- i -

• i() : protocols::farna::BasePairStep , protocols::frag_picker::Contact
• i_next() : protocols::farna::BasePairStep
• i_to_a() : protocols::normalmode::NormalMode
• i_want_this_atom_to_move() : protocols::simple_moves::ConstrainToIdealMover
• id() : protocols::forge::remodel::RemodelConstraintGenerator , protocols::frag_picker::VallResidue , protocols::jd2::archive::Batch , protocols::optimize_weights::OptEVariableExpression , protocols::stepwise::sampler::StepWiseSamplerSized , protocols::wum2::WorkUnit , protocols::wum::WorkUnitBase
• id2list() : protocols::stepwise::sampler::StepWiseSamplerSizedComb
• id2proftag() : protocols::abinitio::FragmentSampler
• id2state() : protocols::stepwise::sampler::StepWiseSamplerSizedAny
• id2string() : protocols::abinitio::FragmentSampler
• id_for_resnum() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerComb
• id_from_index() : protocols::kinematic_closure::ClosureProblem
• ideal_val() : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• idealize_insert() : protocols::grafting::AnchoredGraftMover
• idealize_sidechains() : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• IdealizeHelicesMover() : protocols::rbsegment_relax::IdealizeHelicesMover
• IdealizeMover() : protocols::idealize::IdealizeMover
• identical_info_consistency_check() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• identify_and_set_cdr_cluster() : protocols::antibody::clusters::CDRClusterSet
• identify_antibody() : protocols::antibody::AntibodyInfo
• identify_CDR_from_a_sequence() : protocols::antibody::AntibodyInfo
• identify_light_chain() : protocols::antibody::AntibodyInfo
• identify_motif_build_positions() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• identify_motif_BuildPositions() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• identify_ss() : protocols::fldsgn::topology::SS_Info2
• identities() : protocols::toolbox::task_operations::RestrictIdentitiesOperation
• identity_matrix() : protocols::forge::remodel::RemodelGlobalFrame , protocols::simple_filters::RepeatParameterFilter
• idle() : protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeBase , protocols::jd2::archive::AbstractArchiveBase , protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::ArchiveManager
• ids_span_cut() : protocols::kinematic_closure::ClosureProblem
• if_late_scoring_for_zeros() : protocols::frag_picker::scores::FragmentScoreManager
• ifc() : protocols::kinmatch::FunGroupTK
• IfMover() : protocols::moves::IfMover
• IfThenFilter() : protocols::filters::IfThenFilter
• ig() : protocols::multistate_design::PackingState , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::simple_moves::PackRotamersMover
• IGLigandDesignEdgeUpweighter() : protocols::toolbox::IGLigandDesignEdgeUpweighter
• ignore() : protocols::comparative_modeling::IgnoreSubsetConstraintSet
• ignore_assignments() : protocols::noesy_assign::PeakFileFormat_Base
• ignore_cmdline_enzdes_cstfile() : protocols::forge::components::VarLengthBuild
• ignore_default_task() : protocols::docking::DockingHighRes
• ignore_h_collisions() : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::toolbox::match_enzdes_util::LigandConformer
• ignore_list() : protocols::comparative_modeling::IgnoreSubsetConstraintSet
• ignore_loops() : protocols::fldsgn::NcontactsCalculator
• ignore_negative_intensity() : protocols::noesy_assign::PeakFileFormat_Base
• ignore_pikaa_natro() : protocols::flxbb::LayerDesignOperation
• ignore_residue() : protocols::comparative_modeling::IgnoreSubsetConstraintSet
• ignore_residues_in_csts() : protocols::idealize::IdealizeMover
• ignore_same_sheet() : protocols::fldsgn::NcontactsCalculator
• ignore_same_sselement() : protocols::fldsgn::NcontactsCalculator
• ignore_secstruct() : protocols::farna::RNA_DeNovoProtocol
• ignore_zero_byte() : protocols::simple_filters::FileExistFilter
• ignorefinished() : protocols::jobdist::BaseJobDistributor
• IgnoreSubsetConstraintSet() : protocols::comparative_modeling::IgnoreSubsetConstraintSet
• ImplicitFastClashCheck() : protocols::scoring::ImplicitFastClashCheck
• Import_pose() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• import_tags() : protocols::rosetta_scripts::RosettaScriptsParser
• ImportUnboundRotamersOperation() : protocols::toolbox::task_operations::ImportUnboundRotamersOperation
• impose_constraints() : protocols::idealize::IdealizeMover
• in_blacklist() : protocols::wum::WorkUnitBase
• in_charge() : protocols::loops::GuardedLoopsFromFile
• inbound() : protocols::wum::WorkUnitManager
• inc_alternate_state_total_energy() : protocols::flexpack::interaction_graph::FlexbbNode
• inc_curr_state_total_energy() : protocols::flexpack::interaction_graph::FlexbbNode
• incl_nonopt() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• include_eggshell_points_based_on_known_ligand() : protocols::pockets::NonPlaidFingerprint
• include_lips() : protocols::membrane::AddMembraneMover
• include_native_aa() : protocols::antibody::design::ConservativeDesignOperation
• include_native_restype() : protocols::antibody::design::ResidueProbDesignOperation
• include_neighbors() : protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors
• include_only_center_clusters() : protocols::antibody::CDRSetOptions
• include_only_clusters() : protocols::antibody::CDRSetOptions
• include_only_clusters_add() : protocols::antibody::CDRSetOptions
• include_only_clusters_clear() : protocols::antibody::CDRSetOptions
• include_only_current_cluster() : protocols::antibody::CDRSetOptions
• include_only_germlines() : protocols::antibody::CDRSetOptions
• include_only_germlines_add() : protocols::antibody::CDRSetOptions
• include_only_germlines_clear() : protocols::antibody::CDRSetOptions
• include_only_pdbs() : protocols::antibody::CDRSetOptions
• include_only_pdbs_add() : protocols::antibody::CDRSetOptions
• include_only_pdbs_clear() : protocols::antibody::CDRSetOptions
• include_only_species() : protocols::antibody::CDRSetOptions
• include_only_species_add() : protocols::antibody::CDRSetOptions
• include_only_species_clear() : protocols::antibody::CDRSetOptions
• include_residue() : protocols::toolbox::task_operations::DesignAroundOperation
• include_trp() : protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation
• incorporate_batch() : protocols::abinitio::HedgeArchive
• incorporate_motifs() : protocols::motifs::IRCollection , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• increase_chainbreak_weight_and_update_monte_carlo() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• increase_packer_residue_radius() : protocols::hotspot_hashing::SearchPatternRotSetOp , protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO
• increasing() : protocols::loops::Loop , protocols::nonlocal::Region
• increment_client_rank() : protocols::jd2::MPIFileBufJobDistributor
• increment_count() : protocols::stepwise::screener::StepWiseScreener
• increment_count_nodes_in_flexseg() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• increment_cur_indices() : protocols::helical_bundle::BundleGridSamplerHelper
• increment_helix_count() : protocols::helical_bundle::BundleGridSampler
• increment_pool_size() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• increment_stage() : protocols::abinitio::IterativeBase
• increment_unique_id() : protocols::motifs::IRCollection
• increment_upstream_only_hit_combination() : protocols::match::Matcher
• incremente_n_multi_data() : protocols::scoring::methods::pcs2::PcsEnergyParameterManager , protocols::scoring::methods::pcs2::PcsGridSearchParameterManager
• independent_cycles() : protocols::forge::remodel::RemodelLoopMover
• independent_stage() : protocols::forge::remodel::RemodelLoopMover
• IndependentLoopMover() : protocols::loops::loop_mover::IndependentLoopMover
