Here is a list of all class members with links to the classes they belong to:

- i -

• I : core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens
• i2() : core::scoring::methods::GoapRsdType
• i2_ : core::scoring::methods::GoapRsdType
• i2c : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• i2c_ : core::scoring::PoissonBoltzmannPotential
• i3() : core::scoring::methods::GoapRsdType
• i3_ : core::scoring::methods::GoapRsdType
• i_param : core::scoring::APBSConfig
• I_PARAM() : core::scoring::APBSConfig::I_PARAM
• iA() : core::scoring::TMscore
• iA_ : core::scoring::TMscore
• iB() : core::scoring::TMscore
• iB_ : core::scoring::TMscore
• iBR() : core::pack::annealer::FASTERAnnealer
• ibx : core::scoring::APBSResult
• iby : core::scoring::APBSResult
• ibz : core::scoring::APBSResult
• iCode : core::io::pdb::AtomInformation , core::io::pdb::ResidueInformation
• icode() : core::pose::PDBInfo
• iCode : core::pose::PDBInfo::ResidueRecord , core::pose::PDBPoseMap::ResidueKey
• icode : core::scoring::packstat::SimplePDB_Atom
• iCode1 : core::io::pdb::LinkInformation
• iCode2 : core::io::pdb::LinkInformation
• icoor() : core::chemical::Orbital , core::chemical::ResidueConnection , core::chemical::ResidueType , core::conformation::Residue
• icoor_ : core::chemical::Orbital , core::chemical::ResidueConnection , core::chemical::ResidueType
• ICoorAtomID() : core::chemical::ICoorAtomID
• ICoorOrbitalData() : core::chemical::orbitals::ICoorOrbitalData
• id() : core::environment::EnvCore , core::fragment::FragID , core::fragment::picking_old::vall::VallResidue , core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::optimization::DOF_Node , core::scoring::packstat::CavityBall , core::scoring::packstat::Sphere , core::sequence::Sequence
• id_ : core::environment::EnvCore , core::fragment::picking_old::vall::VallResidue , core::id::EXCN_AtomNotFound , core::scoring::packstat::CavityBall , core::scoring::saxs::FormFactor , core::sequence::Sequence
• id_for_current_rotamer() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• id_for_current_rotamer_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• id_to_index() : core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• id_to_index_ : core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• idCode() : core::io::pdb::HeaderInformation
• idCode_ : core::io::pdb::HeaderInformation
• ideal_bond_length_set() : core::chemical::ChemicalManager
• ideal_bond_length_sets_ : core::chemical::ChemicalManager
• ideal_delta_north_ : core::chemical::rna::RNA_FittedTorsionInfo
• ideal_delta_south_ : core::chemical::rna::RNA_FittedTorsionInfo
• ideal_nu1_north_ : core::chemical::rna::RNA_FittedTorsionInfo
• ideal_nu1_south_ : core::chemical::rna::RNA_FittedTorsionInfo
• ideal_nu2_north_ : core::chemical::rna::RNA_FittedTorsionInfo
• ideal_nu2_south_ : core::chemical::rna::RNA_FittedTorsionInfo
• ideal_xyz() : core::chemical::Atom , core::chemical::Orbital
• ideal_xyz_ : core::chemical::Atom , core::chemical::Orbital
• IdealBondLengthSet() : core::chemical::IdealBondLengthSet
• IdealBondLengthSets : core::chemical::ChemicalManager
• idealize_proline_nvs() : core::scoring::methods::CartesianBondedEnergy
• IdealizeRamaEnergy() : core::scoring::Ramachandran2B
• IdealParametersDatabase() : core::scoring::methods::IdealParametersDatabase
• identify_ss() : core::scoring::SecondaryStructurePotential
• identities() : core::sequence::SequenceAlignment
• identity() : core::id::SequenceMapping
• identity_obs_hub_ : core::conformation::Conformation
• identity_transform() : core::kinematics::Jump , core::kinematics::RT
• IdentityEval() : core::fragment::picking_old::vall::eval::IdentityEval
• IdentityEvent : core::conformation::Conformation , core::conformation::signals::IdentityEvent
• IdentityFunc() : core::scoring::func::IdentityFunc
• ids_ : core::scoring::SecondaryStructurePotential
• ids_initializer() : core::scoring::SecondaryStructurePotential
• idsn_ : core::scoring::SecondaryStructurePotential
• idsn_initializer() : core::scoring::SecondaryStructurePotential
• idx2cart() : core::scoring::electron_density::ElectronDensity , core::scoring::PoissonBoltzmannPotential
• idxoffset2cart() : core::scoring::electron_density::ElectronDensity
• if_hydrogens_ : core::scoring::saxs::SAXSEnergy
• ig_ : core::pack::annealer::DebuggingAnnealer , core::pack::annealer::FASTERAnnealer , core::pack::annealer::FixbbCoupledRotamerSimAnnealer , core::pack::annealer::FixbbLinkingRotamerSimAnnealer , core::pack::annealer::FixbbSimAnnealer , core::pack::annealer::MultiCoolAnnealer
• ig_edge_list_ : core::pack::interaction_graph::InteractionGraphBase
• IG_edge_reweights_ : core::pack::task::PackerTask_
• ig_nodes_ : core::pack::interaction_graph::InteractionGraphBase
• IGEdgeReweightContainer() : core::pack::task::IGEdgeReweightContainer
• IGEdgeReweighter() : core::pack::task::IGEdgeReweighter
• IGEdgeReweights() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• ignore_unrecognized_res() : core::io::pdb::FileDataOptions
• ignore_unrecognized_res_ : core::io::pdb::FileDataOptions
• ignore_waters() : core::io::pdb::FileDataOptions
• ignore_waters_ : core::io::pdb::FileDataOptions
• ignore_zero_occupancy() : core::io::pdb::FileDataOptions
• ignore_zero_occupancy_ : core::io::pdb::FileDataOptions
• implicit_radii_set_ : core::scoring::sasa::SasaCalc
• import() : core::kinematics::MoveMap
• import_exp_chemical_shift_data() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• import_false() : core::kinematics::MoveMap
• import_true() : core::kinematics::MoveMap
