- i -

• i() : protocols::frag_picker::Contact
• I_PARAM() : core::scoring::APBSConfig::I_PARAM
• i_want_this_atom_to_move() : protocols::simple_moves::ConstrainToIdealMover
• iBR() : core::pack::annealer::FASTERAnnealer
• icode() : core::pose::PDBInfo
• icoor() : core::chemical::Atom , core::chemical::ResidueType , core::conformation::Residue , core::chemical::Atom , core::chemical::Orbital , core::chemical::ResidueConnection
• ICoorAtomID() : core::chemical::ICoorAtomID
• ICoorOrbitalData() : core::chemical::orbitals::ICoorOrbitalData
• id() : core::sequence::Sequence , protocols::forge::remodel::RemodelConstraintGenerator , protocols::frag_picker::VallResidue , protocols::jd2::archive::Batch , protocols::optimize_weights::OptEVariableExpression , protocols::wum::WorkUnitBase , protocols::wum2::WorkUnit , core::fragment::FragID , core::fragment::picking_old::vall::VallResidue , core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::scoring::packstat::CavityBall , core::sequence::Sequence
• id2proftag() : protocols::abinitio::FragmentSampler
• id2string() : protocols::abinitio::FragmentSampler
• id_for_current_rotamer() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• id_to_index() : core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• idCode() : core::io::pdb::HeaderInformation
• ideal_bond_length_set() : core::chemical::ChemicalManager
• ideal_delta_north() : core::scoring::rna::RNA_FittedTorsionInfo
• ideal_delta_south() : core::scoring::rna::RNA_FittedTorsionInfo
• ideal_nu1_north() : core::scoring::rna::RNA_FittedTorsionInfo
• ideal_nu1_south() : core::scoring::rna::RNA_FittedTorsionInfo
• ideal_nu2_north() : core::scoring::rna::RNA_FittedTorsionInfo
• ideal_nu2_south() : core::scoring::rna::RNA_FittedTorsionInfo
• ideal_val() : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• ideal_xyz() : core::chemical::Atom , core::chemical::Orbital
• IdealBondLengthSet() : core::chemical::IdealBondLengthSet
• idealize_sidechains() : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• IdealizeMover() : protocols::idealize::IdealizeMover
• IdealizeRamaEnergy() : core::scoring::Ramachandran2B
• IdealParametersDatabase() : core::scoring::methods::IdealParametersDatabase
• identical_info_consistency_check() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• identify_antibody() : protocols::antibody2::AntibodyInfo
• identify_CDR_from_a_sequence() : protocols::antibody2::AntibodyInfo
• identify_motif_build_positions() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• identify_motif_BuildPositions() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• identify_ss() : core::scoring::SecondaryStructurePotential , protocols::fldsgn::topology::SS_Info2
• identities() : core::sequence::SequenceAlignment
• identity() : core::id::SequenceMapping
• identity_transform() : core::kinematics::Jump , core::kinematics::RT
• IdentityEval() : core::fragment::picking_old::vall::eval::IdentityEval
• IdentityEvent() : core::conformation::signals::IdentityEvent
• IdentityFunc() : core::scoring::constraints::IdentityFunc
• idle() : protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeBase , protocols::jd2::archive::AbstractArchiveBase , protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::ArchiveManager
• ids_initializer() : core::scoring::SecondaryStructurePotential
• idsn_initializer() : core::scoring::SecondaryStructurePotential
• idx2cart() : core::scoring::electron_density::ElectronDensity , core::scoring::PoissonBoltzmannPotential
• idxoffset2cart() : core::scoring::electron_density::ElectronDensity
• 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
• IGEdgeReweightContainer() : core::pack::task::IGEdgeReweightContainer
• IGEdgeReweighter() : core::pack::task::IGEdgeReweighter
• IGEdgeReweights() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• 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_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::rna::RNA_DeNovoProtocol
• ignore_unrecognized_res() : core::io::pdb::FileDataOptions
• ignore_waters() : core::io::pdb::FileDataOptions
• ignore_zero_byte() : protocols::simple_filters::FileExistFilter
• ignore_zero_occupancy() : core::io::pdb::FileDataOptions
• ignorefinished() : protocols::jobdist::BaseJobDistributor
• IgnoreSubsetConstraintSet() : protocols::comparative_modeling::IgnoreSubsetConstraintSet
• ImplicitFastClashCheck() : protocols::scoring::ImplicitFastClashCheck
• import() : core::kinematics::MoveMap
• import_exp_chemical_shift_data() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• import_false() : core::kinematics::MoveMap
• Import_pose() : protocols::swa::rna::StepWiseRNA_PoseSetup , protocols::swa::StepWisePoseSetup
• import_true() : core::kinematics::MoveMap
• ImportPoseOptions() : core::import_pose::ImportPoseOptions
• ImportPoseOptionsCreator() : core::import_pose::ImportPoseOptionsCreator
• impose_constraints() : protocols::idealize::IdealizeMover
• improper_torsion_parameters() : core::scoring::methods::ResidueCartBondedParameters
• in_blacklist() : protocols::wum::WorkUnitBase
• in_charge() : protocols::loops::GuardedLoopsFromFile
• in_place_copy() : core::conformation::Conformation
• inbound() : protocols::wum::WorkUnitManager
• inc_alternate_state_total_energy() : protocols::flexpack::interaction_graph::FlexbbNode
• inc_curr_state_total_energy() : protocols::flexpack::interaction_graph::FlexbbNode
• include_current() : core::pack::task::operation::OptH , core::pack::task::ResidueLevelTask , core::pack::task::PackerTask , core::pack::task::ResidueLevelTask_ , core::pack::task::PackerTask_
• include_gly() : core::pack::task::operation::RestrictYSDesign
• include_intra_res_RNA() : core::scoring::hbonds::HBondOptions
• include_neighbors() : protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors
• include_resid() : core::pack::task::operation::RestrictYSDesign
• include_residue() : core::pack::task::operation::RestrictResidueToRepacking , core::pack::task::operation::RestrictAbsentCanonicalAAS , core::pack::task::operation::PreventRepacking , protocols::toolbox::task_operations::DesignAroundOperation
• include_trp() : protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation
• incomplete() : core::chemical::ResConnID
• 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_multi_cool_annealer_history_size() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• increase_packer_residue_radius() : core::pack::rotamer_set::RotamerSetOperation , protocols::hotspot_hashing::SearchPatternRotSetOp , protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO
• increasing() : protocols::loops::Loop , protocols::nonlocal::Region
• increment_both() : core::pack::interaction_graph::RotamerDots
• increment_both_and_cache() : core::pack::interaction_graph::RotamerDots
• increment_client_rank() : protocols::jd2::MPIFileBufJobDistributor
• increment_count() : core::pack::interaction_graph::DotSphere , core::pack::interaction_graph::RotamerDotsCache
• increment_count_nodes_in_flexseg() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• increment_edge_list_iterator() : core::pack::interaction_graph::InteractionGraphBase
• increment_f1_f2_for_atom_pair() : core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::MembraneEnvSmoothEnergy
• increment_from_cached() : core::pack::interaction_graph::RotamerDots
• increment_histogram_bin() : core::scoring::orbitals::OrbitalsStatistics
• increment_inner() : core::fragment::OrderedFragSetIterator_
• increment_outer() : core::fragment::OrderedFragSetIterator_
• increment_pool_size() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• increment_self_overlap() : core::pack::interaction_graph::RotamerDots
• increment_stage() : protocols::abinitio::IterativeBase
• increment_this_and_cache() : core::pack::interaction_graph::RotamerDots
• increment_total_read_count_for_file() : protocols::pack_daemon::DynamicAggregateFunction
• 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_residues() : core::conformation::symmetry::SymmetryInfo
• independent_stage() : protocols::forge::remodel::RemodelLoopMover
• IndependentBBTorsionSRFD() : core::fragment::IndependentBBTorsionSRFD
• IndependentLoopMover() : protocols::loops::loop_mover::IndependentLoopMover
• index() : core::chemical::AtomICoor , core::chemical::ResidueConnection , core::fragment::picking_old::vall::VallSection , protocols::enzdes::EnzdesFlexibleRegion , protocols::genetic_algorithm::EntityElement , protocols::match::upstream::ScaffoldBuildPoint , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• index2frac() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• index2symbol() : core::util::ABEGOManager