• index() : protocols::enzdes::EnzdesFlexibleRegion , protocols::genetic_algorithm::EntityElement , protocols::match::upstream::ScaffoldBuildPoint , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• index_and_mask_for_bin() : protocols::match::Bool3DGrid
• index_and_mask_for_point() : protocols::match::Bool3DGrid
• index_for_new_match() : protocols::match::output::BestMatchesCollection
• index_of_entity() : protocols::pack_daemon::TopEntitySet
• index_pair_in_range() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• indicate_required_context_graphs() : protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::scoring::methods::EnsembleEnergy , protocols::scoring::methods::InterchainEnvEnergy , protocols::scoring::methods::InterchainPairEnergy , protocols::scoring::methods::pcs2::PcsEnergy , 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 , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments , protocols::scoring::methods::saxs::PDDFEnergy , protocols::scoring::methods::SpecialRotamerEnergy
• indices() : protocols::features::BatchFeatures , protocols::features::ProtocolFeatures
• individual_hbonds() : protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::toolbox::task_operations::SelectByDeltaScoreOperation
• infer_anchor_connIDs() : protocols::generalized_kinematic_closure::GeneralizedKIC
• info() : protocols::moves::Mover , protocols::noesy_assign::CrossPeak
• inform_edges_considered_fixedbb_substition_uncommitted() : protocols::flexpack::interaction_graph::FlexbbNode
• inform_edges_of_alt_state_before_bbjump() : protocols::flexpack::interaction_graph::FlexbbNode
• inform_incident_edges_about_partial_state_assignment() : protocols::flexpack::interaction_graph::FlexbbNode
• ingo_clean_ss() : protocols::simple_filters::SheetFilter
• ingo_diamers() : protocols::simple_filters::SheetFilter
• ingo_find_dir() : protocols::simple_filters::SheetFilter
• ingo_find_ord() : protocols::simple_filters::SheetFilter
• ingo_hand() : protocols::simple_filters::SheetFilter
• ingo_ident_sheets() : protocols::simple_filters::SheetFilter
• ingo_lnl() : protocols::simple_filters::SheetFilter
• ingo_locations() : protocols::simple_filters::SheetFilter
• ingo_number_of_strands() : protocols::simple_filters::SheetFilter
• ingo_proper_sheets() : protocols::simple_filters::SheetFilter
• ingo_sheet_stuff() : protocols::simple_filters::SheetFilter
• ingo_start_stop() : protocols::simple_filters::SheetFilter
• ingo_strand_dirs() : protocols::simple_filters::SheetFilter
• ingo_strand_dists_min() : protocols::simple_filters::SheetFilter
• inherit_cuts() : protocols::environment::Environment
• inherit_scorefxn_temperature() : protocols::simple_moves::sidechain_moves::SidechainMCMover
• init() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::KinematicTaskControl , protocols::abinitio::MembraneAbinitio , protocols::abinitio::Protocol , protocols::antibody::AntibodyInfo , protocols::antibody::AntibodyModelerProtocol , protocols::antibody::CDRsMinPackMin , protocols::antibody::design::ResidueProbDesignOperation , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::GraftedStemOptimizer , protocols::antibody::GraftOneCDRLoop , protocols::antibody::H3CterInsert , protocols::antibody::H3PerturbCCD , protocols::antibody::H3RefineCCD , protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , protocols::antibody::ModelCDRH3 , protocols::antibody::RefineBetaBarrel , protocols::antibody::RefineOneCDRLoop , protocols::antibody::SnugDock , protocols::antibody::SnugDockProtocol , protocols::constraints_additional::BindingSiteConstraint , protocols::cyclic_peptide::PeptideStubMover , protocols::docking::DockingHighRes , protocols::docking::DockingInitialPerturbation , protocols::docking::DockingLowRes , protocols::docking::DockingProtocol , protocols::docking::DockMCMProtocol , protocols::docking::TemperedDocking , protocols::electron_density::BfactorFittingMover , protocols::electron_density::DensityMorphingMover , protocols::electron_density::ReportFSC , protocols::electron_density::ScaleMapIntensities , protocols::forge::build::ConnectRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentSwap , protocols::forge::constraints::InverseRotamersRCG , protocols::forge::constraints::InvrotTreeRCG , protocols::forge::remodel::RemodelConstraintGenerator , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::hybridization::CartesianHybridize , protocols::hybridization::CartesianSampler , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup , protocols::hybridization::InsertChunkMover , protocols::hybridization::MRMover , protocols::jumping::MembraneJump , protocols::loophash::MPI_LoopHashRefine_Emperor , protocols::loophash::MPI_LoopHashRefine_Master , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::ccd::RamaCheckBase , protocols::loops::loop_mover::LoopMover , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , 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 , protocols::match::output::MatchScoreWriter , protocols::md::CartesianMD , protocols::moves::ReplicaExchangeMC , protocols::mpi_refinement::MPI_Refine_Emperor , protocols::mpi_refinement::MPI_Refine_Master , protocols::mpi_refinement::Serial_Refine , protocols::optimize_weights::WrapperOptEMultifunc , protocols::pockets::PocketConstraint , protocols::pockets::PocketGrid , protocols::seeded_abinitio::SegmentHybridizer , protocols::sic_dock::SICFast , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::ReportEffectivePKA , protocols::simple_moves::RingConformationMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::symmetry::SequentialSymmetrySlider , protocols::sparta::ANN , protocols::sparta::Sparta::SpartaLib , protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer , protocols::stepwise::sampler::MC_Comb , protocols::stepwise::sampler::MC_OneTorsion , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange , protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_KinematicCloser , protocols::stepwise::sampler::rna::RNA_MC_Sugar , protocols::stepwise::sampler::rna::RNA_MC_Suite , protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler , protocols::stepwise::sampler::StepWiseSamplerAny , protocols::stepwise::sampler::StepWiseSamplerBase , protocols::stepwise::sampler::StepWiseSamplerComb , protocols::stepwise::sampler::StepWiseSamplerOneValue , protocols::stepwise::sampler::StepWiseSamplerSized , protocols::stepwise::sampler::StepWiseSamplerSizedAny , protocols::stepwise::sampler::StepWiseSamplerSizedComb , protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::SurfaceDockingProtocol , protocols::symmetric_docking::SymFoldandDockRbTrialMover , protocols::toolbox::GreedyKCenter , protocols::toolbox::InteratomicVarianceMatrix , protocols::toolbox::KCluster , protocols::toolbox::KMedoid , protocols::toolbox::match_enzdes_util::EnzConstraintParameters , protocols::toolbox::task_operations::RestrictToLoops , protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors , protocols::toolbox::task_operations::RestrictToMoveMapChiOperation , protocols::wum::MPI_WorkUnitManager , protocols::wum::MPI_WorkUnitManager_Slave
• init_after_reading() : protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::FragmentClaimer , 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::TemplateFragmentClaimer , protocols::topology_broker::TemplateJumpClaimer , protocols::topology_broker::TopologyClaimer
• init_allowed_pos() : protocols::loops::loop_closure::kinematic_closure::KinematicWrapper
• init_angle() : protocols::matdes::GetRBDOFValues
• init_atom_equiv() : protocols::comparative_modeling::ThreadingMover