• ImportPoseOptions() : core::import_pose::ImportPoseOptions
• ImportPoseOptionsCreator() : core::import_pose::ImportPoseOptionsCreator
• improper_dihedral() : core::chemical::ResidueType
• improper_dihedral_atom_sets_ : core::chemical::ResidueType
• improper_dihedrals_for_atom() : core::chemical::ResidueType
• improper_dihedrals_for_atom_ : core::chemical::ResidueType
• improper_torsion_parameters() : core::scoring::methods::ResidueCartBondedParameters
• improper_torsion_params_ : core::scoring::methods::ResidueCartBondedParameters
• in_ : core::import_pose::atom_tree_diffs::AtomTreeDiff
• in_bin() : core::scoring::bin_transitions::BinTransitionData
• in_FASTER_mode_ : core::pack::interaction_graph::FASTERNode
• in_paired_strands() : core::scoring::dssp::Dssp
• in_place_copy() : core::conformation::Conformation
• in_span() : core::conformation::membrane::SpanningTopology
• incident_edge_list_ : core::graph::Node , core::pack::interaction_graph::NodeBase
• incident_edge_vector_ : core::pack::interaction_graph::NodeBase
• include_c_s_only_in_hsasa_ : core::scoring::sasa::SasaCalc
• include_current() : core::pack::task::operation::OptH , core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• include_current_ : core::pack::task::operation::OptH , core::pack::task::ResidueLevelTask_
• include_gly() : core::pack::task::operation::RestrictYSDesign
• include_hydrogens_ : core::scoring::sasa::SasaCalc
• include_lips() : core::conformation::membrane::MembraneInfo
• include_lips_ : core::scoring::membrane::MPLipoEnergy
• include_magnetic_anisotropy_effect_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• include_neighbor_base_stacks_ : core::scoring::rna::RNA_FilteredBaseBaseInfo
• include_probe_radius_ : core::scoring::sasa::SasaCalc , core::scoring::sasa::SasaMethod
• include_resid() : core::pack::task::operation::RestrictYSDesign
• include_residue() : core::pack::task::operation::PreventRepacking , core::pack::task::operation::RestrictAbsentCanonicalAAS , core::pack::task::operation::RestrictResidueToRepacking
• include_ring_current_effect_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• include_subunit_ : core::conformation::symmetry::SymmData
• include_virtual_side_chain() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• include_virtual_side_chain_ : core::pack::task::ResidueLevelTask_
• incomplete() : core::chemical::ResConnID
• increase_multi_cool_annealer_history_size() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• increase_packer_residue_radius() : core::pack::rotamer_set::RotamerSetOperation
• increment_both() : core::pack::interaction_graph::RotamerDots
• increment_both_and_cache() : core::pack::interaction_graph::RotamerDots
• increment_count() : core::pack::interaction_graph::DotSphere , core::pack::interaction_graph::RotamerDotsCache
• increment_edge_list_iterator() : core::pack::interaction_graph::InteractionGraphBase
• increment_f1_f2_for_atom_pair() : core::scoring::membrane::FaMPEnvSmoothEnergy , 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_self_overlap() : core::pack::interaction_graph::RotamerDots
• increment_this_and_cache() : core::pack::interaction_graph::RotamerDots
• independent_residues() : core::conformation::symmetry::SymmetryInfo
• IndependentBBTorsionSRFD() : core::fragment::IndependentBBTorsionSRFD
• index() : core::chemical::ResidueConnection , core::chemical::sdf::MolFileIOAtom , core::chemical::sdf::MolFileIOBond , core::fragment::picking_old::vall::VallSection , core::graph::DS_Node , core::scoring::motif::MotifHit
• index2frac() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• index2symbol() : core::util::ABEGOManager
• index_ : core::chemical::ResidueConnection , core::chemical::sdf::MolFileIOAtom , core::chemical::sdf::MolFileIOBond , core::fragment::picking_old::vall::VallSection , core::graph::UEVertex< V, E > , core::pack::dunbrack::ProbSortClass
• index_atom_map_ : core::chemical::sdf::MolFileIOMolecule
• index_str_ : core::pack::task::residue_selector::ResidueIndexSelector
• index_to_id() : core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• index_to_id_ : core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• index_valid() : core::chemical::sdf::MolFileIOMolecule
• IndexList : core::fragment::CacheWrapper< T, XCacheUnit >
• indicate_required_context_graphs() : core::pack::dunbrack::cenrot::CenRotDunEnergy , 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::cryst::XtalMLEnergy , 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::elec::FA_ElecEnergy , core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density::FastDensEnergy , core::scoring::electron_density::PattersonCorrEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::hackaro::HackAroEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::interface_::DDPscore , core::scoring::loop_graph::LoopCloseEnergy , core::scoring::membrane::FaMPEnvEnergy , core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::membrane::FaMPSolvEnergy , core::scoring::membrane::MPCbetaEnergy , core::scoring::membrane::MPEnvEnergy , core::scoring::membrane::MPLipoEnergy , core::scoring::membrane::MPNonHelixPenalty , core::scoring::membrane::MPPairEnergy , core::scoring::membrane::MPTerminiPenalty , core::scoring::membrane::MPTMProjPenalty , core::scoring::methods::BurialEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::CenRotEnvEnergy , core::scoring::methods::CenRotPairEnergy , core::scoring::methods::ChainbreakEnergy , core::scoring::methods::ChemicalShiftAnisotropyEnergy , core::scoring::methods::ContactOrderEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::D2H_SA_Energy , 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::FreeDOF_Energy , core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::GoapEnergy , core::scoring::methods::HybridVDW_Energy , core::scoring::methods::IntermolEnergy , core::scoring::methods::LinearChainbreakEnergy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::LK_hack , core::scoring::methods::LK_PolarNonPolarEnergy , 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::MissingEnergy , 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::NMerSVMEnergy , core::scoring::methods::OmegaTetherEnergy , core::scoring::methods::OtherPoseEnergy , 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::ProQ_Energy , core::scoring::methods::Rama2BOffsetEnergy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::RamachandranEnergy , core::scoring::methods::ReferenceEnergy , core::scoring::methods::ReferenceEnergyNoncanonical , core::scoring::methods::ResidualDipolarCouplingEnergy , core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl , core::scoring::methods::RG_Energy_Fast , core::scoring::methods::RG_LocalEnergy , 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::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::data::RNA_ChemicalMappingEnergy , core::scoring::rna::data::RNA_DataBackboneEnergy , core::scoring::rna::RG_Energy_RNA , core::scoring::rna::RNA_BulgeEnergy , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_FullAtomVDW_BasePhosphate , core::scoring::rna::RNA_JR_SuiteEnergy , 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_SuiteEnergy , core::scoring::rna::RNA_TorsionEnergy , core::scoring::rna::RNA_VDW_Energy , core::scoring::rna::StackElecEnergy , core::scoring::saxs::FastSAXSEnergy , core::scoring::saxs::SAXSEnergy , core::scoring::ScoreFunction , core::scoring::sym_e::symEnergy , core::scoring::vdwaals::VDW_Energy
• indices() : core::pack::task::operation::ResidueIndexIs , core::pack::task::operation::ResiduePDBIndexIs
• indices_ : core::pack::task::operation::ResidueIndexIs , core::pack::task::operation::ResiduePDBIndexIs
• INFINITE_SEPARATION : core::scoring::trie::TrieCountPairBase
• info() : core::scoring::ScoreFunction
• inform_non_changing_node_of_neighbors_change() : core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G >
• init() : core::chemical::carbohydrates::CarbohydrateInfo , core::chemical::ResidueProperties , core::chemical::ResidueTypeSet , core::chemical::RingConformerSet , core::pose::Pose , core::pose::rna::RNA_IdealCoord , core::pose::rna::RNA_SuiteName , core::scoring::electron_density::ElectronDensity , core::scoring::fiber_diffraction::FiberDiffraction , core::scoring::membrane::FaMPEnvEnergy , core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::BBDepCartBondedParameters , core::scoring::methods::IdealParametersDatabase , core::scoring::mm::MMBondAngleResidueTypeParam , core::scoring::motif::MotifHashManager , core::scoring::motif::ResPairMotifQuery , core::scoring::packstat::Array2D , core::scoring::sasa::LeGrandSasa , core::scoring::sasa::SasaCalc
• Init() : core::scoring::sc::MolecularSurfaceCalculator
• init_ : core::scoring::MembraneTopology
• init_cst_score_types() : core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::KofNConstraint
• init_defaults() : core::conformation::symmetry::SymmetryInfo
• 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_from_comand_line() : core::pack::task::operation::OptH
• init_from_command_line_ : core::pack::task::operation::OptH
• init_from_file() : core::kinematics::MoveMap , core::pack::dunbrack::SingleLigandRotamerLibrary , core::scoring::methods::BurialEnergy
• init_from_lines() : core::import_pose::PDBSilentStruct , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RigidBodySilentStruct , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreFileSilentStruct , core::io::silent::ScoreJumpFileSilentStruct , core::io::silent::SilentStruct
• init_from_options() : core::import_pose::ImportPoseOptions , core::io::pdb::FileDataOptions , core::io::pdb::PDB_DReaderOptions
• init_from_pose() : core::io::pdb::FileData
• init_hASA_variables() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• init_length() : core::fragment::Frame
• init_matrix() : core::sequence::NWAligner
• init_membrane_center_normal() : core::scoring::MembranePotential
• init_posehash() : core::pose::xyzStripeHashPose
• init_potentials_from_rna_torsion_database_files() : core::scoring::rna::RNA_TorsionPotential
• init_rama_sampling_table() : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• init_res_list() : core::scoring::methods::ReferenceEnergyNoncanonical
• init_rna_torsion_gaussian_parameters() : core::chemical::rna::RNA_FittedTorsionInfo
• init_SASA_radii_from_database() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• init_type() : core::sequence::MatrixScoringScheme
• init_uniform_sampling_table() : core::scoring::Ramachandran