• 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_to_id() : core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• indicate_required_context_graphs() : core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density::FastDensEnergy , core::scoring::electron_density::PattersonCorrEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::CoarseEtableEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::hackaro::HackAroEnergy , core::scoring::hackelec::HackElecEnergy , core::scoring::hackelec::HackElecEnergyAroAll , core::scoring::hackelec::HackElecEnergyAroAro , core::scoring::hackelec::RNAHackElecEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::interface::DDPscore , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::BurialEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::ChainbreakEnergy , core::scoring::methods::ChemicalShiftAnisotropyEnergy , core::scoring::methods::ContactOrderEnergy , core::scoring::methods::CSD_TorsionEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::DipolarCouplingEnergy , core::scoring::methods::DirectReadoutEnergy , core::scoring::methods::DistanceChainbreakEnergy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::EnvEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::HybridVDW_Energy , core::scoring::methods::LinearChainbreakEnergy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::LK_CosThetaEnergy , core::scoring::methods::LK_hack , core::scoring::methods::MembraneCbetaEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MembraneEnvEnergy , core::scoring::methods::MembraneEnvPenalties , core::scoring::methods::MembraneEnvSmoothEnergy , core::scoring::methods::MembraneLipo , core::scoring::methods::MetalloPlacementEnergy , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::NMerPSSMEnergy , core::scoring::methods::NMerRefEnergy , core::scoring::methods::OmegaTetherEnergy , core::scoring::methods::P_AA_Energy , core::scoring::methods::P_AA_pp_Energy , core::scoring::methods::PackStatEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::PeptideBondEnergy , core::scoring::methods::pHEnergy , core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::PyContextIndependentTwoBodyEnergy , core::scoring::methods::RamachandranEnergy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::ReferenceEnergy , core::scoring::methods::ReferenceEnergyNoncanonical , core::scoring::methods::ResidualDipolarCouplingEnergy , core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl , core::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments , core::scoring::methods::RG_Energy , core::scoring::methods::RG_Energy_Fast , core::scoring::methods::RMS_Energy , core::scoring::methods::SA_Energy , core::scoring::methods::SecondaryStructureEnergy , core::scoring::methods::SequenceDependentRefEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::SmoothEnvEnergy , core::scoring::methods::SuckerEnergy , core::scoring::methods::SymmetricLigandEnergy , core::scoring::methods::UnfoldedStateEnergy , core::scoring::methods::VDW_Energy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::methods::WaterAdductIntraEnergy , core::scoring::methods::YHHPlanarityEnergy , core::scoring::nv::NVscore , core::scoring::orbitals::OrbitalsScore , core::scoring::packing::HolesEnergy , core::scoring::packing::HolesEnergyRes , core::scoring::packing::SurfEnergy , core::scoring::packing::SurfVolEnergy , core::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergy , core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential , core::scoring::rna::RG_Energy_RNA , core::scoring::rna::RNA_BaseBaseEnergy , core::scoring::rna::RNA_BulgeEnergy , core::scoring::rna::RNA_DataBackboneEnergy , core::scoring::rna::RNA_FA_Stack , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_FullAtomVDW_BasePhosphate , core::scoring::rna::RNA_LJ_BaseEnergy , core::scoring::rna::RNA_Mg_Energy , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::RNA_SugarCloseEnergy , core::scoring::rna::RNA_TorsionEnergy , core::scoring::rna::RNA_VDW_Energy , core::scoring::saxs::FastSAXSEnergy , core::scoring::saxs::SAXSEnergy , core::scoring::ScoreFunction , core::scoring::sym_e::symEnergy , protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::scoring::methods::EnsembleEnergy , protocols::scoring::methods::InterchainEnvEnergy , protocols::scoring::methods::InterchainPairEnergy , protocols::scoring::methods::pcs::PCS_Energy , protocols::scoring::methods::pcs2::PcsEnergy , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments , protocols::scoring::methods::saxs::PDDFEnergy , protocols::scoring::methods::SpecialRotamerEnergy , core::pack::dunbrack::DunbrackEnergy , core::pack::interaction_graph::HPatchEnergy , core::pack::interaction_graph::SurfaceEnergy , core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::constraints::ConstraintsEnergy , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::disulfides::CentroidDisulfideEnergy , core::scoring::disulfides::DisulfideMatchingEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::dna::DNAChiEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy
• indices() : core::pack::task::operation::ResidueIndexIs , core::pack::task::operation::ResiduePDBIndexIs , protocols::features::BatchFeatures , protocols::features::ProtocolFeatures
• info() : core::scoring::ScoreFunction , 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
• inform_non_changing_node_of_neighbors_change() : core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G >
• 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_scorefxn_temperature() : protocols::simple_moves::sidechain_moves::SidechainMCMover
• Init() : core::scoring::sc::MolecularSurfaceCalculator
• init() : core::chemical::carbohydrates::CarbohydrateInfo , core::pose::Pose , core::scoring::electron_density::ElectronDensity , core::scoring::methods::BBDepCartBondedParameters , core::scoring::methods::IdealParametersDatabase , core::scoring::mm::MMBondAngleResidueTypeParam , core::scoring::packstat::Array2D , protocols::abinitio::ClassicAbinitio , protocols::abinitio::KinematicTaskControl , protocols::abinitio::MembraneAbinitio , protocols::abinitio::Protocol , protocols::antibody2::AntibodyInfo , protocols::antibody2::AntibodyModelerProtocol , protocols::antibody2::CDRsMinPackMin , protocols::antibody2::GraftCDRLoopsProtocol , protocols::antibody2::GraftOneCDRLoop , protocols::antibody2::H3CterInsert , protocols::antibody2::H3PerturbCCD , protocols::antibody2::H3RefineCCD , protocols::antibody2::LHRepulsiveRamp , protocols::antibody2::LHRepulsiveRampLegacy , protocols::antibody2::LHSnugFitLegacy , protocols::antibody2::ModelCDRH3 , protocols::antibody2::RefineBetaBarrel , protocols::antibody2::RefineOneCDRLoop , protocols::antibody2::SnugDock , protocols::antibody2::SnugDockProtocol , protocols::constraints_additional::BindingSiteConstraint , protocols::docking::DockingHighRes , protocols::docking::DockingInitialPerturbation , protocols::docking::DockingLowRes , protocols::docking::DockingProtocol , protocols::docking::DockMCMProtocol , protocols::docking::TemperedDocking , 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::CartesianHybridize , protocols::hybridization::CartesianSampler , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol , protocols::jumping::MembraneJump , protocols::loophash::MPI_LoopHashRefine_Emperor , protocols::loophash::MPI_LoopHashRefine_Master , protocols::loops::loop_closure::ccd::LoopClosure , 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::moves::ReplicaExchangeMC , protocols::pockets::PocketConstraint , protocols::pockets::PocketGrid , protocols::rna::RNA_IdealCoord , protocols::seeded_abinitio::SegmentHybridizer , protocols::sic_dock::SICFast , protocols::simple_moves::carbohydrates::RingConformationMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::symmetry::SequentialSymmetrySlider , protocols::sparta::ANN , protocols::sparta::Sparta::SpartaLib , protocols::toolbox::InteratomicVarianceMatrix , protocols::toolbox::KCluster , protocols::toolbox::KMedoid , protocols::toolbox::GreedyKCenter , protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors , protocols::wum::DatabaseQueryWorkUnitManager< T > , 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::RigidChunkClaimer , protocols::topology_broker::SequenceClaimer , protocols::topology_broker::TemplateFragmentClaimer , protocols::topology_broker::TemplateJumpClaimer , protocols::topology_broker::TopologyClaimer