• init_bbgmover() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• init_calibrator() : protocols::noesy_assign::PeakCalibrator , protocols::noesy_assign::StructureDependentPeakCalibrator
• init_centroids() : protocols::make_rot_lib::MakeRotLibMover
• init_clash_check() : protocols::scoring::ImplicitFastClashCheck
• init_d77_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
• init_data() : protocols::analysis::InterfaceAnalyzerMover
• init_disp() : protocols::matdes::GetRBDOFValues
• init_fast() : protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• init_for_copy() : protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors
• init_for_equal_operator_and_copy_constructor() : protocols::antibody::design::ConservativeDesignOperation , protocols::antibody::design::ResidueProbDesignOperation , protocols::antibody::SnugDock , protocols::antibody::SnugDockProtocol , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::loops::loop_mover::refine::RepackTrial , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial
• init_from_cmd() : protocols::docking::membrane::MPDockingMover , protocols::loophash::WorkUnit_LoopHash , protocols::membrane::AddMembraneMover , protocols::membrane::RotationMover , protocols::membrane::symmetry::SymmetricAddMembraneMover , protocols::membrane::TransformIntoMembraneMover , protocols::membrane::TranslationMover , protocols::membrane::TranslationRotationMover , protocols::membrane::visualize::VisualizeEmbeddingMover , protocols::membrane::visualize::VisualizeMembraneMover , protocols::mpi_refinement::WorkUnit_CombinePose , protocols::mpi_refinement::WorkUnit_LoopHash , protocols::mpi_refinement::WorkUnit_NormalMode , protocols::mpi_refinement::WorkUnit_RamaPerturber , protocols::mpi_refinement::WorkUnit_Sampler
• init_from_decoy_set() : protocols::abinitio::HedgeArchive , protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeBase , protocols::jd2::archive::AbstractArchiveBase , protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::EvaluatedArchive , protocols::jd2::archive::VarianceStatisticsArchive
• init_from_file() : protocols::simple_filters::PredictedBurialEvaluator
• init_from_options() : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody_legacy::AntibodyModeler , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperingBase , protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingInitialPerturbation , protocols::docking::DockingPrepackProtocol , protocols::docking::DockingProtocol , protocols::docking::DockTaskFactory , protocols::docking::EllipsoidalRandomizationMover , protocols::docking::TemperedDocking , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::features::strand_assembly::StrandBundleFeatures , protocols::jd2::archive::NormalizedEvaluatedArchive , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• init_jd() : protocols::jd2::JobDistributor
• init_jumps() : protocols::topology_broker::FragmentJumpClaimer
• init_k48r_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
• init_kic_loop() : protocols::simple_moves::BBGaussianMover
• init_mc() : protocols::docking::DockMCMCycle , protocols::loops::loop_closure::ccd::LoopClosure
• init_mini_pose() : protocols::jumping::ResiduePairJump
• init_minmover() : protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• init_on_new_input() : protocols::analysis::InterfaceAnalyzerMover , protocols::anchored_design::AnchoredDesignMover , protocols::antibody::design::AntibodyDesignMover , protocols::antibody_legacy::AntibodyModeler , protocols::floppy_tail::FloppyTailMover
• init_options() : protocols::antibody::SnugDock , protocols::antibody::SnugDockProtocol , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::RamaCheckBase , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , 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::motifs::LigandMotifSearch , protocols::motifs::MotifDnaPacker , protocols::motifs::MotifSearch
• init_parameters() : protocols::motif_grafting::movers::MotifGraftMover
• init_per_residue_data() : protocols::analysis::InterfaceAnalyzerMover
• init_pose() : protocols::abinitio::ResolutionSwitcher
• init_PredErrorSurface() : protocols::sparta::Sparta::SpartaLib
• init_rdcs() : protocols::simple_filters::SelectRDC_Evaluator
• init_rot_to_pack() : protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• init_rotamer_recovery_with_options() : protocols::rotamer_recovery::RotamerRecovery
• init_rotamers() : protocols::make_rot_lib::MakeRotLibMover
• init_standard() : protocols::dna::DnaInterfacePacker , protocols::motifs::MotifDnaPacker , protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• init_strength() : protocols::environment::claims::TorsionClaim , protocols::environment::claims::XYZClaim
• init_task() : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• init_with_options() : protocols::backrub::BackrubMover , protocols::rotamer_recovery::RotamerRecovery
• init_with_pose() : protocols::sic_dock::xyzStripeHashPoseWithMeta
• initForEqualOperatorAndCopyConstructor() : protocols::antibody::GraftedStemOptimizer , protocols::antibody::GraftOneCDRLoop , protocols::docking::DockingProtocol , protocols::loops::loop_mover::LoopMover
• initHBond() : protocols::sparta::PDB
• initial_cter_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
• initial_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
• initial_repack() : protocols::ub_e2c::ubi_e2c_modeler
• initial_template_index() : protocols::hybridization::HybridizeSetup
• initialize() : protocols::abinitio::abscript::AbscriptMover , protocols::abinitio::abscript::FragmentCM , protocols::abinitio::abscript::RigidChunkCM , protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeBase , protocols::abinitio::IterativeFullatom , protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD , protocols::dna::DnaInterfaceMultiStateDesign , protocols::environment::ClientMover , protocols::environment::CoMTrackerCM , protocols::environment::ScriptCM , protocols::farna::BasePairStepLibrary , protocols::farna::MultipleDomainMover , protocols::farna::RNA_StructureParameters , protocols::features::ProteinSilentReport , protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::SheetFoldTypeManager , protocols::fldsgn::topology::SheetSet , protocols::fldsgn::topology::SS_Info2 , protocols::fldsgn::topology::StrandPairing , protocols::flexpack::interaction_graph::FlexbbInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flxbb::FilterStructs , protocols::frag_picker::nonlocal::NonlocalFrags , protocols::frag_picker::SidechainContactDistCutoff , protocols::hybridization::HybridizeFoldtreeDynamic , protocols::jd2::archive::AbstractArchiveBase , protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::NormalizedEvaluatedArchive , protocols::loops::loop_mover::LoopCM , protocols::match::downstream::ActiveSiteGrid , protocols::match::HitHasher , protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::match::OccupiedSpaceHash , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::moves::MoveMapMover , protocols::nonlocal::HelixRotate , protocols::nonlocal::SheetTranslate , protocols::nonlocal::SingleFragmentMover , protocols::pack_daemon::IterativeVectorExpression , protocols::pockets::PocketGrid , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::qsar::scoring_grid::ConstantScoreBase , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::rbsegment_relax::RBSegmentRelax , protocols::rigid::UniformRigidBodyCM , protocols::scoring::InterfaceInfo , protocols::simple_filters::DdGScan , protocols::simple_moves::GenericMonteCarloMover , protocols::stepwise::modeler::align::StepWisePoseAligner , protocols::stepwise::modeler::packer::StepWiseMasterPacker , protocols::stepwise::modeler::StepWiseModeler , protocols::stepwise::monte_carlo::StepWiseMonteCarlo , protocols::stepwise::sampler::protein::ProteinFragmentStepWiseSampler , protocols::stepwise::setup::StepWiseCSA_JobDistributor , protocols::stepwise::setup::StepWiseJobDistributor , protocols::stepwise::setup::StepWiseMonteCarloJobDistributor , protocols::toolbox::AllowInsert , protocols::toolbox::SelectResiduesByLayer
