactory , protocols::loops::loops_definers::LoopsDefinerFactory , protocols::matdes::SymDofMoverSampler , protocols::moves::MoverFactory , protocols::noesy_assign::CovalentCompliance , protocols::noesy_assign::MethylNameLibrary , protocols::noesy_assign::PeakAssignmentParameters , protocols::qsar::scoring_grid::GridFactory , protocols::qsar::scoring_grid::GridManager , protocols::rosetta_scripts::PosePropertyReporterFactory , protocols::rosetta_scripts::PoseSelectorFactory , protocols::rotamer_recovery::RotamerRecoveryFactory , protocols::scoring::InterchainPotential , protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton , protocols::scoring::methods::pcs2::PcsEnergyParameterManager , protocols::scoring::methods::pcs2::PcsGridSearchParameterManager , protocols::scoring::methods::pcs2::PcsInputCenterManager , protocols::scoring::methods::pcs::PCS_data_input_manager , protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::topology_broker::TopologyClaimerFactory
• create_sliced_pose() : protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters
• create_small_mover() : protocols::medal::MedalMover
• create_starting_pose() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• create_state_variable_expressions() : protocols::pack_daemon::DynamicAggregateFunction
• create_sub_to_full_map() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• create_subpose() : protocols::simple_moves::CutChainMover
• create_surface_packer_task() : protocols::surface_docking::SurfaceDockingProtocol
• create_tags_map() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• create_task_for_allhotspot_packing() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• create_task_for_hotspot_packing() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• create_task_operation() : protocols::dna::RestrictDesignToProteinDNAInterfaceCreator , protocols::dna::WatsonCrickRotamerCouplingsCreator , protocols::enzdes::AddLigandMotifRotamersOperationCreator , protocols::enzdes::AddRigidBodyLigandConfsCreator , protocols::enzdes::DetectProteinLigandInterfaceOperationCreator , protocols::enzdes::ProteinLigandInterfaceUpweighterOperationCreator , protocols::enzdes::SetCatalyticResPackBehaviorCreator , protocols::flxbb::LayerDesignOperationCreator , protocols::forge::remodel::RemodelRotamerLinksCreator , protocols::matdes::BuildingBlockInterfaceOperationCreator , protocols::toolbox::task_operations::AlignedThreadOperationCreator , protocols::toolbox::task_operations::CrystalContactsOperationCreator , protocols::toolbox::task_operations::DatabaseThreadCreator , protocols::toolbox::task_operations::DesignAroundOperationCreator , protocols::toolbox::task_operations::DsspDesignOperationCreator , protocols::toolbox::task_operations::ImportUnboundRotamersOperationCreator , protocols::toolbox::task_operations::InteractingRotamerExplosionCreator , protocols::toolbox::task_operations::JointSequenceOperationCreator , protocols::toolbox::task_operations::LimitAromaChi2OperationCreator , protocols::toolbox::task_operations::LinkResiduesCreator , protocols::toolbox::task_operations::ModifyAnnealerCreator , protocols::toolbox::task_operations::PreventChainFromRepackingOperationCreator , protocols::toolbox::task_operations::PreventResiduesFromRepackingOperationCreator , protocols::toolbox::task_operations::ProteinInterfaceDesignOperationCreator , protocols::toolbox::task_operations::ReadResfileFromDBCreator , protocols::toolbox::task_operations::RestrictByCalculatorsOperationCreator , protocols::toolbox::task_operations::RestrictChainToRepackingOperationCreator , protocols::toolbox::task_operations::RestrictConservedLowDdgOperationCreator , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperationCreator , protocols::toolbox::task_operations::RestrictIdentitiesOperationCreator , protocols::toolbox::task_operations::RestrictInterGroupVectorOperationCreator , protocols::toolbox::task_operations::RestrictNativeResiduesOperationCreator , protocols::toolbox::task_operations::RestrictNonSurfaceToRepackingOperationCreator , protocols::toolbox::task_operations::RestrictResiduesToRepackingOperationCreator , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperationCreator , protocols::toolbox::task_operations::RestrictToCDRH3LoopCreator , protocols::toolbox::task_operations::RestrictToInterfaceCreator , protocols::toolbox::task_operations::RestrictToInterfaceOperationCreator , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperationCreator , protocols::toolbox::task_operations::RestrictToLoopsAndNeighborsCreator , protocols::toolbox::task_operations::RestrictToLoopsCreator , protocols::toolbox::task_operations::RestrictToNeighborhoodOperationCreator , protocols::toolbox::task_operations::RestrictToTerminiOperationCreator , protocols::toolbox::task_operations::RetrieveStoredTaskOperationCreator , protocols::toolbox::task_operations::SelectByDeltaScoreOperationCreator , protocols::toolbox::task_operations::SelectByDensityFitOperationCreator , protocols::toolbox::task_operations::SelectBySASAOperationCreator , protocols::toolbox::task_operations::SelectResiduesWithinChainOperationCreator , protocols::toolbox::task_operations::SeqprofConsensusOperationCreator , protocols::toolbox::task_operations::SetIGTypeOperationCreator , protocols::toolbox::task_operations::ThreadSequenceOperationCreator
• 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::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• create_VDW_screen_bin() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• create_vrt_if_necessary() : protocols::environment::claims::JumpClaim
• create_weighted_scorefunction() : protocols::optimize_weights::IterativeOptEDriver
• create_WUs() : protocols::mpi_refinement::MPI_Refine_Master
• create_xyz_constraints_median() : protocols::toolbox::DecoySetEvaluation
• CreateAngleConstraint() : protocols::cyclic_peptide::CreateAngleConstraint
• 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
• CreateDistanceConstraint() : protocols::cyclic_peptide::CreateDistanceConstraint
• creates_undefined_backbone() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• CreateTorsionConstraint() : protocols::cyclic_peptide::CreateTorsionConstraint
• cross_angle() : protocols::fldsgn::topology::HelixPairing
• cross_over() : protocols::fldsgn::topology::BetaAlphaBetaMotif
• crossover() : protocols::genetic_algorithm::EntityRandomizer
• CrossPeak() : protocols::noesy_assign::CrossPeak
• crosspeak() : protocols::noesy_assign::PeakAssignment
• 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
• CrystalContactsOperation() : protocols::toolbox::task_operations::CrystalContactsOperation
• CS2ndShift() : protocols::frag_picker::CS2ndShift
• CSP_fraction() : protocols::ub_e2c::ubi_e2c_modeler
• CSScore() : protocols::frag_picker::scores::CSScore
• cst_block() : protocols::toolbox::match_enzdes_util::CstResInteractions , protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• cst_cache() : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• cst_cleanup() : protocols::protein_interface_design::movers::PlaceStubMover
• cst_file() : protocols::abinitio::abscript::ConstraintPreparer
• cst_files() : protocols::relax::RelaxProtocolBase
• cst_interactions() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• cst_io() : protocols::match::output::OutputWriter
• cst_minimize() : protocols::enzdes::EnzdesBaseProtocol
• cst_on_pose() : protocols::md::MDBase
• cst_on_pose_dynamic() : protocols::md::CartesianMD
• cst_on_pose_simple() : protocols::md::CartesianMD
• cst_sd() : protocols::relax::AtomCoordinateCstMover
• cst_sdev() : protocols::normalmode::NormalModeRelaxMover
• cst_sidechain() : protocols::relax::AtomCoordinateCstMover
• cst_type() : protocols::protein_interface_design::movers::TaskAwareCsts
• cst_weight() : protocols::simple_moves::AddConstraintsToCurrentConformationMover
• cst_width() : protocols::relax::AtomCoordinateCstMover
• CSTalosIO() : protocols::frag_picker::CSTalosIO
• cstAtoms() : protocols::jumping::ResiduePairJump , protocols::jumping::ResiduePairJumpSingle
• cstAtoms_defined() : protocols::jumping::ResiduePairJump , protocols::jumping::ResiduePairJumpSingle
• cstfile() : protocols::enzdes::AddOrRemoveMatchCsts
• cstfile_name() : protocols::match::MatcherTask , protocols::match::output::PDBWriter
• cstInfoMap_defined() : protocols::jumping::ResiduePairJump
• CstResInteractions() : protocols::toolbox::match_enzdes_util::CstResInteractions
• Cter_insert_flexibility() : protocols::grafting::AnchoredGraftMover
• Cter_loop_end() : protocols::grafting::AnchoredGraftMover
• Cter_loop_start() : protocols::grafting::AnchoredGraftMover
• Cter_overhang_length() : protocols::grafting::GraftMoverBase
• Cter_scaffold_flexibility() : protocols::grafting::AnchoredGraftMover
• ctor() : protocols::loops::loop_closure::kinematic_closure::KinematicWrapper