• init_all_suite() : protocols::rna::RNA_suite_list
• init_allowed_pos() : protocols::loops::loop_closure::kinematic_closure::KinematicWrapper
• init_atom_equiv() : protocols::comparative_modeling::ThreadingMover
• init_calibrator() : protocols::noesy_assign::PeakCalibrator , protocols::noesy_assign::StructureDependentPeakCalibrator
• init_clash_check() : protocols::scoring::ImplicitFastClashCheck
• init_cst_score_types() : core::scoring::constraints::KofNConstraint , core::scoring::constraints::AmbiguousConstraint
• init_d77_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
• init_dist_map() : core::kinematics::ShortestPathInFoldTree
• init_dna_bform_data() : core::scoring::dna::DNABFormPotential
• init_dna_torsion_parameters() : core::scoring::dna::DNATorsionPotential
• init_fade_functions() : core::scoring::rna::RNA_TorsionPotential
• init_ff() : core::scoring::saxs::SAXSEnergy
• init_for_equal_operator_and_copy_constructor() : protocols::antibody2::SnugDock , protocols::antibody2::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 , protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors
• init_from_cmd() : protocols::loophash::WorkUnit_LoopHash
• init_from_comand_line() : core::pack::task::operation::OptH
• 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() : core::kinematics::MoveMap , core::pack::dunbrack::SingleLigandRotamerLibrary , core::scoring::methods::BurialEnergy , protocols::simple_filters::PredictedBurialEvaluator
• init_from_lines() : core::import_pose::PDBSilentStruct , core::io::silent::BinaryProteinSilentStruct , core::io::silent::BinaryRNASilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreFileSilentStruct , core::io::silent::SilentStruct
• init_from_options() : core::import_pose::ImportPoseOptions , core::io::pdb::FileDataOptions , core::io::pdb::PDB_DReaderOptions , protocols::antibody::AntibodyModeler , protocols::antibody2::AntibodyModelerProtocol , protocols::antibody2::GraftCDRLoopsProtocol , 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::TemperedDocking , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::features::strand_assembly::StrandBundleFeatures , protocols::jd2::archive::NormalizedEvaluatedArchive , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• init_from_pose() : core::io::pdb::FileData
• init_hASA_variables() : core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >
• init_jd() : protocols::jd2::JobDistributor
• init_jumps() : protocols::topology_broker::JumpClaimer
• init_k48r_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
• init_length() : core::fragment::Frame
• init_master() : protocols::wum::MPI_Relax
• init_matrix() : core::sequence::NWAligner
• init_mc() : protocols::docking::DockMCMCycle , protocols::loops::loop_closure::ccd::LoopClosure
• init_membrane_center_normal() : core::scoring::MembranePotential
• init_mini_pose() : protocols::jumping::ResiduePairJump
• init_minmover() : protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• init_on_new_input() : protocols::anchored_design::AnchoredDesignMover , protocols::antibody::AntibodyModeler , protocols::floppy_tail::FloppyTailMover
• init_options() : protocols::antibody2::SnugDock , protocols::antibody2::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 , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifDnaPacker , protocols::motifs::MotifSearch
• init_pose() : protocols::abinitio::ResolutionSwitcher
• init_potentials_from_rna_torsion_database_files() : core::scoring::rna::RNA_TorsionPotential
• init_PredErrorSurface() : protocols::sparta::Sparta::SpartaLib
• init_rama_sampling_table() : core::scoring::Ramachandran
• init_rama_sampling_table_left() : core::scoring::Ramachandran2B
• init_rama_sampling_table_right() : core::scoring::Ramachandran2B
• init_rama_sampling_tables_by_torsion_bin() : core::scoring::Ramachandran , core::scoring::Ramachandran2B
• init_rdcs() : protocols::simple_filters::SelectRDC_Evaluator
• init_res_list() : core::scoring::methods::ReferenceEnergyNoncanonical
• init_rna_torsion_gaussian_parameters() : core::scoring::rna::RNA_FittedTorsionInfo
• init_rot_to_pack() : protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• init_rotamer_recovery_with_options() : protocols::rotamer_recovery::RotamerRecovery
• init_SASA_radii_from_database() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• init_slave() : protocols::wum::MPI_Relax
• init_standard() : protocols::dna::DnaInterfacePacker , protocols::motifs::MotifDnaPacker
• init_task() : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• init_type() : core::sequence::MatrixScoringScheme
• init_with_options() : protocols::backrub::BackrubMover , protocols::rotamer_recovery::RotamerRecovery
• init_with_pose() : protocols::sic_dock::xyzStripeHashPose , protocols::sic_dock::xyzStripeHashPoseWithMeta
• initForEqualOperatorAndCopyConstructor() : protocols::antibody2::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
• initialize() : core::chemical::AtomTypeDatabaseIO , core::chemical::ResidueDatabaseIO , core::conformation::symmetry::SymmetryInfo , core::fragment::AnnotatedFragData , core::optimization::DescentDirectionAlgorithm , core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SimpleNode , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , core::scoring::CenListInfo , core::scoring::FACTSResidueInfo , core::scoring::FACTSPoseInfo , core::scoring::FACTSRotamerSetInfo , core::scoring::GenBornResidueInfo , core::scoring::GenBornPoseInfo , core::scoring::GenBornRotamerSetInfo , core::scoring::hackelec::HackElecEnergy , core::scoring::hbonds::HBondDatabase , core::scoring::Membrane_FAEmbed , core::scoring::MembraneEmbed , core::scoring::MembraneTopology , core::scoring::methods::LinearChainbreakEnergy , core::scoring::ResidueNblistData , core::scoring::SecondaryStructureWeights , core::scoring::SigmoidWeightedCenList< T > , core::util::ABEGOManager , 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::features::ProteinSilentReport , protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::SheetSet , protocols::fldsgn::topology::SheetFoldTypeManager , 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::match::downstream::ActiveSiteGrid , protocols::match::HitHasher , protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::match::OccupiedSpaceHash , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , 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::GridBase , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::rbsegment_relax::RBSegmentRelax , protocols::rna::MultipleDomainMover , protocols::rna::RNA_DataReader , protocols::rna::RNA_StructureParameters , protocols::scoring::InterfaceInfo , protocols::seeded_abinitio::PlaceFragments , protocols::simple_moves::GenericMonteCarloMover , protocols::swa::protein::StepWiseProteinJumpSampleGenerator , protocols::toolbox::AllowInsert , protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• initialize_acc_strength() : core::scoring::hbonds::HBondDatabase
• initialize_active_site_definition_from_command_line() : protocols::match::MatcherTask
• initialize_active_site_grid() : protocols::match::Matcher
• initialize_all_atoms() : protocols::protein_interface_design::filters::AtomicContactCountFilter
• initialize_all_grids() : protocols::qsar::scoring_grid::GridManager
• initialize_allow_insert() : protocols::rna::RNA_StructureParameters
• initialize_and_read_srsrdl() : core::pack::dunbrack::RotamerLibrary
• initialize_and_sample_loops() : protocols::hybridization::HybridizeProtocol
• initialize_atom_atom_overlap_cache() : core::pack::interaction_graph::HPatchNode< V, E, G >
• initialize_atom_atom_overlaps() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• initialize_atom_numbers_for_backbone_score_calculations() : core::scoring::rna::RNA_LowResolutionPotential
• initialize_atom_numbers_sugar() : core::scoring::rna::RNA_DataBackboneEnergy
• initialize_auto_tune_cluster_rmsds() : protocols::swa::StepWiseClusterer
• initialize_base_centroids_and_stubs() : core::scoring::rna::RNA_CentroidInfo
• Initialize_base_stub_list() : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• initialize_bg_bg_atom_atom_overlaps() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• initialize_bg_bg_overlap() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• initialize_bg_bg_overlaps() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• initialize_bicubic_splines() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
• initialize_bump_grids() : protocols::match::Matcher