• initialize_active_site_definition_from_command_line() : protocols::match::MatcherTask
• initialize_active_site_grid() : protocols::match::Matcher
• initialize_actual_rep_cutoff() : protocols::stepwise::screener::PartitionContactScreener
• initialize_all_atoms() : protocols::protein_interface_design::filters::AtomicContactCountFilter
• initialize_all_grids() : protocols::qsar::scoring_grid::GridManager
• initialize_allow_insert() : protocols::farna::RNA_StructureParameters
• initialize_and_sample_loops() : protocols::hybridization::HybridizeProtocol
• initialize_auto_tune_cluster_rmsds() : protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• Initialize_base_stub_list() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• initialize_betaresidue_minima() : protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber
• initialize_bump_grids() : protocols::match::Matcher
• initialize_by_dimer_pairs() : protocols::fldsgn::topology::StrandPairingSet
• initialize_by_prepack() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• initialize_cdr_set() : protocols::antibody::design::AntibodyGraftDesignMover
• initialize_checkers() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_chunks() : protocols::nonlocal::SingleFragmentMover
• initialize_cluster_list() : protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• initialize_conformers() : protocols::match::downstream::LigandConformerBuilder
• initialize_constraint_forest() : protocols::abinitio::AbrelaxApplication
• initialize_constraints() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol
• initialize_constraints_from_file() : protocols::optimize_weights::ConstraintedOptimizationWeightFunc
• initialize_corresponding_atom_id_map() : protocols::stepwise::legacy::screener::SimpleRMSD_Screener , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• initialize_cross_chain() : protocols::protein_interface_design::filters::AtomicContactCountFilter
• initialize_cross_jump() : protocols::protein_interface_design::filters::AtomicContactCountFilter
• initialize_cuts() : protocols::topology_broker::TopologyBroker
• initialize_daemon_with_all_states() : protocols::pack_daemon::DynamicAggregateFunctionDriver
• initialize_database() : protocols::features::ReportToDB
• initialize_defaults() : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• initialize_distance_range() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• initialize_dofs() : protocols::topology_broker::AsymFoldandDockClaimer , protocols::topology_broker::BasicJumpClaimer , 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::RigidChunkClaimer , protocols::topology_broker::StartStructClaimer , protocols::topology_broker::TMHTopologySamplerClaimer , protocols::topology_broker::TopologyBroker , protocols::topology_broker::TopologyClaimer
• initialize_downstream_algorithms() : protocols::match::Matcher
• initialize_enzdes_input_data_from_command_line() : protocols::match::MatcherTask
• initialize_espGrid() : protocols::pockets::ElectrostaticpotentialGrid
• initialize_euler_angle_grid_parameters() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_evaluator() : protocols::stepwise::screener::PartitionContactScreener
• initialize_exchange_schedule_from_file() : protocols::canonical_sampling::HamiltonianExchange
• initialize_filter() : protocols::flxbb::FlxbbDesign
• initialize_for_movie() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• initialize_frag_source_pose() : protocols::coarse_rna::CoarseRNA_Fragments
• initialize_fragments() : protocols::seeded_abinitio::CloseFold
• initialize_free_and_fixed() : protocols::optimize_weights::IterativeOptEDriver
• initialize_from_command_line() : protocols::match::MatcherTask , protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::modeler::options::StepWiseModelerOptions , protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions , protocols::stepwise::options::StepWiseBasicOptions , protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst
• initialize_from_correspondence_file() : protocols::pack_daemon::EntityCorrespondence
• initialize_from_directory() : protocols::stepwise::modeler::precomputed::PrecomputedLibraryMover
• initialize_from_enzcst_io() : protocols::toolbox::match_enzdes_util::InvrotTreeNode
• initialize_from_enzcst_io_and_invrots() : protocols::toolbox::match_enzdes_util::InvrotTreeNode
• initialize_from_file() : protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperingBase , protocols::match::Matcher
• initialize_from_gridlig_file() : protocols::match::downstream::ActiveSiteGrid
• initialize_from_input_file() : protocols::pack_daemon::DynamicAggregateFunctionDriver , protocols::pack_daemon::EntityFunc
• initialize_from_matcher_task() : protocols::match::output::OutputWriter , protocols::match::output::PDBWriter
• initialize_from_residue() : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::match::upstream::OriginalBackboneBuildPoint , protocols::toolbox::match_enzdes_util::LigandConformer
• initialize_from_residue_type() : protocols::match::upstream::UpstreamResTypeGeometry
• initialize_from_rotation_matrix() : protocols::stepwise::sampler::rigid_body::EulerAngles
• initialize_from_task() : protocols::match::Matcher
• initialize_full_rigid_body_sampler() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_ghost_pose() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• initialize_internal_correspondence_data() : protocols::simple_moves::GreenPacker
• initialize_internal_data() : protocols::enzdes::ResidueConformerFilter
• initialize_is_fixed_res() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• Initialize_is_virtual_base() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• initialize_library() : protocols::nonlocal::BiasedFragmentMover , protocols::nonlocal::SingleFragmentMover
• initialize_lores_silent_file() : protocols::farna::RNA_DeNovoProtocol
• initialize_max_memory_pose_num() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• initialize_minimizer() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• initialize_modeler_scorefxn() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection
• initialize_movemap() : protocols::relax::RelaxProtocolBase
• initialize_movers() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol , protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• initialize_moving_residue_pose_list() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_next_suite_atoms() : protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• initialize_o2prime_green_packer() : protocols::stepwise::modeler::rna::o2prime::O2PrimePacker
• initialize_o2prime_packer_task() : protocols::stepwise::modeler::rna::o2prime::O2PrimePacker
• initialize_occupied_space_bounding_box_from_command_line() : protocols::match::MatcherTask
• initialize_occupied_space_hash() : protocols::match::Matcher
• initialize_optE_type_name_map() : protocols::optimize_weights::OptEPositionDataFactory
• initialize_orientation_atoms_from_command_line() : protocols::match::MatcherTask
• initialize_output_options_from_command_line() : protocols::match::MatcherTask
• initialize_pack_daemons() : protocols::pack_daemon::DynamicAggregateFunctionDriver
• initialize_packer() : protocols::stepwise::modeler::packer::StepWiseMasterPacker
• initialize_parameters() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker , protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler , protocols::stepwise::modeler::StepWiseMinimizer