• initialize() : core::chemical::AtomTypeDatabaseIO , core::chemical::gasteiger::GasteigerAtomTypeData , core::chemical::ResidueDatabaseIO , core::conformation::symmetry::SymmetryInfo , core::fragment::AnnotatedFragData , core::io::rna::RNA_DataReader , 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::SimpleInteractionGraph , core::pack::interaction_graph::SimpleNode , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , core::scoring::CenListInfo , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::FAElecContextData , core::scoring::elec::GroupElec , core::scoring::etable::coulomb::Coulomb , core::scoring::FACTSPoseInfo , core::scoring::FACTSResidueInfo , core::scoring::FACTSRotamerSetInfo , core::scoring::GenBornPoseInfo , core::scoring::GenBornResidueInfo , core::scoring::GenBornRotamerSetInfo , core::scoring::hbonds::HBondDatabase , core::scoring::Membrane_FAEmbed , core::scoring::MembraneEmbed , core::scoring::MembraneTopology , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::LinearChainbreakEnergy , core::scoring::methods::LKB_ResidueInfo , core::scoring::methods::LKB_ResPairMinData , core::scoring::methods::ProQ_Energy , core::scoring::ResidueNblistData , core::scoring::rna::data::RNA_DMS_LowResolutionPotential , core::scoring::rna::data::RNA_DMS_Potential , core::scoring::SecondaryStructureWeights , core::scoring::SigmoidWeightedCenList< T > , core::util::ABEGOManager
• initialize_acc_strength() : core::scoring::hbonds::HBondDatabase
• initialize_and_read_srsrdl() : core::pack::dunbrack::RotamerLibrary
• 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::data::RNA_DataBackboneEnergy
• initialize_base_centroids_and_stubs() : core::scoring::rna::RNA_CentroidInfo
• 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, N >
• initialize_carbontypes_to_linearize_fasol() : core::scoring::etable::Etable
• initialize_DMS_low_resolution_potential() : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• initialize_DMS_potential() : core::scoring::rna::data::RNA_DMS_Potential
• initialize_don_strength() : core::scoring::hbonds::HBondDatabase
• initialize_dot_coords() : core::pack::interaction_graph::RotamerDots
• initialize_dun02_aa_parameters() : core::pack::dunbrack::RotamerLibrary
• initialize_dun10_aa_parameters() : core::pack::dunbrack::RotamerLibrary
• initialize_extra_rotamer_flags_from_command_line() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• initialize_from() : core::scoring::ScoreFunctionInfo
• initialize_from_command_line() : core::pack::rotamer_set::UnboundRotamersOperation , core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• initialize_from_file() : core::scoring::ScoreFunction
• initialize_from_input_atomset() : core::scoring::etable::Etable
• initialize_from_options() : core::scoring::hbonds::HBondOptions , core::scoring::methods::EnergyMethodOptions , core::scoring::methods::FreeDOF_Options , core::scoring::methods::NMerPSSMEnergy , core::scoring::methods::NMerRefEnergy , core::scoring::methods::NMerSVMEnergy , core::scoring::rna::RNA_EnergyMethodOptions
• initialize_from_residues() : core::scoring::ResiduePairNeighborList
• initialize_from_tokens() : core::pack::task::ALLAA , core::pack::task::ALLAAwc , core::pack::task::ALLAAxc , core::pack::task::APOLA , core::pack::task::APOLAR , core::pack::task::AUTO , core::pack::task::EMPTY , core::pack::task::EX , core::pack::task::EX_CUTOFF , core::pack::task::FIX_HIS_TAUTOMER , core::pack::task::NATAA , core::pack::task::NATRO , core::pack::task::NC , core::pack::task::NO_ADDUCTS , core::pack::task::NOTAA , core::pack::task::PIKAA , core::pack::task::PIKNA , core::pack::task::PIKRNA , core::pack::task::POLAR , core::pack::task::RESET , core::pack::task::ResfileCommand , core::pack::task::SCAN , core::pack::task::TARGET , core::pack::task::USE_INPUT_SC
• initialize_func() : core::scoring::func::GaussianChainFunc
• 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_intrascale() : core::scoring::FACTSRsdTypeInfo
• initialize_matrix() : core::scoring::bin_transitions::BinTransitionCalculator
• initialize_methods_arrays() : core::scoring::ScoreFunction
• initialize_more_precise_base_pair_cutoffs() : core::scoring::rna::RNA_LowResolutionPotential
• initialize_name_map() : core::pose::datacache::CacheableDataType
• initialize_num_neighbors_counting_self() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• initialize_overlap_cache() : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >
• initialize_overlap_with_background() : core::pack::interaction_graph::HPatchNode< V, E, G >
• initialize_parameters() : core::scoring::FACTSRsdTypeInfo , core::scoring::func::GaussianChainDoubleFunc , core::scoring::func::GaussianChainFunc , core::scoring::func::GaussianChainQuadrupleFunc , core::scoring::func::GaussianChainSingleFunc , core::scoring::func::GaussianChainTripleFunc , core::sequence::ProfSimScoringScheme
• initialize_potential_from_file() : core::scoring::rna::RNA_TorsionPotential
• initialize_rama_sampling_tables() : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• initialize_residue_type() : core::scoring::methods::LKB_ResidueInfo
• 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_repulsive_weights() : core::scoring::rna::RNA_LowResolutionPotential
• initialize_rna_stagger() : core::scoring::rna::RNA_LowResolutionPotential
• initialize_sasa_arrays() : core::pack::interaction_graph::RotamerDots
• initialize_self_overlap() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• initialize_srsrdl() : core::pack::dunbrack::RotamerLibrary
• initialize_target_evaluator() : core::scoring::cryst::PhenixInterface
• initialize_vertex() : core::chemical::RerootRestypeVisitor
• initialized() : core::scoring::hbonds::HBondDatabase , core::scoring::MembraneTopology , core::scoring::methods::LKB_ResPairMinData
• initialized_ : core::pose::xyzStripeHashPose , core::scoring::hbonds::HBondDatabase , core::scoring::hbonds::HBondTypeManager , core::scoring::MembraneTopology , core::scoring::methods::LKB_ResPairMinData , core::scoring::ScoreTypeManager
• initialized_databases_ : core::scoring::hbonds::HBondDatabase
• initialized_SASA_radii : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• initializeSymmOps() : core::scoring::electron_density::ElectronDensity , core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• inner_ : core::fragment::OrderedFragSetIterator_