• initialize_by_dimer_pairs() : protocols::fldsgn::topology::StrandPairingSet
• initialize_carbontypes_to_linearize_fasol() : core::scoring::etable::Etable
• initialize_charge() : core::scoring::FACTSResidueInfo
• initialize_chunks() : protocols::nonlocal::SingleFragmentMover
• initialize_cluster_list() : protocols::swa::StepWiseClusterer
• initialize_conformers() : protocols::match::downstream::LigandConformerBuilder
• initialize_constants() : core::scoring::FACTSResidueInfo
• initialize_constraint_forest() : protocols::abinitio::AbrelaxApplication
• initialize_constraints() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::rna::RNA_DeNovoProtocol
• initialize_constraints_from_file() : protocols::optimize_weights::ConstraintedOptimizationWeightFunc
• initialize_corresponding_atom_id_map() : protocols::swa::PoseFilter_RMSD_Screen , protocols::swa::StepWiseClusterer
• initialize_counters() : protocols::swa::RigidBodySampler
• 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::DynamicAggregateFunction
• initialize_database() : protocols::features::ReportToDB
• initialize_defaults() : protocols::swa::InputStreamWithResidueInfo
• initialize_dofs() : protocols::topology_broker::AsymFoldandDockClaimer , protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::DisulfJumpClaimer , protocols::topology_broker::FibrilModelingClaimer , protocols::topology_broker::FoldandDockClaimer , protocols::topology_broker::FragmentClaimer , protocols::topology_broker::JumpClaimer , protocols::topology_broker::MembraneTopologyClaimer , protocols::topology_broker::MetalloClaimer , protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::SequenceClaimer , protocols::topology_broker::StartStructClaimer , protocols::topology_broker::TopologyBroker , protocols::topology_broker::TopologyClaimer
• initialize_don_strength() : core::scoring::hbonds::HBondDatabase
• initialize_dot_coords() : core::pack::interaction_graph::RotamerDots
• initialize_downstream_algorithms() : protocols::match::Matcher
• initialize_dun02_aa_parameters() : core::pack::dunbrack::RotamerLibrary
• initialize_dun10_aa_parameters() : core::pack::dunbrack::RotamerLibrary
• initialize_enzdes_input_data_from_command_line() : protocols::match::MatcherTask
• initialize_extra_rotamer_flags_from_command_line() : core::pack::task::ResidueLevelTask , core::pack::task::PackerTask , core::pack::task::ResidueLevelTask_ , core::pack::task::PackerTask_
• initialize_extra_rotamer_perturbations() : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• initialize_fa_rep() : protocols::swa::rna::RNA_LoopCloseSampler
• initialize_filter() : protocols::flxbb::FlxbbDesign
• initialize_for_regular_packer() : protocols::swa::protein::StepWiseProteinPacker , protocols::swa::protein::StepWiseProteinResidueSampler
• initialize_frag_source_pose() : protocols::coarse_rna::CoarseRNA_Fragments
• initialize_fragments() : protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::PlaceFragments
• initialize_free_and_fixed() : protocols::optimize_weights::IterativeOptEDriver
• initialize_from() : core::scoring::ScoreFunctionInfo
• initialize_from_command_line() : core::pack::rotamer_set::UnboundRotamersOperation , core::pack::task::ResidueLevelTask , core::pack::task::PackerTask , core::pack::task::ResidueLevelTask_ , core::pack::task::PackerTask_ , protocols::match::MatcherTask , protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst
• initialize_from_correspondence_file() : protocols::pack_daemon::EntityCorrespondence
• 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() : core::scoring::ScoreFunction , 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_atomset() : core::scoring::etable::Etable
• initialize_from_input_file() : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• initialize_from_matcher_task() : protocols::match::output::OutputWriter , protocols::match::output::PDBWriter
• initialize_from_options() : core::scoring::methods::EnergyMethodOptions , core::scoring::methods::NMerPSSMEnergy , core::scoring::methods::NMerRefEnergy
• 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_residues() : core::scoring::ResiduePairNeighborList
• initialize_from_scratch() : protocols::swa::protein::StepWiseProteinPoseSetup
• initialize_from_task() : protocols::match::Matcher
• initialize_from_tokens() : core::pack::task::ResfileCommand , core::pack::task::NATRO , core::pack::task::NATAA , core::pack::task::ALLAA , core::pack::task::ALLAAxc , core::pack::task::ALLAAwc , core::pack::task::PIKAA , core::pack::task::PIKNA , core::pack::task::PIKRNA , core::pack::task::NOTAA , core::pack::task::EMPTY , core::pack::task::POLAR , core::pack::task::APOLAR , core::pack::task::APOLA , core::pack::task::EX , core::pack::task::NC , core::pack::task::EX_CUTOFF , core::pack::task::USE_INPUT_SC , core::pack::task::AUTO , core::pack::task::SCAN , core::pack::task::TARGET , core::pack::task::NO_ADDUCTS , core::pack::task::FIX_HIS_TAUTOMER
• initialize_ghost_pose() : protocols::swa::protein::StepWiseProteinScreener , protocols::swa::StepWiseScreener
• initialize_green_packer() : protocols::swa::protein::StepWiseProteinPacker , protocols::swa::protein::StepWiseProteinResidueSampler , protocols::swa::StepWiseResidueSampler
• initialize_HBEval() : core::scoring::hbonds::HBondDatabase
• initialize_HBFadeInterval() : core::scoring::hbonds::HBondDatabase
• initialize_HBPoly1D() : core::scoring::hbonds::HBondDatabase
• initialize_header_information() : core::io::pdb::FileData
• initialize_internal_correspondence_data() : protocols::simple_moves::GreenPacker
• initialize_is_fixed_res() : protocols::swa::protein::StepWiseProteinLoopBridger , protocols::swa::protein::StepWiseProteinScreener
• Initialize_is_virtual_base() : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• initialize_library() : protocols::nonlocal::BiasedFragmentMover , protocols::nonlocal::SingleFragmentMover
• initialize_lores_silent_file() : protocols::rna::RNA_DeNovoProtocol
• initialize_max_memory_pose_num() : protocols::swa::rna::StepWiseRNA_Clusterer
• initialize_methods_arrays() : core::scoring::ScoreFunction
• initialize_more_precise_base_pair_cutoffs() : core::scoring::rna::RNA_LowResolutionPotential
• initialize_movemap() : protocols::relax::RelaxProtocolBase
• initialize_movers() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::rna::RNA_DeNovoProtocol
• initialize_moving_residues_including_junction() : protocols::swa::protein::StepWiseProteinPacker , protocols::swa::protein::StepWiseProteinResidueSampler , protocols::swa::StepWiseResidueSampler
• initialize_name_map() : core::pose::datacache::CacheableDataType
• initialize_next_suite_atoms() : protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover
• initialize_num_neighbors_counting_self() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• initialize_number_of_atoms() : core::scoring::FACTSResidueInfo
• initialize_o2star_green_packer() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• initialize_o2star_packer_task() : protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler
• 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_overlap_cache() : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >
• initialize_overlap_with_background() : core::pack::interaction_graph::HPatchNode< V, E, G >
• initialize_pack_daemons() : protocols::pack_daemon::DynamicAggregateFunction
• initialize_parameters() : core::scoring::FACTSResidueInfo , core::sequence::ProfSimScoringScheme , protocols::swa::protein::StepWiseProteinPoseMinimizer
• initialize_parameters_and_input() : protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::StepWiseClusterer
• initialize_phi_psi_offsets() : protocols::swa::StepWisePoseSetup
• initialize_pose() : protocols::features::ReportToDB
• initialize_pose_from_streams() : protocols::swa::StepWisePoseSetup
• initialize_potential_from_file() : core::scoring::rna::RNA_TorsionPotential
• initialize_probabilities() : protocols::nonlocal::BiasedFragmentMover
• initialize_protein_input_silent_file_data_from_pose_list() : protocols::swa::protein::StepWiseProteinPoseMinimizer
• initialize_quick_alignment_pose() : protocols::swa::rna::StepWiseRNA_Clusterer
• initialize_random_chunks() : protocols::rna::RNA_ChunkLibrary
• initialize_rb_fragments() : protocols::rbsegment_relax::FragInsertAndAlignMover
• initialize_reference_axes_and_centroid() : protocols::swa::RigidBodySampler
• initialize_refinement_pattern() : protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• initialize_rep_scorefxn() : protocols::swa::rna::RNA_LoopCloseSampler