• initialize_parameters_and_input() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• initialize_phi_psi_offsets() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• initialize_phosphate_move_list() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• initialize_pose() : protocols::features::ReportToDB , protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_pose_from_streams() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• initialize_pose_if_empty() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• initialize_pose_level_screeners() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_pose_variants_for_chain_closure() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler
• initialize_probabilities() : protocols::nonlocal::BiasedFragmentMover
• initialize_protein_bond_sampler() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_protein_packer() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_quick_alignment_pose() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• initialize_random_chunks() : protocols::farna::RNA_ChunkLibrary
• initialize_rb_fragments() : protocols::rbsegment_relax::FragInsertAndAlignMover
• initialize_refinement_pattern() : protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• initialize_relevant_residues() : protocols::features::ReportToDB
• initialize_repeat_pose() : protocols::simple_moves::RepeatPropagationMover
• initialize_reporters() : protocols::features::ReportToDB
• initialize_rescoords() : protocols::match::upstream::ProteinUpstreamBuilder
• initialize_residue_level_screeners() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_residues() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler
• initialize_residues_for_type() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler
• initialize_rigid_body_movers() : protocols::farna::MultipleDomainMover
• initialize_rigid_body_rotamer() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_rna_bond_sampler() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_rna_chunk_library() : protocols::farna::RNA_ChunkLibrary
• initialize_rotamer() : protocols::features::RotamerInitializer< T, N >
• initialize_rotamer_behavior_for_residue_level_task() : protocols::ddg::ddGMover
• initialize_sampler() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_samples() : protocols::helical_bundle::BundleGridSamplerHelper
• initialize_scaffold_active_site_residue_list_from_command_line() : protocols::match::MatcherTask
• initialize_scaffold_build_points() : protocols::match::Matcher
• initialize_scanner() : protocols::pack_daemon::DynamicAggregateFunction
• initialize_scanner_and_function_names() : protocols::pack_daemon::EntityFunc
• initialize_scorefunction() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• initialize_scorefunctions() : protocols::stepwise::modeler::StepWiseModeler
• initialize_scorefxn() : protocols::farna::RNA_DeNovoProtocol , protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• initialize_screeners() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_secstruct() : protocols::farna::RNA_StructureParameters
• initialize_sequence() : protocols::topology_broker::TopologyBroker
• initialize_simulation() : protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover , protocols::canonical_sampling::AsyncMPITemperingBase , protocols::canonical_sampling::BiasEnergy , protocols::canonical_sampling::DbTrajectoryRecorder , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperatureController , protocols::canonical_sampling::TemperingBase , protocols::canonical_sampling::ThermodynamicMover , protocols::canonical_sampling::ThermodynamicObserver , protocols::canonical_sampling::TrajectoryRecorder , protocols::canonical_sampling::TrialCounterObserver , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• initialize_starting_rama_scores() : protocols::loops::loop_closure::ccd::RamaCheckBase
• initialize_surface_energies() : protocols::surface_docking::SurfaceDockingProtocol
• initialize_tag_is_done() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol
• initialize_task_factory() : protocols::features::RotamerRecoveryFeatures
• initialize_task_level_behavior() : protocols::ddg::ddGMover
• Initialize_terminal_res() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• initialize_trajectory_reporter() : protocols::features::TrajectoryReportToDB
• initialize_tree_nodes_from_enzcst_io() : protocols::toolbox::match_enzdes_util::InvrotTarget
• initialize_typGrid() : protocols::pockets::ElectrostaticpotentialGrid
• initialize_upstream_downstream_collision_filter_data_from_command_line() : protocols::match::MatcherTask
• initialize_upstream_nonbonded_min_separation_d2() : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• initialize_upstream_residue() : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• initialize_upstream_residue_collision_filter_data_from_command_line() : protocols::match::MatcherTask
• initialize_useful_info() : protocols::stepwise::modeler::StepWiseConnectionSampler
• initialize_value_evaluators_from_file() : protocols::enzdes::EnzdesScorefileFilter
• initialize_variables() : 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::phosphate::PhosphateMover , protocols::stepwise::options::StepWiseBasicOptions
• initialize_VDW_rep_checker() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• initialize_velocity() : protocols::md::CartesianMD
• initialize_weights() : protocols::moves::TrialMover
• initialize_worker() : protocols::boinc::Boinc
• initialize_working_parameters_and_root() : protocols::stepwise::modeler::StepWiseModeler
• initialize_xyz_grid_parameters() : protocols::stepwise::modeler::StepWiseConnectionSampler
• InitializeByBins() : protocols::simple_moves::bin_transitions::InitializeByBins
• initialized() : protocols::branch_angle::BranchAngleOptimizer , protocols::dna::DnaInterfaceFinder , protocols::dna::DnaInterfacePacker , protocols::farna::RNA_SecStructInfo , protocols::rbsegment_relax::RBSegment , protocols::rotamer_recovery::PerNativeRRReporterHuman
• initiate_wu_sendrecv() : protocols::wum2::EndPoint
• initOrbitalShift() : protocols::sparta::PDB
• initPB() : protocols::simple_filters::DdgFilter
• inner_cycles() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• inner_job() : protocols::jd2::Job
• inner_job_nonconst() : protocols::jd2::Job
• inner_loop() : protocols::abinitio::DoubleLayerKinematicAbinitio , protocols::abinitio::KinematicTaskControl
• inner_loop_refinement() : protocols::surface_docking::FullatomRelaxMover
• InnerJob() : protocols::jd2::InnerJob
• InnerMultiThreadingJob() : protocols::jd2::InnerMultiThreadingJob
• inprogress() : protocols::jobdist::BaseJobDistributor
• input_conformation() : protocols::match::upstream::OriginalBackboneBuildPoint
• input_loops_into_tuples() : protocols::anchored_design::AnchorMoversData
• input_res() : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• input_res_vectors() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• input_source() : protocols::comparative_modeling::GenericJobInputter , protocols::comparative_modeling::ThreadingJobInputter , protocols::features::DatabaseJobInputter , protocols::jd2::AtomTreeDiffJobInputter , protocols::jd2::BatchJobInputter , protocols::jd2::JD2ResourceManagerJobInputter , protocols::jd2::JobInputter , protocols::jd2::LazySilentFileJobInputter , protocols::jd2::PDBJobInputter , protocols::jd2::PoseInputStreamJobInputter , protocols::jd2::ScreeningJobInputter , protocols::jd2::SilentFileJobInputter , protocols::make_rot_lib::MakeRotLibJobInputter
• input_struct_definition() : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• input_tag() : protocols::jd2::InnerJob , protocols::jd2::Job , protocols::jobdist::BasicJob