• inner_end_ : core::fragment::OrderedFragSetIterator_
• inneriterations_ : core::pack::annealer::SimAnnealerBase
• inneriterations_scaling_ : core::pack::annealer::SimAnnealerBase
• InnerIterator : core::fragment::OrderedFragSetIterator_
• InPlaceIntListOP : core::pack::interaction_graph::DoubleLazyInteractionGraph
• input_domain_map() : core::pose::full_model_info::FullModelInfo
• input_etable() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• input_file : update_ResidueType_enum_files.EnumInfo
• input_rotamer_coords_ : core::pack::rotamer_set::ContinuousRotamerSet
• input_rotamer_rotblock_ : core::pack::rotamer_set::ContinuousRotamerSet
• input_rotamer_samplingrot_index_ : core::pack::rotamer_set::ContinuousRotamerSet
• input_streams_ : core::import_pose::pose_stream::MetaPoseInputStream
• 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_
• insert() : core::graph::EdgeList , core::pose::PDBPoseMap , core::scoring::constraints::ResidueConstraints , core::scoring::motif::Xfrag , core::scoring::saxs::DistanceHistogram
• 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_chain_ending() : core::conformation::Conformation
• insert_char() : core::sequence::CompositeSequence , core::sequence::Sequence , core::sequence::SequenceCoupling , core::sequence::SequenceProfile
• insert_conformation_by_jump() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation
• insert_cut() : core::environment::FoldTreeSketch
• insert_dssp_ss_into_pose() : core::scoring::dssp::Dssp
• insert_edge_ss_into_pose() : core::scoring::dssp::Dssp
• insert_fold_tree_by_jump() : core::kinematics::FoldTree
• insert_fragID_list() : core::fragment::FragSet
• insert_fragment() : core::conformation::Conformation , core::kinematics::AtomTree
• insert_gap() : core::sequence::Sequence
• insert_ideal_geometry_at_polymer_bond() : core::conformation::Conformation
• insert_ideal_geometry_at_residue_connection() : core::conformation::Conformation
• insert_jump() : core::environment::FoldTreeSketch
• insert_polymer_residue() : core::conformation::Conformation , core::kinematics::FoldTree
• insert_position() : core::fragment::picking_old::vall::eval::EnergyEval
• insert_position_ : core::fragment::picking_old::vall::eval::EnergyEval
• insert_residue_by_bond() : core::conformation::Conformation , core::pose::Pose
• insert_residue_by_chemical_bond() : core::kinematics::FoldTree
• insert_residue_by_jump() : core::conformation::Conformation , core::kinematics::FoldTree , core::pose::Pose
• insert_score_function_method_options_rows() : core::scoring::methods::EnergyMethodOptions
• insert_single_fragment() : core::kinematics::AtomTree
• insert_source_residue() : core::id::SequenceMapping
• insert_ss_into_pose() : core::scoring::dssp::Dssp
• insert_ss_into_pose_no_IG_helix() : core::scoring::dssp::Dssp
• insert_target_residue() : core::id::SequenceMapping
• Instance() : core::pose::metrics::CalculatorFactory
• instance_ : core::chemical::orbitals::OrbitalTypeMapper , core::pack::task::operation::ResFilterFactory , core::pack::task::operation::TaskOperationFactory , core::pack::task::residue_selector::ResidueSelectorFactory , core::scoring::motif::MotifHashManager , core::SVNVersion
• instance_node_2_file_node_ : core::pack::interaction_graph::PDInteractionGraph
• inter_clash1() : core::scoring::motif::ResPairMotifQuery
• inter_clash1_ : core::scoring::motif::ResPairMotifQuery
• inter_clash1_xform() : core::scoring::motif::ResPairMotifQuery
• inter_clash1_xform_ : core::scoring::motif::ResPairMotifQuery
• inter_clash2() : core::scoring::motif::ResPairMotifQuery
• inter_clash2_ : core::scoring::motif::ResPairMotifQuery
• inter_clash2_xform() : core::scoring::motif::ResPairMotifQuery
• inter_clash2_xform_ : core::scoring::motif::ResPairMotifQuery
• inter_residue_connection_partner() : core::conformation::Conformation
• interacting_atompair_list_ : core::scoring::custom_pair_distance::AtomPairFuncList
• interaction_cutoff() : core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::SuckerEnergy
• interaction_defined() : core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy
• INTERACTION_RADIUS : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfacePotential
• InteractionGraphBase() : core::pack::interaction_graph::InteractionGraphBase
• InteractionGraphBaseOP : core::pack::annealer::FixbbCoupledRotamerSimAnnealer , core::pack::annealer::FixbbLinkingRotamerSimAnnealer , core::pack::annealer::FixbbSimAnnealer
• InteractionType : core::scoring::dna::DNA_BasePotential
• intercept() : core::scoring::packing::HolesParams , core::util::Line
• intercept_ : core::scoring::packing::HolesParams
• intercepts_ : core::scoring::packing::HolesParams
• interchangeability_group() : core::chemical::ResidueType
• interchangeability_group_ : core::chemical::ResidueType
• interchangeability_group_map() : core::chemical::ResidueTypeSet
• interchangeability_group_map_ : core::chemical::ResidueTypeSet
• interface_atoms_ : core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• INTERFACE_INFO : core::pose::datacache::CacheableDataType
• interface_number() : core::conformation::symmetry::SymmetryInfo
• interface_only() : core::scoring::motif::ResPairMotifQuery
• interface_only_ : core::scoring::motif::ResPairMotifQuery
• interface_residues_ : core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• InterfaceDefinitionCalculator() : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• InterfaceDeltaEnergeticsCalculator() : core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator
• InterfaceNeighborDefinitionCalculator() : core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator
• interfaces_ : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• InterfaceSasaDefinitionCalculator() : core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• InterGroupInterfaceByVectorSelector() : core::pack::task::residue_selector::InterGroupInterfaceByVectorSelector
• IntermolEnergy() : core::scoring::methods::IntermolEnergy
• INTERNAL : core::chemical::ICoorAtomID
• internal_allowed_ : core::scoring::packstat::Slice
• internal_coords_need_updating_ : core::kinematics::AtomTree
• internalize_new_domain_map() : core::scoring::Energies
• interp_ : core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::SuckerEnergy
• interpolate_ : core::scoring::rna::RNA_LowResolutionPotential
• interpolate_bbdep_nrchi_sample() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• interpolate_bins() : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::TableLookupEvaluator
• interpolate_rotamers() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N >
• interpolated_analytic_etable_evaluation() : core::scoring::etable::Etable
• interpolator_ : core::scoring::func::SplineFunc
• interres_evaluator() : core::scoring::etable::AnalyticEtableEnergy , core::scoring::etable::TableLookupEtableEnergy
• interres_evaluator_ : core::scoring::etable::AnalyticEtableEnergy , core::scoring::etable::TableLookupEtableEnergy
• interres_path_distance_cutoff_ : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• intersubunit_hbond_energy() : core::scoring::symmetry::SymmetricScoreFunction
• intgrp_ : core::chemical::SetInterchangeabilityGroup_String
• intgrp_addendum_ : core::chemical::AppendInterchangeabilityGroup_String
• intra_elec_scale() : core::scoring::FACTSRsdTypeInfo
• intra_elec_scale_ : core::scoring::FACTSRsdTypeInfo
• intra_residue_constraints_ : core::scoring::constraints::ConstraintSet
• intra_residue_energy() : core::scoring::constraints::Constraints
• intra_solv_scale() : core::scoring::FACTSRsdTypeInfo
• intra_solv_scale_ : core::scoring::FACTSRsdTypeInfo
• intrares_elec_correction_scale() : core::scoring::methods::EnergyMethodOptions
• intrares_elec_correction_scale_ : core::scoring::methods::EnergyMethodOptions
• intrares_evaluator() : core::scoring::etable::AnalyticEtableEnergy , core::scoring::etable::TableLookupEtableEnergy
• intrares_evaluator_ : core::scoring::etable::AnalyticEtableEnergy , core::scoring::etable::TableLookupEtableEnergy
• intrares_path_distance_cutoff_ : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• intrares_scale_ : core::scoring::elec::FA_GrpElecEnergy
• intrares_side_chain_score() : core::scoring::rna::RNA_TorsionPotential
• intrares_side_chain_score_ : core::scoring::rna::RNA_TorsionPotential
• intrares_upper_atom_neighbors() : core::scoring::NeighborList
• intrares_upper_nblist_ : core::scoring::NeighborList
• intrascale_by_level_ : core::scoring::FACTSPotential
• inv_cov_ : core::scoring::rna::RNA_SuitePotential
• inv_die() : core::scoring::FACTSPotential
• inv_die_ : core::scoring::FACTSPotential
• inv_dist6() : core::scoring::constraints::AmbiguousNMRDistanceConstraint
• inv_dots_ : core::pack::interaction_graph::InvRotamerDots
• inv_rho_mask : core::scoring::electron_density::ElectronDensity
• INVALIDATE : core::conformation::signals::IdentityEvent , core::conformation::signals::LengthEvent
• invDcnst() : core::scoring::RDC_Rohl
• inverse() : core::kinematics::RT
• 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
• invoke() : core::scoring::etable::BB_BB_EnergyInvoker< Evaluator > , core::scoring::etable::count_pair::Invoker , core::scoring::etable::SC_BB_EnergyInvoker< Evaluator > , core::scoring::etable::SC_SC_EnergyInvoker< Evaluator > , core::scoring::etable::SC_Whole_EnergyInvoker< Evaluator > , core::scoring::etable::WholeWholeEnergyInvoker< Evaluator >
• Invoker() : core::scoring::etable::count_pair::Invoker
• InvRotamerDots() : core::pack::interaction_graph::InvRotamerDots
• INWARDS : core::scoring::dssp::Pairing
• ionc : core::scoring::APBSConfig
• ionq : core::scoring::APBSConfig
• ionr : core::scoring::APBSConfig
• iparam19 : core::scoring::APBSConfig::I_PARAM
• ipos_ : core::fragment::FragID_Iterator
• iptsn_ : core::scoring::SecondaryStructurePotential
• is_acc_chem_type() : core::scoring::hbonds::HBondTypeManager
• is_acceptor() : core::chemical::Atom , core::chemical::AtomType
• is_acceptor_ : core::chemical::Atom , core::chemical::AtomType
• is_acetylated() : core::chemical::carbohydrates::CarbohydrateInfo
• is_acetylated_nterminus() : core::chemical::ResidueType
• is_acyclic() : core::chemical::carbohydrates::CarbohydrateInfo
• is_adduct() : core::chemical::ResidueType
• is_aldose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_alpha_aa() : core::chemical::ResidueType
• is_alpha_sugar() : core::chemical::carbohydrates::CarbohydrateInfo
• is_amino_sugar() : core::chemical::carbohydrates::CarbohydrateInfo
• is_ancestor_virtual() : core::conformation::symmetry::SymmData
• is_anti() : core::scoring::dssp::Pairing
• is_apolar() : core::conformation::Residue
• is_applicable() : core::fragment::BBTorsionAndAnglesSRFD , core::fragment::BBTorsionSRFD , core::fragment::DownJumpSRFD , core::fragment::FragData , core::fragment::Frame , core::fragment::IndependentBBTorsionSRFD , core::fragment::SecstructSRFD , core::fragment::SingleResidueFragData , core::fragment::UpJumpSRFD
• is_aromatic() : core::chemical::AtomType , core::chemical::ResidueType , core::conformation::Residue
• is_aromatic_ : core::chemical::AtomType