• initialize_reporters() : protocols::features::ReportToDB
• initialize_rescoords() : protocols::match::upstream::ProteinUpstreamBuilder
• initialize_residue_type() : core::scoring::methods::LKB_ResidueInfo
• initialize_residues() : protocols::topology_broker::StartStructClaimer , protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::MetalloClaimer , protocols::topology_broker::SequenceClaimer , protocols::topology_broker::TopologyClaimer
• initialize_rigid_body_movers() : protocols::rna::MultipleDomainMover
• initialize_rna_axis() : core::scoring::rna::RNA_LowResolutionPotential
• initialize_rna_backbone_backbone() : core::scoring::rna::RNA_LowResolutionPotential
• initialize_rna_backbone_backbone_weights() : core::scoring::rna::RNA_LowResolutionPotential
• initialize_RNA_backbone_oxygen_atoms() : core::scoring::rna::RNA_LowResolutionPotential
• initialize_rna_base_backbone_xy() : core::scoring::rna::RNA_LowResolutionPotential
• initialize_rna_basepair_xy() : core::scoring::rna::RNA_LowResolutionPotential
• initialize_rna_chunk_library() : protocols::rna::RNA_ChunkLibrary
• initialize_rna_repulsive_weights() : core::scoring::rna::RNA_LowResolutionPotential
• initialize_rna_stagger() : core::scoring::rna::RNA_LowResolutionPotential
• initialize_rotamer() : protocols::features::RotamerInitializer< T >
• initialize_rotamer_behavior_for_residue_level_task() : protocols::ddg::ddGMover
• initialize_rotamer_generator() : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• initialize_rotamer_generator_list() : protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• initialize_rotamers() : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• initialize_sample_base_states() : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• initialize_sasa_arrays() : core::pack::interaction_graph::RotamerDots
• 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_scorefunctions() : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler
• initialize_scorefxn() : protocols::rna::RNA_DeNovoProtocol
• initialize_secstruct() : protocols::rna::RNA_StructureParameters
• initialize_self_overlap() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• initialize_sequence() : protocols::topology_broker::TopologyBroker
• initialize_simulation() : protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::canonical_sampling::TrajectoryRecorder , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::HamiltonianExchange , protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperatureController , protocols::canonical_sampling::TemperingBase , protocols::canonical_sampling::ThermodynamicMover , protocols::canonical_sampling::ThermodynamicObserver , protocols::canonical_sampling::TrialCounterObserver , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::simple_moves::sidechain_moves::SidechainMover
• initialize_srsrdl() : core::pack::dunbrack::RotamerLibrary
• initialize_tag_is_done() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::rna::RNA_DeNovoProtocol
• initialize_task_factory() : protocols::features::RotamerRecoveryFeatures
• initialize_task_level_behavior() : protocols::ddg::ddGMover
• Initialize_terminal_res() : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• initialize_tree_nodes_from_enzcst_io() : protocols::toolbox::match_enzdes_util::InvrotTarget
• 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::RigidLigandBuilder , protocols::match::downstream::LigandConformerBuilder
• initialize_upstream_residue_collision_filter_data_from_command_line() : protocols::match::MatcherTask
• initialize_value_evaluators_from_file() : protocols::enzdes::EnzdesScorefileFilter
• initialize_VDW_rep_screener() : protocols::swa::rna::StepWiseRNA_Clusterer
• initialize_weights() : protocols::moves::TrialMover
• initialize_worker() : protocols::boinc::Boinc
• initialized() : core::scoring::MembraneTopology , core::scoring::hbonds::HBondDatabase , core::scoring::MembraneTopology , protocols::branch_angle::BranchAngleOptimizer , protocols::dna::DnaInterfaceFinder , protocols::dna::DnaInterfacePacker , protocols::rbsegment_relax::RBSegment , protocols::rna::RNA_SecStructInfo , protocols::rotamer_recovery::PerNativeRRReporterHuman
• initializeSymmOps() : core::scoring::electron_density::ElectronDensity , core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• 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
• InnerJob() : protocols::jd2::InnerJob
• InnerMultiThreadingJob() : protocols::jd2::InnerMultiThreadingJob
• inprogress() : protocols::jobdist::BaseJobDistributor
• input_conformation() : protocols::match::upstream::OriginalBackboneBuildPoint
• input_etable() : core::scoring::etable::MembEtable , core::scoring::etable::Etable , core::scoring::etable::MembEtable
• input_loops_into_tuples() : protocols::anchored_design::AnchorMoversData
• input_res() : protocols::swa::InputStreamWithResidueInfo
• input_res_vectors() : protocols::swa::rna::StepWiseRNA_JobParameters
• input_source() : protocols::jd2::BatchJobInputter , protocols::jd2::JD2ResourceManagerJobInputter , protocols::jd2::JobInputter , protocols::jd2::LazySilentFileJobInputter , protocols::jd2::PDBJobInputter , protocols::jd2::PoseInputStreamJobInputter , protocols::jd2::SilentFileJobInputter , protocols::jd2::AtomTreeDiffJobInputter , protocols::comparative_modeling::GenericJobInputter , protocols::comparative_modeling::ThreadingJobInputter , protocols::features::DatabaseJobInputter
• input_struct_definition() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• input_stub_atom0() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• input_stub_atom0_id() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• input_stub_atom1() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• input_stub_atom1_id() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• input_stub_atom2() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• input_stub_atom2_id() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• input_stub_atom3() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• input_stub_atom3_id() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• input_tag() : protocols::jd2::InnerJob , protocols::jd2::Job , protocols::jobdist::BasicJob
• InputStreamWithResidueInfo() : protocols::swa::InputStreamWithResidueInfo
• Inputter() : protocols::inputter::Inputter
• InputterStream() : protocols::inputter::InputterStream
• inq() : protocols::wum2::EndPoint
• insert() : core::graph::EdgeList , core::pose::PDBPoseMap , core::scoring::constraints::ResidueConstraints , core::scoring::saxs::DistanceHistogram , protocols::comparative_modeling::AlignmentSet , protocols::frag_picker::BoundedCollector< StrictWeakOrdering > , protocols::frag_picker::CandidatesCollector , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaCollector , protocols::frag_picker::quota::SecondaryStructurePool , protocols::frags::TorsionFragment , protocols::match::upstream::OriginalBackboneBuildPoint , protocols::match::upstream::ScaffoldBuildPoint , protocols::frag_picker::scores::AdaptiveScoreHistogram , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::frag_picker::GrabAllCollector
• insert_after() : core::graph::NegSpaceElement< T >
• insert_aligned_residue() : core::id::SequenceMapping
• insert_aligned_residue_safe() : core::id::SequenceMapping
• insert_atom() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• insert_base_pair_jumps() : protocols::rna::RNA_StructureParameters
• insert_chain_ending() : core::conformation::Conformation
• insert_char() : core::sequence::CompositeSequence , core::sequence::Sequence , core::sequence::SequenceProfile , core::sequence::SequenceCoupling
• insert_chunk_into_pose() : protocols::rna::ChunkSet , protocols::rna::RNA_ChunkLibrary
• insert_conformation_by_jump() : core::conformation::symmetry::SymmetricConformation , core::conformation::Conformation
• insert_connection_scheme() : protocols::forge::build::SegmentInsert
• insert_dofs_by_residue() : protocols::simple_moves::DOFHistogramRecorder
• insert_fold_tree_by_jump() : core::kinematics::FoldTree
• insert_fragID_list() : core::fragment::FragSet
• insert_fragment() : core::conformation::Conformation , core::kinematics::AtomTree , protocols::frags::SingleResidueTorsionFragmentLibrary , protocols::rna::FullAtomRNA_Fragments , protocols::coarse_rna::CoarseRNA_Fragments
• insert_gap() : core::sequence::Sequence
• 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() : core::conformation::Conformation
• insert_ideal_geometry_at_residue_connection() : core::conformation::Conformation
• insert_loop_at_index() : protocols::loops::LoopsFileData