• InputStreamStepWiseSampler() : protocols::stepwise::sampler::input_streams::InputStreamStepWiseSampler
• InputStreamWithResidueInfo() : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• Inputter() : protocols::inputter::Inputter
• InputterStream() : protocols::inputter::InputterStream
• inq() : protocols::wum2::EndPoint
• insert() : protocols::comparative_modeling::AlignmentSet , protocols::frag_picker::BoundedCollector< StrictWeakOrdering > , protocols::frag_picker::CandidatesCollector , protocols::frag_picker::GrabAllCollector , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaCollector , protocols::frag_picker::quota::SecondaryStructurePool , protocols::frag_picker::scores::AdaptiveScoreHistogram , protocols::frags::TorsionFragment , protocols::match::upstream::OriginalBackboneBuildPoint , protocols::match::upstream::ScaffoldBuildPoint , protocols::protein_interface_design::movers::PlacementAuctionMover
• insert_base_pair_jumps() : protocols::farna::RNA_StructureParameters
• insert_chain_ending() : protocols::environment::ProtectedConformation
• insert_chunk_into_pose() : protocols::farna::ChunkSet , protocols::farna::RNA_ChunkLibrary
• insert_conformation_by_jump() : protocols::environment::ProtectedConformation
• insert_connection_scheme() : protocols::forge::build::SegmentInsert
• insert_ddG_rows() : protocols::features::DdGFeatures
• insert_dof_element() : protocols::environment::claims::TorsionClaim
• insert_dofs_by_residue() : protocols::simple_moves::DOFHistogramRecorder
• insert_fragment() : protocols::coarse_rna::CoarseRNA_Fragments , protocols::environment::ProtectedConformation , protocols::farna::FullAtomRNA_Fragments , protocols::frags::SingleResidueTorsionFragmentLibrary
• insert_grid() : protocols::qsar::scoring_grid::GridManager
• insert_hbond_dehydron_row() : protocols::features::HBondFeatures
• insert_hbond_geom_coords() : protocols::features::HBondFeatures
• insert_hbond_lennard_jones_row() : protocols::features::HBondFeatures
• insert_hbond_row() : protocols::features::HBondFeatures
• insert_hit() : protocols::match::HitHasher
• insert_hit_geometry() : protocols::match::OccupiedSpaceHash
• insert_ideal_geometry_at_polymer_bond() : protocols::environment::ProtectedConformation
• insert_ideal_geometry_at_residue_connection() : protocols::environment::ProtectedConformation
• insert_loop_at_index() : protocols::loops::LoopsFileData
• insert_map() : protocols::simple_moves::FragmentMover
• insert_match_into_pose() : protocols::match::output::PoseMatchOutputWriter
• insert_movemap() : protocols::grafting::AnchoredGraftMover
• insert_one_body_residue_score_rows() : protocols::features::ResidueScoresFeatures
• insert_pair() : protocols::toolbox::task_operations::RestrictInterGroupVectorOperation
• insert_piece() : protocols::grafting::GraftMoverBase
• insert_pose() : protocols::forge::build::SegmentInsert
• insert_pose_torsion_override_movemap() : protocols::forge::build::SegmentInsert
• insert_random_smallestmer_per_loop() : protocols::forge::remodel::RemodelLoopMover
• insert_residue_pdb_confidence_rows() : protocols::features::PdbDataFeatures
• insert_residue_pdb_identification_rows() : protocols::features::PdbDataFeatures
• insert_residue_rows() : protocols::features::ResidueFeatures
• insert_residue_scores_rows() : protocols::features::ResidueScoresFeatures
• insert_residue_total_scores_rows() : protocols::features::ResidueTotalScoresFeatures
• insert_rms() : protocols::simple_moves::ScoreMover
• insert_sampled_torsion_string_into_taboo_map() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• insert_score_function_weights_rows() : protocols::features::ScoreFunctionFeatures
• insert_score_type_rows() : protocols::features::ScoreTypeFeatures
• insert_site_atoms_row() : protocols::features::HBondFeatures
• insert_site_environment_row() : protocols::features::HBondFeatures
• insert_site_pdb_row() : protocols::features::HBondFeatures
• insert_site_row() : protocols::features::HBondFeatures
• insert_size() : protocols::simple_moves::FragmentMover
• insert_ss_into_pose() : protocols::jd2::parser::BluePrint
• insert_string_real_rows() : protocols::features::JobDataFeatures
• insert_string_rows() : protocols::features::JobDataFeatures
• insert_string_string_rows() : protocols::features::JobDataFeatures
• insert_structure_score_rows() : protocols::features::StructureScoresFeatures
• insert_task_operation_residue_effects_row() : protocols::features::TaskOperationFeatures
• insert_task_operations_row() : protocols::features::TaskOperationFeatures
• insert_template_frags() : protocols::abinitio::AbrelaxApplication
• insert_two_body_long_range_residue_score_rows() : protocols::features::ResidueScoresFeatures
• insert_two_body_residue_score_rows() : protocols::features::ResidueScoresFeatures
• insert_unrecognized_atoms_rows() : protocols::features::UnrecognizedAtomFeatures
• insert_unrecognized_neighbors_rows() : protocols::features::UnrecognizedAtomFeatures
• insert_unrecognized_residues_rows() : protocols::features::UnrecognizedAtomFeatures
• InsertChunkMover() : protocols::hybridization::InsertChunkMover
• insertion() : protocols::jd2::parser::BluePrint
• insertion_char() : protocols::forge::build::SegmentInsert
• insertion_code() : protocols::antibody::PDBLandmark , protocols::loops::ResidueIndexDescription
• insertion_end_residue() : protocols::forge::build::SegmentInsert
• insertion_length() : protocols::grafting::GraftMoverBase
• insertion_point_absolute_index() : protocols::forge::build::SegmentInsert
• insertion_start_residue() : protocols::forge::build::SegmentInsert
• InsertPoseIntoPoseMover() : protocols::grafting::simple_movers::InsertPoseIntoPoseMover
• InSetExpression() : protocols::pack_daemon::InSetExpression
• instance() : protocols::boinc::Boinc , protocols::checkpoint::Timer
• instantiate_filter() : protocols::rosetta_scripts::RosettaScriptsParser
• instantiate_mover() : protocols::rosetta_scripts::RosettaScriptsParser
• instantiate_rampfunc() : protocols::moves::RampingMover
• instantiate_residue_if_rebuilding_bulge() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• instantiate_sugar() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator
• instantiate_sugars_at_cutpoint_closed() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator
• instantiate_sugars_recursively() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator
• instantiate_taskoperation() : protocols::rosetta_scripts::RosettaScriptsParser
• instantiated_phosphate() : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• instantiated_some_phosphate() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• instruct_daemons_to_drop_entity() : protocols::pack_daemon::MPIMultistateFitnessFunction , protocols::pack_daemon::MultistateFitnessFunction
• instruct_daemons_to_keep_last_entity() : protocols::pack_daemon::MPIMultistateFitnessFunction , protocols::pack_daemon::MultistateFitnessFunction
• instruction_size() : protocols::fldsgn::BluePrintBDR
• integration_test_mode() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• IntegrationTestBreaker() : protocols::stepwise::screener::IntegrationTestBreaker
• intensity() : protocols::noesy_assign::Resonance
• inter_chain() : protocols::simple_moves::AddConstraintsToCurrentConformationMover
• InteractingRotamerExplosion() : protocols::toolbox::task_operations::InteractingRotamerExplosion
• InteratomicVarianceMatrix() : protocols::toolbox::InteratomicVarianceMatrix
• InterbondAngleScore() : protocols::frag_picker::scores::InterbondAngleScore
• InterchainEnvEnergy() : protocols::scoring::methods::InterchainEnvEnergy
• InterchainPairEnergy() : protocols::scoring::methods::InterchainPairEnergy