• ctrl_strength() : protocols::environment::claims::TorsionClaim , protocols::environment::claims::XYZClaim
• cull_mutatable_residues() : protocols::vip::VIP_Mover
• cull_violators() : protocols::abinitio::Template
• cummulative_time() : protocols::md::MDBase
• cumulate_jobs() : protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::TrajectoryRecorder
• cumulate_replicas() : protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::TrajectoryRecorder
• cumulative_peak_volume() : protocols::noesy_assign::CrossPeak
• cur_energy() : protocols::flexpack::interaction_graph::FlexbbEdge
• curr_bb() : protocols::flexpack::interaction_graph::FlexbbNode
• curr_gen_entity() : protocols::genetic_algorithm::GeneticAlgorithmBase
• curr_state_one_body_energy() : protocols::flexpack::interaction_graph::FlexbbNode
• 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_batch_id() : protocols::jd2::JobDistributor
• current_cycle_number() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• current_dna_design_string() : protocols::dna::DnaInterfacePacker
• current_generation() : protocols::genetic_algorithm::GeneticAlgorithmBase
• current_generation_begin() : protocols::genetic_algorithm::GeneticAlgorithmBase
• current_generation_complete() : protocols::genetic_algorithm::GeneticAlgorithmBase
• current_generation_end() : protocols::genetic_algorithm::GeneticAlgorithmBase
• current_job() : protocols::jd2::JobDistributor , protocols::jd2::MSDJobDistributor , protocols::jobdist::BaseJobDistributor
• current_job_finished() : protocols::jd2::FileSystemJobDistributor , protocols::jd2::JobDistributor
• current_job_id() : protocols::jd2::JobDistributor
• current_kinematics() : protocols::abinitio::KinematicTaskControl
• current_mem() : protocols::wum2::EndPoint , protocols::wum2::WUQueue
• current_nstruct() : protocols::jobdist::BaseJobDistributor
• current_output_name() : protocols::jd2::JobDistributor
• current_pose() : protocols::topology_broker::TopologyBroker
• current_score() : protocols::simple_moves::GenericMonteCarloMover
• current_scorefxn() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• current_size() : protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaPool , protocols::frag_picker::quota::SecondaryStructurePool
• current_state() : protocols::flexpack::interaction_graph::FlexbbNode
• current_state_info() : protocols::flexpack::interaction_graph::FlexbbNode
• current_temp() : protocols::canonical_sampling::TemperingBase
• current_trial() : protocols::canonical_sampling::MetropolisHastingsMover , protocols::flxbb::FilterStructs
• current_working_sequence() : protocols::dna::DnaInterfacePacker
• custom_angle() : protocols::backrub::BackrubMover
• CustomScoreSelector() : protocols::frag_picker::CustomScoreSelector
• cut() : protocols::environment::claims::JumpClaim , protocols::loops::Loop
• cut_residue() : protocols::kinematic_closure::ClosureProblem
• CutBiasClaim() : protocols::environment::claims::CutBiasClaim
• CutBiasClaimer() : protocols::topology_broker::CutBiasClaimer
• CutBiasElement() : protocols::environment::claims::CutBiasElement
• CutChainMover() : protocols::simple_moves::CutChainMover
• CutClaim() : protocols::topology_broker::claims::CutClaim
• CutElement() : protocols::environment::claims::CutElement
• cutoff() : protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::PDDFScoreFilter , protocols::simple_filters::SAXSScoreFilter , protocols::simple_filters::ScoreCutoffFilter , protocols::simple_moves::FragmentCost
• cutoff_distance() : protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors
• cutpoint_closed_list() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• cutpoint_open_list() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• cutpoint_res() : protocols::loops::LoopFromFileData
• cutpoint_separation() : protocols::antibody_legacy::CDRH3Modeler
• cutpoints() : protocols::star::Extender
• cutpoints_separation() : protocols::antibody_legacy::CDRH3Modeler
• cutpos_list() : protocols::coarse_rna::CoarseRNA_LoopCloser
• cuts() : protocols::environment::AutoCutData , protocols::jumping::JumpSample
• CycleMover() : protocols::moves::CycleMover
• cycles() : protocols::grafting::AnchoredGraftMover , protocols::moves::IteratedConvergenceMover , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• CyclicMover() : protocols::moves::CyclicMover
• CyclizationMover() : protocols::simple_moves::CyclizationMover