• insert_map() : protocols::simple_moves::FragmentMover
• insert_match_into_pose() : protocols::match::output::PoseMatchOutputWriter
• insert_one_body_residue_score_rows() : protocols::features::ResidueScoresFeatures
• insert_pair() : protocols::toolbox::task_operations::RestrictInterGroupVectorOperation
• insert_piece() : protocols::grafting::GraftMoverBase
• insert_polymer_residue() : core::conformation::Conformation , core::kinematics::FoldTree
• insert_pose() : protocols::forge::build::SegmentInsert
• insert_pose_torsion_override_movemap() : protocols::forge::build::SegmentInsert
• insert_position() : core::fragment::picking_old::vall::eval::EnergyEval
• insert_random_smallestmer_per_loop() : protocols::forge::remodel::RemodelLoopMover
• insert_residue_by_jump() : core::conformation::Conformation , core::kinematics::FoldTree , core::pose::Pose
• 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_method_options_rows() : core::scoring::methods::EnergyMethodOptions
• insert_score_function_weights_rows() : protocols::features::ScoreFunctionFeatures
• insert_score_type_rows() : protocols::features::ScoreTypeFeatures
• insert_single_fragment() : core::kinematics::AtomTree
• 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_source_residue() : core::id::SequenceMapping
• insert_ss_into_pose() : core::scoring::dssp::Dssp , 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_target_residue() : core::id::SequenceMapping
• 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::loops::ResidueIndexDescription
• insertion_end_residue() : protocols::forge::build::SegmentInsert
• insertion_point_absolute_index() : protocols::forge::build::SegmentInsert
• insertion_start_residue() : protocols::forge::build::SegmentInsert
• InSetExpression() : protocols::pack_daemon::InSetExpression
• instance() : protocols::checkpoint::Timer
• Instance() : core::pose::metrics::CalculatorFactory
• instance() : protocols::boinc::Boinc
• instantiate_rampfunc() : protocols::moves::RampingMover
• 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
• intensity() : protocols::noesy_assign::Resonance
• inter_residue_connection_partner() : core::conformation::Conformation
• interaction_cutoff() : core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::SuckerEnergy , core::scoring::methods::GaussianOverlapEnergy
• interaction_defined() : core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy
• InteractionGraphBase() : core::pack::interaction_graph::InteractionGraphBase
• InteratomicVarianceMatrix() : protocols::toolbox::InteratomicVarianceMatrix
• InterbondAngleScore() : protocols::frag_picker::scores::InterbondAngleScore
• intercept() : core::scoring::packing::HolesParams
• InterchainEnvEnergy() : protocols::scoring::methods::InterchainEnvEnergy
• InterchainPairEnergy() : protocols::scoring::methods::InterchainPairEnergy
• InterchainPotential() : protocols::scoring::InterchainPotential
• interface() : protocols::scoring::InterfaceInfo
• Interface() : protocols::scoring::Interface
• interface() : protocols::dna::RestrictDesignToProteinDNAInterface
• Interface() : protocols::ligand_docking::ligand_options::Interface , protocols::scoring::Interface
• interface_calc() : protocols::anchored_design::AnchorMoversData
• interface_distance_cutoff() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• interface_from_pose() : protocols::scoring::InterchainPotential
• interface_interaction_energy() : protocols::simple_filters::RotamerBoltzmannWeight
• interface_nres() : protocols::scoring::InterfaceInfo , protocols::scoring::Interface
• interface_number() : core::conformation::symmetry::SymmetryInfo
• 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
• InterfaceDefinitionCalculator() : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• InterfaceDeltaEnergeticsCalculator() : core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator
• InterfaceHolesFilter() : protocols::protein_interface_design::filters::InterfaceHolesFilter
• InterfaceInfo() : protocols::ligand_docking::ligand_options::InterfaceInfo , protocols::scoring::InterfaceInfo , protocols::ligand_docking::ligand_options::InterfaceInfo , protocols::scoring::InterfaceInfo
• InterfaceNeighborDefinitionCalculator() : core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator
• InterfaceRecapitulationMover() : protocols::protein_interface_design::movers::InterfaceRecapitulationMover
• InterfaceSasaDefinitionCalculator() : core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• 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::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::comparative_modeling::LoopRelaxMover , protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::comparative_modeling::LoopRelaxMover
• internalize_new_domain_map() : core::scoring::Energies
• InternalWorkingResidueParameter() : protocols::swa::rna::InternalWorkingResidueParameter
• interpolate_bbdep_nrchi_sample() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• interpolate_bins() : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::TableLookupEvaluator , core::scoring::etable::BaseEtableEnergy< Derived >
• interpolate_on_statistics() : protocols::noesy_assign::PeakCalibrator
• interpolate_rotamers() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
• interpolate_too_big() : protocols::noesy_assign::PeakCalibrator
• interpolate_too_small() : protocols::noesy_assign::PeakCalibrator
• interpolated_analytic_etable_evaluation() : core::scoring::etable::Etable
• interres_evaluator() : core::scoring::etable::AnalyticEtableEnergy , core::scoring::etable::TableLookupEtableEnergy , core::scoring::etable::AnalyticEtableEnergy
• intersects() : protocols::forge::build::Interval
• intersubunit_hbond_energy() : core::scoring::symmetry::SymmetricScoreFunction
• Interval() : protocols::forge::build::Interval
• interval() : protocols::forge::build::Bridge , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild
• Interval() : protocols::forge::build::Interval , protocols::jumping::Interval
• interval() : protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::SegmentSwap
• Interval() : protocols::jumping::Interval
• interval() : protocols::forge::build::BuildInstruction
• 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
• intra_residue_energy() : core::scoring::constraints::Constraints
• intrares_evaluator() : core::scoring::etable::TableLookupEtableEnergy , core::scoring::etable::AnalyticEtableEnergy
• intrares_upper_atom_neighbors() : core::scoring::NeighborList
• inv_dist6() : core::scoring::constraints::AmbiguousNMRDistanceConstraint
• invalidate_score_variations() : protocols::jd2::archive::EvaluatedArchive , protocols::jd2::archive::NormalizedEvaluatedArchive
• invDcnst() : core::scoring::RDC_Rohl
• inverse() : core::kinematics::RT
• 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
• invert_to_boolmasks() : core::pack::interaction_graph::RotamerDots
• invert_to_compact_array() : core::pack::interaction_graph::DotSphere
• invert_vector() : core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::DisallowIfNonnativeRLT
• InvGeometricFunc() : protocols::moves::InvGeometricFunc
• invoke() : core::scoring::etable::SC_BB_EnergyInvoker< Evaluator > , core::scoring::etable::count_pair::Invoker , core::scoring::etable::WholeWholeEnergyInvoker< Evaluator > , core::scoring::etable::SC_Whole_EnergyInvoker< Evaluator > , core::scoring::etable::BB_BB_EnergyInvoker< Evaluator > , core::scoring::etable::SC_SC_EnergyInvoker< Evaluator >
• Invoker() : core::scoring::etable::count_pair::Invoker
• InvRotamerDots() : core::pack::interaction_graph::InvRotamerDots
• 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
• iprod() : protocols::frag_picker::scores::RDCScore
• IRCollection() : protocols::motifs::IRCollection
• irrelevant_jump() : protocols::topology_broker::RigidChunkClaimer::JumpCalculator
• is4D() : protocols::noesy_assign::CrossPeak
• is_acc_chem_type() : core::scoring::hbonds::HBondTypeManager
• is_acceptor() : core::chemical::AtomType
• is_acetylated_nterminus() : core::chemical::ResidueType
• is_active_node() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• is_acyclic() : core::chemical::carbohydrates::CarbohydrateInfo
• is_adduct() : core::chemical::ResidueType
• is_aldose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_alpha_sugar() : core::chemical::carbohydrates::CarbohydrateInfo
• is_ancestor_virtual() : core::conformation::symmetry::SymmData
• is_anti() : core::scoring::dssp::Pairing
• is_any_pdb_empty() : protocols::ddg::ddGMover