• InterchainPotential() : protocols::scoring::InterchainPotential
• interface() : protocols::dna::RestrictDesignToProteinDNAInterface
• Interface() : protocols::ligand_docking::ligand_options::Interface , protocols::scoring::Interface
• interface() : protocols::scoring::InterfaceInfo
• interface_calc() : protocols::anchored_design::AnchorMoversData
• interface_detection_dis() : protocols::antibody::design::AntibodyDesignModeler , protocols::antibody::design::AntibodyDesignMoverGenerator
• interface_distance_cutoff() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• interface_exists() : protocols::features::InterfaceFeatures
• interface_from_pose() : protocols::scoring::InterchainPotential
• interface_interaction_energy() : protocols::simple_filters::RotamerBoltzmannWeight
• interface_nres() : protocols::scoring::Interface , protocols::scoring::InterfaceInfo
• interface_radius() : protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover
• InterfaceAnalyzerMover() : protocols::analysis::InterfaceAnalyzerMover
• InterfaceBindingEnergyDensityFilter() : protocols::simple_filters::InterfaceBindingEnergyDensityFilter
• InterfaceBuilder() : protocols::ligand_docking::InterfaceBuilder
• InterfaceBuilderLoader() : protocols::ligand_docking::InterfaceBuilderLoader
• InterfaceFeatures() : protocols::features::InterfaceFeatures
• InterfaceFeaturesCreator() : protocols::features::InterfaceFeaturesCreator
• InterfaceHolesFilter() : protocols::protein_interface_design::filters::InterfaceHolesFilter
• InterfaceInfo() : protocols::ligand_docking::ligand_options::InterfaceInfo , protocols::scoring::InterfaceInfo
• InterfacePackingFilter() : protocols::matdes::InterfacePackingFilter
• InterfaceRecapitulationMover() : protocols::protein_interface_design::movers::InterfaceRecapitulationMover
• InterfaceSasaFilter() : protocols::simple_filters::InterfaceSasaFilter
• InterfaceScoreCalculator() : protocols::ligand_docking::InterfaceScoreCalculator
• InterfaceSidechainMinMover() : protocols::docking::InterfaceSidechainMinMover
• InterfaceTaskOperation() : protocols::toolbox::task_operations::InterfaceTaskOperation
• InterGroupNeighborsCalculator() : protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator
• InterlockAroma() : protocols::flxbb::InterlockAroma
• InterlockingAromaFilter() : protocols::fldsgn::filters::InterlockingAromaFilter
• intermediate_structs() : protocols::jd2::archive::Batch
• intermedrelax() : protocols::comparative_modeling::LoopRelaxMover , protocols::protein_interface_design::movers::LoopMoverFromCommandLine
• InternalWorkingResidueParameter() : protocols::stepwise::modeler::rna::InternalWorkingResidueParameter
• interpolate_on_statistics() : protocols::noesy_assign::PeakCalibrator
• interpolate_too_big() : protocols::noesy_assign::PeakCalibrator
• interpolate_too_small() : protocols::noesy_assign::PeakCalibrator
• InterRepeatContactFilter() : protocols::simple_filters::InterRepeatContactFilter
• intersects() : protocols::forge::build::Interval
• interval() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight
• Interval() : protocols::forge::build::Interval
• interval() : protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• Interval() : protocols::jumping::Interval
• intervals() : protocols::forge::build::BuildManager
• intervals_containing_defined_positions() : protocols::forge::build::BuildManager
• intervals_containing_new_positions() : protocols::forge::build::BuildManager
• intervals_containing_preexisting_positions() : protocols::forge::build::BuildManager
• intervals_containing_undefined_positions() : protocols::forge::build::BuildManager
• intervals_without_valid_original_equivalents() : protocols::forge::build::BuildManager
• intialize_free_and_fixed_energy_terms() : protocols::optimize_weights::IterativeOptEDriver
• IntraRepeatContactFilter() : protocols::simple_filters::IntraRepeatContactFilter
• invalidate_score_variations() : protocols::jd2::archive::EvaluatedArchive , protocols::jd2::archive::NormalizedEvaluatedArchive
• inverse_rotamers_against_residue() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
• InverseRotamersRCG() : protocols::forge::constraints::InverseRotamersRCG
• invert() : protocols::filters::CompoundFilter , protocols::loops::Loops , protocols::membrane::geometry::Embedding , protocols::membrane::geometry::EmbeddingDef , protocols::toolbox::task_operations::StoreCompoundTaskMover
• invert_direction() : protocols::normalmode::NormalModeRelaxMover
• invert_helix() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• InvGeometricFunc() : protocols::moves::InvGeometricFunc
• InvrotCollector() : protocols::toolbox::match_enzdes_util::InvrotCollector
• invrots() : protocols::toolbox::match_enzdes_util::InvrotCollector
• InvrotTarget() : protocols::toolbox::match_enzdes_util::InvrotTarget
• InvrotTree() : protocols::toolbox::match_enzdes_util::InvrotTree
• InvrotTreeNode() : protocols::toolbox::match_enzdes_util::InvrotTreeNode
• InvrotTreeNodeBase() : protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase
• InvrotTreeRCG() : protocols::forge::constraints::InvrotTreeRCG
• inward_normal_to_plane() : protocols::docking::EllipsoidalRandomizationMover
• IonizableResidue() : protocols::simple_moves::IonizableResidue
• ionized_restypes() : protocols::simple_moves::IonizableResidue
• IRCollection() : protocols::motifs::IRCollection
• IRmsdFilter() : protocols::protein_interface_design::filters::IRmsdFilter
• irrelevant_jump() : protocols::topology_broker::RigidChunkClaimer::JumpCalculator
• is4D() : protocols::noesy_assign::CrossPeak
• is_active_node() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• is_any_pdb_empty() : protocols::ddg::ddGMover
• is_archive_rank() : protocols::jd2::archive::MPIArchiveJobDistributor
• is_atom_bin_in_range() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• is_attached() : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• is_backbone() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• is_backbone_only_cst() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• is_barrel() : protocols::fldsgn::topology::Sheet
• is_base_paired() : protocols::dna::DNAParameters
• is_beta_aminoacid() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• is_buried_ring() : protocols::pockets::GenPharmacophore
• is_camelid() : protocols::antibody::Ab_TemplateInfo , protocols::antibody::AntibodyInfo
• is_cancelled() : protocols::jd2::archive::Batch
• is_catalytic_position() : protocols::enzdes::EnzdesBaseProtocol
• is_claim() : protocols::environment::claims::EnvClaim
• is_complete() : protocols::ddg::ddGMover
• is_compliant() : protocols::noesy_assign::CovalentCompliance
• is_copy() : protocols::helical_bundle::PerturbBundleOptions
• is_covalent() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• is_crystal_contact() : protocols::toolbox::task_operations::CrystalContactsOperation
• is_cut() : protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops
• is_dominant() : protocols::mpi_refinement::MultiObjective
• is_elimination_candidate() : protocols::noesy_assign::CrossPeak
• is_empty() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• is_excluded() : protocols::mpi_refinement::Scheduler
• is_extended() : protocols::loops::Loop
• is_finished() : protocols::jobdist::AtomTreeDiffJobDistributor , protocols::jobdist::BaseJobDistributor , protocols::jobdist::PlainPdbJobDistributor , protocols::jobdist::PlainRawJobDistributor , protocols::jobdist::PlainSilentFileJobDistributor
• is_flexible() : protocols::enzdes::EnzdesFlexBBProtocol
• is_folded() : protocols::noesy_assign::FoldResonance
• is_folded_down() : protocols::noesy_assign::FoldResonance
• is_folded_up() : protocols::noesy_assign::FoldResonance
• is_foldtype() : protocols::fldsgn::topology::SheetFoldTypeManager
• is_fullatom() : protocols::coarse_rna::CoarseRNA_Fragments , protocols::farna::FullAtomRNA_Fragments , protocols::farna::RNA_Fragments
• is_geometry_initialized() : protocols::fldsgn::topology::SS_Base
• is_good() : protocols::abinitio::Template , protocols::abinitio::Templates
• is_helix() : protocols::features::SecondaryStructureSegmentFeatures
• is_helix_jump() : protocols::abinitio::TemplateJumpSetup
• is_hydrophobic() : protocols::fldsgn::MyAtom
• is_in_grid() : protocols::qsar::scoring_grid::ConstantScoreBase , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::GridManager , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationMetaGrid
• is_in_list() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::PerturbBundle
• is_in_neighborhood() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• is_in_taboo_map() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• is_init() : protocols::stepwise::sampler::StepWiseSamplerBase
• is_initialized() : protocols::features::ProteinSilentReport , protocols::fldsgn::BluePrintBDR
• is_interface() : protocols::scoring::Interface , protocols::scoring::InterfaceInfo
• is_interface_ddg() : protocols::ddg::ddGMover
• is_interface_residue() : protocols::ligand_docking::InterfaceBuilder
• is_internal() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• is_it_time() : protocols::moves::PyMolMover
• is_jump() : protocols::stepwise::monte_carlo::SWA_Move
• is_lefthanded() : protocols::fldsgn::topology::BetaAlphaBetaMotif
• is_ligand_present() : protocols::flexpep_docking::FlexPepDockingFlags
• is_loop() : protocols::features::HelixCapFeatures , protocols::features::SecondaryStructureSegmentFeatures
• is_loop_residue() : protocols::loops::Loops
• is_master_node() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• is_medium_base_stack_and_medium_base_pair() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• is_member() : protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::StrandPairing
• is_movable() : protocols::nonlocal::Chunk
• is_moving_res() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• is_multi_trial() : protocols::canonical_sampling::ThermodynamicMover , protocols::simple_moves::sidechain_moves::SidechainMCMover
• is_mutant_calc_complete() : protocols::ddg::ddGMover
• is_my_structure() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• is_native_pairing() : protocols::abinitio::PairingStatistics
• is_native_rotamer_well() : protocols::optimize_weights::PNatRotOptEPositionData
• is_new_cluster_center_with_working_parameters() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• is_new_structure() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• is_nonpivot_residue() : protocols::kinematic_closure::ClosureProblem
• is_normalization_enabled() : protocols::qsar::scoring_grid::GridManager
• is_observing() : protocols::viewer::ConformationViewer
• is_old_individual_suite_cluster() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• is_on() : protocols::checkpoint::Timer
• is_open_channel() : protocols::jd2::MpiFileBuffer
• is_optE_type_name() : protocols::optimize_weights::OptEPositionDataFactory
• is_pair() : protocols::scoring::Interface , protocols::scoring::InterfaceInfo
• is_parallel() : protocols::fldsgn::topology::DimerPairing , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::StrandPairing
• is_perturbable() : protocols::helical_bundle::PerturbBundleOptions
• is_pivot_residue() : protocols::kinematic_closure::ClosureProblem
• is_positive_state() : protocols::multistate_design::SingleState
• is_pre_proline() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• is_prepend() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• is_prepend_map() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• is_properly_initialized() : protocols::ddg::ddGMover
• is_protected() : protocols::environment::ProtectedConformation
• is_proton() : protocols::noesy_assign::Resonance
• is_qsar_map_attached() : protocols::qsar::scoring_grid::GridManager
• is_registered() : protocols::environment::Environment
• is_remodelable() : protocols::enzdes::EnzdesFlexBBProtocol
• is_representative_resonance() : protocols::noesy_assign::FloatingResonance
• is_set_s_kk() : protocols::cluster::DataPoint
• is_sibling_sugar_rotamer_pose() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• is_simple_full_length_job_params() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• is_solution_trivial() : protocols::kinematic_closure::BalancedKicMover
• is_sparis_foldtype() : protocols::fldsgn::topology::SheetFoldTypeManager
• is_start_zero_score() : protocols::jd2::archive::NormalizedEvaluatedArchive
• is_strong_base_stack() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• is_symmetric_partner_of() : protocols::noesy_assign::PeakAssignment
• is_terminal() : protocols::loops::Loop
• is_top() : protocols::dna::DnaChains
• is_under_memory_limit() : protocols::wum::WorkUnitQueue
• is_valid() : protocols::jumping::JumpSample , protocols::noesy_assign::FragsToAtomDist::DistanceRecord , protocols::nonlocal::HelixRotate , protocols::nonlocal::SheetTranslate
• is_valid_chunk() : protocols::frag_picker::FragmentPicker
• is_valid_quota_pool_name() : protocols::frag_picker::quota::QuotaConfig
• is_virt_sample_sugar_tag() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• is_worker_running() : protocols::boinc::Boinc
• is_working_cutpoint_closed() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• is_working_res() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• is_wt_calc_complete() : protocols::ddg::ddGMover
• isAcceptor() : protocols::sparta::PDB
• isClose() : protocols::pockets::CCluster , protocols::pockets::PCluster
• isCompound() : protocols::rbsegment_relax::RBSegment
• isDeepTargetPocketPoint() : protocols::pockets::PocketGrid
• isDonor() : protocols::sparta::PDB
• isEmpty() : protocols::rbsegment_relax::RBSegment
• isGenericRB() : protocols::rbsegment_relax::RBSegment
• isHelix() : protocols::rbsegment_relax::RBSegment
• isInContact() : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• isProteinPoint() : protocols::pockets::PocketGrid
• isSheet() : protocols::rbsegment_relax::RBSegment
• isSimple() : protocols::rbsegment_relax::RBSegment
• isSolventExposed() : protocols::pockets::CCluster , protocols::pockets::PCluster
• isSSBonded() : protocols::sparta::PDB
• isSurfacePoint() : protocols::pockets::PocketGrid
• isTarget() : protocols::pockets::CCluster , protocols::pockets::PCluster
• isTargetPocketPoint() : protocols::pockets::PocketGrid
• isTooSmall() : protocols::pockets::PocketGrid
• isVarFloat() : protocols::sparta::GDB
• isVarInt() : protocols::sparta::GDB
• isVarString() : protocols::sparta::GDB
• Item() : protocols::simple_moves::LoggedFragmentMover::Item
• iter() : protocols::mpi_refinement::Scheduler
• iterate() : protocols::frag_picker::ContactCounts
• iterate_checkpoint_count() : protocols::boinc::Boinc
• iterate_neighbor() : protocols::frag_picker::ContactCounts
• IteratedConvergenceMover() : protocols::moves::IteratedConvergenceMover
• iteration() : protocols::vip::VIP_Mover
• iterations() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• IterativeAbrelax() : protocols::abinitio::IterativeAbrelax
• IterativeBase() : protocols::abinitio::IterativeBase
• IterativeCentroid() : protocols::abinitio::IterativeCentroid
• IterativeFullatom() : protocols::abinitio::IterativeFullatom
• IterativeOptEDriver() : protocols::optimize_weights::IterativeOptEDriver
• IterativeVectorExpression() : protocols::pack_daemon::IterativeVectorExpression
• itoa() : protocols::sparta::ANN
• ivm() : protocols::toolbox::InteratomicVarianceMatrix