• is_apolar() : core::conformation::Residue
• is_applicable() : core::fragment::FragData , core::fragment::BBTorsionSRFD , core::fragment::FragData , core::fragment::IndependentBBTorsionSRFD , core::fragment::SecstructSRFD , core::fragment::SingleResidueFragData , core::fragment::UpJumpSRFD , core::fragment::DownJumpSRFD , core::fragment::BBTorsionAndAnglesSRFD , core::fragment::SingleResidueFragData , core::fragment::DownJumpSRFD , core::fragment::Frame
• is_archive_rank() : protocols::jd2::archive::MPIArchiveJobDistributor
• is_aro() : core::scoring::rna::RNA_FullAtomStackingEnergy
• is_aromatic() : core::chemical::ResidueType , core::conformation::Residue , core::chemical::AtomType
• is_asymmetric_seqpos() : core::conformation::symmetry::SymmetryInfo
• Is_atom_bin_in_range() : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• is_attached() : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver , core::pose::datacache::LengthEventCollector , core::pose::datacache::CacheableObserver , core::pose::datacache::ObserverCache , core::pose::datacache::SpecialSegmentsObserver
• is_backbone() : core::scoring::hbonds::hbtrie::HBAtom , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo , protocols::toolbox::match_enzdes_util::EnzCstTemplateRes , core::scoring::hbonds::hbtrie::HBAtom
• is_backbone_only_cst() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• is_barrel() : protocols::fldsgn::topology::Sheet
• is_base_paired() : protocols::dna::DNAParameters
• is_below_buried_residue_no_hsasa_cutoff() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• is_beta_sugar() : core::chemical::carbohydrates::CarbohydrateInfo
• is_bonded() : core::conformation::Residue
• is_branch_point() : core::chemical::ResidueType
• is_bulge() : core::scoring::dssp::StrandPairing
• is_camelid() : protocols::antibody2::Ab_TemplateInfo
• is_Camelid() : protocols::antibody2::AntibodyInfo
• is_cancelled() : protocols::jd2::archive::Batch
• is_carbohydrate() : core::chemical::ResidueType , core::conformation::Residue
• is_catalytic_position() : protocols::enzdes::EnzdesBaseProtocol
• is_centroid() : core::conformation::Conformation , core::pose::Pose
• is_charged() : core::conformation::Residue , core::chemical::ResidueType
• is_chemical_bond() : core::kinematics::Edge
• is_coarse() : core::conformation::Residue , core::chemical::ResidueType
• is_compatible() : core::fragment::SecstructSRFD , core::fragment::UpJumpSRFD , core::fragment::BBTorsionSRFD , core::fragment::Frame , core::fragment::FragData , core::fragment::SingleResidueFragData , core::fragment::DownJumpSRFD , core::fragment::BBTorsionAndAnglesSRFD
• is_complete() : protocols::ddg::ddGMover
• is_compliant() : protocols::noesy_assign::CovalentCompliance
• is_connect() : core::chemical::ICoorAtomID
• is_conserved() : core::pose::datacache::PositionConservedResiduesStore
• is_continuous() : core::fragment::Frame , core::fragment::NonContinuousFrame
• is_covalent() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo , protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• Is_current_sugar_virtual() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• is_cut() : protocols::seeded_abinitio::DefineMovableLoops , protocols::seeded_abinitio::CloseFold
• is_cutpoint() : core::kinematics::FoldTree
• Is_cutpoint_closed_atom() : core::scoring::rna::RNA_TorsionPotential
• Is_cutpoint_closed_torsion() : core::scoring::rna::RNA_TorsionPotential
• is_cyclic() : core::chemical::carbohydrates::CarbohydrateInfo
• is_D_sugar() : core::chemical::carbohydrates::CarbohydrateInfo
• is_deriv_type() : core::scoring::hbonds::HBondTypeManager
• is_disulfide() : core::scoring::disulfides::CentroidDisulfidePotential
• is_DNA() : core::conformation::Residue
• is_dna() : core::scoring::hbonds::hbtrie::HBAtom
• is_DNA() : core::chemical::ResidueType
• is_don_chem_type() : core::scoring::hbonds::HBondTypeManager
• is_donor() : core::chemical::AtomType
• is_elimination_candidate() : protocols::noesy_assign::CrossPeak
• is_empty() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters , core::scoring::constraints::ConstraintSet
• is_end_element() : core::graph::EdgeList
• is_experimental_technique() : core::io::pdb::HeaderInformation
• is_extended() : protocols::loops::Loop
• is_finished() : protocols::jobdist::PlainPdbJobDistributor , protocols::jobdist::AtomTreeDiffJobDistributor , protocols::jobdist::PlainRawJobDistributor , protocols::jobdist::BaseJobDistributor , protocols::jobdist::PlainSilentFileJobDistributor
• Is_five_prime_chain_break_sugar_virtual() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• 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_from() : boost::unordered_object_pool< T, UserAllocator >
• is_fullatom() : core::conformation::Conformation , protocols::coarse_rna::CoarseRNA_Fragments , protocols::rna::RNA_Fragments , protocols::rna::FullAtomRNA_Fragments , core::pose::Pose
• is_furanose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_gap() : core::sequence::Sequence
• is_gapped() : core::sequence::SequenceAlignment
• is_geo_dim_type() : core::scoring::hbonds::HBondTypeManager
• is_geometry_initialized() : protocols::fldsgn::topology::SS_Base
• is_glob() : core::scoring::saxs::FormFactor
• is_glycoside() : core::chemical::carbohydrates::CarbohydrateInfo
• is_good() : protocols::abinitio::Templates , protocols::abinitio::Template , core::sequence::ScoringScheme
• is_h2o() : core::chemical::AtomType
• is_haro() : core::chemical::AtomType
• is_heavy() : core::scoring::packing::PoseBalls
• is_heavyatom() : core::chemical::AtomType
• is_helix() : protocols::features::SecondaryStructureSegmentFeatures
• is_helix_jump() : protocols::abinitio::TemplateJumpSetup
• is_heptose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_het() : core::pose::PDBInfo
• is_hexose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_hybridization_type() : core::scoring::hbonds::HBondTypeManager
• is_hydrogen() : core::chemical::AtomType , core::scoring::etable::etrie::EtableAtom , core::scoring::hackelec::ElecAtom , core::scoring::hbonds::hbtrie::HBAtom , core::scoring::trie::TrieNode< AT, CPDATA > , core::scoring::mm::mmtrie::MMEnergyTableAtom , core::scoring::hackelec::ElecAtom , core::scoring::etable::etrie::EtableAtom
• is_hydrophobic() : protocols::fldsgn::MyAtom
• is_identity() : core::id::SequenceMapping
• is_identity_ignore_gaps() : core::id::SequenceMapping
• is_in_grid() : protocols::qsar::scoring_grid::GridBase , core::grid::CartGrid< T > , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::qsar::scoring_grid::GridManager , protocols::qsar::scoring_grid::SingleGrid
• is_in_neighborhood() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• is_in_taboo_map() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• is_initialized() : protocols::features::ProteinSilentReport , protocols::fldsgn::BluePrintBDR
• is_interface() : protocols::scoring::Interface , protocols::scoring::InterfaceInfo , protocols::scoring::Interface
• is_interface_ddg() : protocols::ddg::ddGMover
• is_interface_residue() : protocols::ligand_docking::InterfaceBuilder
• is_internal() : core::chemical::AtomICoor
• Is_internal() : protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::StepWiseJobParameters
• is_internal() : core::chemical::ICoorAtomID
• is_inwards() : core::scoring::dssp::Pairing
• is_it_time() : protocols::moves::PyMolMover
• is_jump() : core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom , core::kinematics::Edge , core::kinematics::tree::Atom
• is_jump_point() : core::kinematics::FoldTree
• is_ketose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_known_atom() : core::scoring::saxs::FormFactorManager
• is_L_sugar() : core::chemical::carbohydrates::CarbohydrateInfo
• is_ladder() : core::scoring::dssp::StrandPairing
• is_lefthanded() : protocols::fldsgn::topology::BetaAlphaBetaMotif
• is_ligand() : core::conformation::Residue , core::chemical::ResidueType
• is_ligand_present() : protocols::flexpep_docking::FlexPepDockingFlags
• is_loaded() : core::scoring::methods::dfire::DFIRE_Potential
• is_loop() : protocols::features::SecondaryStructureSegmentFeatures , core::graph::Edge
• is_loop_residue() : protocols::loops::Loops
• is_lower_terminus() : core::conformation::Residue , core::chemical::ResidueType
• is_magnesium() : core::scoring::rna::RNA_ScoringInfo
• Is_magnetic_anisotropy_source_atom() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• is_master_node() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• is_member() : protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::StrandPairing
• is_mergeable() : core::fragment::Frame
• is_methylated_cterminus() : core::chemical::ResidueType
• is_movable() : protocols::nonlocal::Chunk
• is_moving_res() : protocols::swa::StepWiseJobParameters
• is_multi_trial() : protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::canonical_sampling::ThermodynamicMover
• is_mutant_calc_complete() : protocols::ddg::ddGMover
• is_my_structure() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• is_NA() : core::conformation::Residue , core::chemical::ResidueType
• is_native_pairing() : protocols::abinitio::PairingStatistics
• is_native_rotamer_well() : protocols::optimize_weights::PNatRotOptEPositionData
• Is_new_cluster_center_with_job_parameters() : protocols::swa::rna::StepWiseRNA_Clusterer
• is_new_structure() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• is_null() : core::scoring::methods::CartBondedParameters , core::scoring::methods::BBIndepCartBondedParameters
• is_observing() : core::pose::metrics::PoseMetricContainer , protocols::viewer::ConformationViewer , core::pose::PDBInfo
• Is_old_individual_suite_cluster() : protocols::swa::rna::StepWiseRNA_Clusterer
• is_on() : protocols::checkpoint::Timer
• is_open_channel() : protocols::jd2::MpiFileBuffer
• is_optE_type_name() : protocols::optimize_weights::OptEPositionDataFactory
• is_original_type() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• is_orthogonal() : core::kinematics::Stub
• is_outwards() : core::scoring::dssp::Pairing
• is_pair() : protocols::scoring::InterfaceInfo , protocols::scoring::Interface
• is_parallel() : protocols::fldsgn::topology::DimerPairing , core::scoring::dssp::Pairing , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::StrandPairing
• is_patched() : core::sequence::AnnotatedSequence
• is_pentose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_peptide() : core::kinematics::Edge
• Is_phosphate_atom_list() : core::chemical::rna::RNA_ResidueType
• is_polar() : core::chemical::ResidueType , core::conformation::Residue
• is_polar_hydrogen() : core::chemical::AtomType
• is_polymer() : core::kinematics::Edge , core::chemical::ResidueType , core::conformation::Residue
• is_polymer_bonded() : core::conformation::Residue
• is_polymer_lower() : core::chemical::ICoorAtomID
• is_polymer_upper() : core::chemical::ICoorAtomID
• is_positive_state() : protocols::multistate_design::SingleState
• is_pre_proline() : protocols::swa::StepWiseJobParameters
• Is_prepend() : protocols::swa::StepWiseJobParameters , protocols::swa::rna::StepWiseRNA_JobParameters
• Is_prepend_map() : protocols::swa::rna::StepWiseRNA_JobParameters
• Is_previous_sugar_virtual() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• is_properly_initialized() : protocols::ddg::ddGMover
• is_protein() : core::chemical::ResidueType , core::scoring::hbonds::hbtrie::HBAtom , core::conformation::Residue , core::scoring::hbonds::hbtrie::HBAtom
• is_proton() : protocols::noesy_assign::Resonance
• is_proton_chi() : core::chemical::ResidueType
• is_pseudo_bonded() : core::conformation::Residue
• is_pyranose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_qsar_map_attached() : protocols::qsar::scoring_grid::GridManager
• is_remodelable() : protocols::enzdes::EnzdesFlexBBProtocol
• is_residue_typeset() : core::conformation::Conformation
• is_RNA() : core::chemical::ResidueType , core::conformation::Residue
• is_RNA_base_atom() : core::chemical::rna::RNA_ResidueType
• Is_RNA_base_atom_list() : core::chemical::rna::RNA_ResidueType
• is_root() : core::kinematics::FoldTree
• is_rotamer_terminal() : core::scoring::trie::TrieNode< AT, CPDATA >
• is_sc() : core::scoring::hbonds::hbtrie::HBCPData
• is_score_type() : core::scoring::ScoreTypeManager
• is_septanose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_seq_sep_type() : core::scoring::hbonds::HBondTypeManager
• is_set_s_kk() : protocols::cluster::DataPoint
• Is_sibling_ribose_rotamer_pose() : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• is_similar_aa() : core::conformation::Residue
• is_similar_rotamer() : core::conformation::Residue
• Is_simple_full_length_job_params() : protocols::swa::rna::StepWiseRNA_JobParameters
• is_simple_tree() : core::kinematics::FoldTree
• is_single() : core::kinematics::TreeVizBuilder
• is_single_precision() : core::io::silent::ProteinSilentStruct_Template< T >
• is_sparis_foldtype() : protocols::fldsgn::topology::SheetFoldTypeManager
• is_start_zero_score() : protocols::jd2::archive::NormalizedEvaluatedArchive
• is_surface() : core::conformation::Residue , core::chemical::ResidueType
• is_surface_exposed() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• is_symmetric() : core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::BinaryProteinSilentStruct
• is_symmetric_partner_of() : protocols::noesy_assign::PeakAssignment
• is_terminal() : protocols::loops::Loop
• is_terminus() : core::chemical::ResidueType , core::conformation::Residue
• is_tetrose() : core::chemical::carbohydrates::CarbohydrateInfo
• Is_three_prime_chain_break_sugar_virtual() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• is_top() : protocols::dna::DnaChains
• is_torsion_exists() : protocols::rna::RNA_IdealCoord
• is_triose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_under_memory_limit() : protocols::wum::WorkUnitQueue
• is_upper_terminus() : core::chemical::ResidueType , core::conformation::Residue
• is_uronic_acid() : core::chemical::carbohydrates::CarbohydrateInfo
• is_valid() : protocols::nonlocal::HelixRotate , core::fragment::FragData , protocols::jumping::JumpSample , protocols::nonlocal::SheetTranslate , protocols::noesy_assign::FragsToAtomDist::DistanceRecord , core::fragment::FragID , core::fragment::Frame
• is_valid_chunk() : protocols::frag_picker::FragmentPicker
• is_valid_quota_pool_name() : protocols::frag_picker::quota::QuotaConfig
• Is_virt_sample_ribose_tag() : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• is_virtual() : core::conformation::Residue , core::chemical::AtomType , core::conformation::symmetry::SymmetryInfo , core::chemical::ResidueType
• Is_virtual_atom_list() : core::chemical::rna::RNA_ResidueType
• is_virtual_residue() : core::chemical::ResidueType , core::conformation::Residue
• is_weight_type() : core::scoring::hbonds::HBondTypeManager
• is_worker_running() : protocols::boinc::Boinc
• is_working_cutpoint_closed() : protocols::swa::StepWisePoseSetup
• is_working_res() : protocols::swa::StepWiseJobParameters , protocols::swa::rna::StepWiseRNA_JobParameters
• is_wt_calc_complete() : protocols::ddg::ddGMover
• isAcceptor() : protocols::sparta::PDB
• isbb() : core::scoring::hackelec::ElecAtom
• isClose() : protocols::pockets::PCluster
• isCompound() : protocols::rbsegment_relax::RBSegment
• isDonor() : protocols::sparta::PDB
• isEmpty() : protocols::rbsegment_relax::RBSegment , core::grid::CartGrid< T >
• isFullyOccupied() : core::grid::CartGrid< T >
• isGenericRB() : protocols::rbsegment_relax::RBSegment
• isHelix() : protocols::rbsegment_relax::RBSegment
• isInContact() : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• isMapLoaded() : core::scoring::electron_density::ElectronDensity , core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• IsProteinCAPredicate() : core::scoring::IsProteinCAPredicate
• isSheet() : protocols::rbsegment_relax::RBSegment
• isSimple() : protocols::rbsegment_relax::RBSegment
• isSSBonded() : protocols::sparta::PDB
• isTarget() : protocols::pockets::PCluster
• isTooSmall() : protocols::pockets::PocketGrid
• isVarFloat() : protocols::sparta::GDB
• isVarInt() : protocols::sparta::GDB
• isVarString() : protocols::sparta::GDB
• Item() : protocols::simple_moves::LoggedFragmentMover::Item
• iter_begin() : core::conformation::PseudoBondCollection
• iter_end() : core::conformation::PseudoBondCollection
• iterate() : protocols::frag_picker::ContactCounts
• iterate_bump_selector() : core::pack::rotamer_set::BumpSelector
• iterate_checkpoint_count() : protocols::boinc::Boinc
• iterate_neighbor() : protocols::frag_picker::ContactCounts
• iterate_tensor_weights() : core::scoring::ResidualDipolarCoupling
• IteratedConvergenceMover() : protocols::moves::IteratedConvergenceMover
• 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
• iterator() : core::io::raw_data::RawFileData::iterator , core::io::silent::SilentFileData::iterator , core::io::raw_data::RawFileData::iterator , core::io::silent::SilentFileData::iterator
• itoa() : protocols::sparta::ANN
• ivm() : protocols::toolbox::InteratomicVarianceMatrix