• is_asymmetric_seqpos() : core::conformation::symmetry::SymmetryInfo
• is_attached() : core::pose::datacache::CacheableObserver , core::pose::datacache::LengthEventCollector , core::pose::datacache::ObserverCache , core::pose::datacache::SpecialSegmentsObserver
• is_backbone() : core::scoring::hbonds::hbtrie::HBAtom
• is_backbone_ : core::scoring::hbonds::hbtrie::HBAtom
• is_below_buried_residue_no_hsasa_cutoff() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• 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_aa() : core::chemical::ResidueType
• is_beta_sugar() : core::chemical::carbohydrates::CarbohydrateInfo
• is_bonded() : core::conformation::Residue
• is_bonded_values_ : core::scoring::rna::data::RNA_DMS_Potential
• is_branch_lower_terminus() : core::chemical::ResidueType , core::conformation::Residue
• is_branch_point() : core::chemical::ResidueType , core::conformation::Residue
• is_bulge() : core::scoring::dssp::StrandPairing
• is_bulged() : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• is_bulged_ : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• is_canonical_d_aminoacid() : core::scoring::P_AA , core::scoring::Ramachandran
• is_carbohydrate() : core::chemical::ResidueType , core::conformation::Residue
• is_centroid() : core::conformation::Conformation , core::pose::Pose
• is_changed() : core::scoring::FACTSPoseInfo
• is_charged() : core::chemical::ResidueType , core::conformation::Residue
• is_chargedH() : core::scoring::FACTSRsdTypeInfo
• is_chargedH_ : core::scoring::FACTSRsdTypeInfo
• is_chemical_bond() : core::kinematics::Edge
• is_cis_omg() : core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N >
• is_coarse() : core::chemical::ResidueType , core::conformation::Residue
• is_compatible() : core::fragment::BBTorsionAndAnglesSRFD , core::fragment::BBTorsionSRFD , core::fragment::DownJumpSRFD , core::fragment::FragData , core::fragment::Frame , core::fragment::SecstructSRFD , core::fragment::SingleResidueFragData , core::fragment::UpJumpSRFD
• is_conjugatable() : core::chemical::Element
• is_conjugated() : core::chemical::gasteiger::GasteigerAtomTypeData
• is_connect() : core::chemical::ICoorAtomID
• is_conserved() : core::pose::datacache::PositionConservedResiduesStore
• is_continuous() : core::fragment::Frame , core::fragment::NonContinuousFrame
• is_cutpoint() : core::kinematics::FoldTree
• is_cutpoint_ : core::kinematics::FoldTree
• is_cyclic() : core::chemical::carbohydrates::CarbohydrateInfo , core::chemical::ResidueType
• is_d_aa() : core::chemical::ResidueType
• is_d_aminoacid() : core::scoring::methods::ReferenceEnergy
• is_D_sugar() : core::chemical::carbohydrates::CarbohydrateInfo
• is_deriv_type() : core::scoring::hbonds::HBondTypeManager
• is_disulfide() : core::scoring::disulfides::CentroidDisulfidePotential
• is_disulfide_bonded() : core::chemical::ResidueType
• is_DNA() : core::chemical::ResidueType , core::conformation::Residue
• is_dna() : core::scoring::hbonds::hbtrie::HBAtom
• is_dna_ : core::scoring::hbonds::hbtrie::HBAtom
• is_don_chem_type() : core::scoring::hbonds::HBondTypeManager
• is_donor() : core::chemical::AtomType
• is_donor_ : core::chemical::AtomType
• is_empty() : core::scoring::constraints::ConstraintSet
• is_end_element() : core::graph::EdgeList
• is_experimental_technique() : core::io::pdb::HeaderInformation
• is_fake() : core::chemical::Atom , core::chemical::Bond , core::chemical::Element
• is_freedof() : core::scoring::FACTSRsdTypeInfo
• is_freedof_ : core::scoring::FACTSRsdTypeInfo
• is_fullatom() : core::conformation::Conformation , core::pose::Pose
• is_furanose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_gap() : core::sequence::Sequence
• is_gapped() : core::sequence::SequenceAlignment
• is_gasteiger_atom_type() : core::chemical::gasteiger::GasteigerAtomTypeData
• is_gasteiger_type_ : core::chemical::gasteiger::GasteigerAtomTypeData
• is_geo_dim_type() : core::scoring::hbonds::HBondTypeManager
• is_glob() : core::scoring::saxs::FormFactor
• is_glycoside() : core::chemical::carbohydrates::CarbohydrateInfo
• is_glycoside_ : core::chemical::carbohydrates::CarbohydrateInfo
• is_good() : core::sequence::ScoringScheme
• is_h2o() : core::chemical::AtomType
• is_h2o_ : core::chemical::AtomType
• is_haro() : core::chemical::Atom , core::chemical::AtomType
• is_haro_ : core::chemical::Atom
• is_heavy() : core::scoring::packing::PoseBalls
• is_heavy_ : core::scoring::packing::PoseBalls
• is_heavyatom() : core::chemical::AtomType
• 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::Atom , core::chemical::AtomType , core::scoring::elec::ElecAtom , core::scoring::etable::etrie::EtableAtom , core::scoring::hbonds::hbtrie::HBAtom , core::scoring::mm::mmtrie::MMEnergyTableAtom , core::scoring::trie::TrieNode< AT, CPDATA > , core::scoring::vdwaals::VDWAtom
• is_hydrogen_ : core::chemical::Atom , core::scoring::elec::ElecAtom , core::scoring::etable::etrie::EtableAtom , core::scoring::hbonds::hbtrie::HBAtom , core::scoring::mm::mmtrie::MMEnergyTableAtom , core::scoring::trie::TrieNode< AT, CPDATA > , core::scoring::vdwaals::VDWAtom
• is_identity() : core::id::SequenceMapping
• is_identity_ignore_gaps() : core::id::SequenceMapping
• is_in_between() : core::pose::rna::RNA_SuiteName
• is_in_grid() : core::grid::CartGrid< T >
• is_in_list() : core::scoring::bin_transitions::BinTransitionData
• is_internal() : core::chemical::AtomICoor , core::chemical::ICoorAtomID
• is_inwards() : core::scoring::dssp::Pairing
• is_jump() : core::kinematics::Edge , core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom
• is_jump_point() : core::kinematics::FoldTree
• is_jump_point_ : core::kinematics::FoldTree
• is_ketose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_known_atom() : core::scoring::saxs::FormFactorManager
• is_l_aa() : core::chemical::ResidueType
• is_L_sugar() : core::chemical::carbohydrates::CarbohydrateInfo
• is_ladder() : core::scoring::dssp::StrandPairing
• is_ligand() : core::chemical::ResidueType , core::conformation::Residue
• is_lipid() : core::chemical::ResidueType
• is_loaded() : core::scoring::methods::dfire::DFIRE_Potential
• is_loop() : core::graph::Edge
• is_lower_terminus() : core::chemical::ResidueType , core::conformation::Residue
• is_magnesium() : core::scoring::rna::RNA_ScoringInfo
• is_magnesium_ : core::scoring::rna::RNA_ScoringInfo
• Is_magnetic_anisotropy_source_atom() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• is_map_loaded : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• is_membrane() : core::chemical::ResidueType , core::conformation::Conformation
• is_mergeable() : core::fragment::Frame
• is_metal() : core::chemical::ResidueType , core::conformation::Residue
• is_metalbinding() : core::chemical::ResidueType , core::conformation::Residue
• is_methylated_cterminus() : core::chemical::ResidueType
• is_N_acetylated() : core::chemical::carbohydrates::CarbohydrateInfo
• is_NA() : core::chemical::ResidueType , core::conformation::Residue
• is_nonose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_normally_connected() : core::scoring::Ramachandran
• is_nub() : core::chemical::RigidDistanceVisitor
• is_null() : core::scoring::methods::BBIndepCartBondedParameters , core::scoring::methods::CartBondedParameters
• is_O_acetylated() : core::chemical::carbohydrates::CarbohydrateInfo
• is_observing() : core::pose::metrics::PoseMetricContainer , core::pose::PDBInfo
• is_octose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_orbital_acceptor_ : core::chemical::orbitals::OrbitalType
• is_orbital_donor_ : core::chemical::orbitals::OrbitalType
• is_original_type() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• is_orthogonal() : core::kinematics::Stub
• is_outwards() : core::scoring::dssp::Pairing
• is_parallel() : core::scoring::dssp::Pairing
• is_patched() : core::sequence::AnnotatedSequence
• is_pentose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_peptide() : core::kinematics::Edge
• is_peptoid() : core::chemical::ResidueType , core::conformation::Residue
• is_phosphate() : core::chemical::rna::RNA_ResidueType
• is_phosphate_ : core::chemical::rna::RNA_ResidueType
• is_polar() : core::chemical::ResidueType , core::conformation::Residue
• is_polar_hydrogen() : core::chemical::Atom , core::chemical::AtomType
• is_polar_hydrogen_ : core::chemical::Atom , core::chemical::AtomType
• is_polymer() : core::chemical::ResidueType , core::conformation::Residue , core::kinematics::Edge
• is_polymer_bonded() : core::conformation::Residue
• is_polymer_lower() : core::chemical::ICoorAtomID
• is_polymer_upper() : core::chemical::ICoorAtomID
• is_protected() : core::conformation::Conformation
• is_protected_values_ : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• is_protein() : core::chemical::ResidueType , core::conformation::Residue , core::scoring::hbonds::hbtrie::HBAtom
• is_protein_ : core::scoring::hbonds::hbtrie::HBAtom
• is_proton_chi() : core::chemical::ResidueType
• is_proton_chi_ : core::chemical::ResidueType
• is_pseudo_bonded() : core::conformation::Residue
• is_pyranose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_residue_typeset() : core::conformation::Conformation
• is_reversible() : core::scoring::motif::ResPairMotif
• is_RNA() : core::chemical::ResidueType , core::conformation::Residue
• is_RNA_base() : core::chemical::rna::RNA_ResidueType
• is_rna_base() : core::scoring::rna::StackElecEnergy
• is_RNA_base_ : core::chemical::rna::RNA_ResidueType
• is_RNA_base_atom() : 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_sc_ : core::scoring::hbonds::hbtrie::HBCPData
• is_sc_bb_clash() : core::pack::task::residue_selector::ClashBasedRepackShellSelector
• is_sc_sc_clash() : core::pack::task::residue_selector::ClashBasedRepackShellSelector
• is_score_precomputed : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• is_score_type() : core::scoring::ScoreTypeManager
• is_septanose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_seq_sep_type() : core::scoring::hbonds::HBondTypeManager
• is_similar_aa() : core::conformation::Residue
• is_similar_rotamer() : core::conformation::Residue
• is_simple_tree() : core::kinematics::FoldTree
• is_single() : core::kinematics::TreeVizBuilder
• is_single_precision() : core::io::silent::ProteinSilentStruct_Template< T >
• is_surface() : core::chemical::ResidueType , core::conformation::Residue
• is_surface_ : core::scoring::solid_surface::SurfaceEnergies
• is_surface_exposed() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• is_symmetric() : core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RigidBodySilentStruct
• is_term_ : core::scoring::trie::TrieNode< AT, CPDATA >
• is_terminus() : core::chemical::ResidueType , core::conformation::Residue
• is_tetrose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_torsion_exists() : core::pose::rna::RNA_IdealCoord
• is_trans_omg() : core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N >
• is_triose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_ulose() : core::chemical::carbohydrates::CarbohydrateInfo
• is_upper_terminus() : core::chemical::ResidueType , core::conformation::Residue
• is_uronic_acid() : core::chemical::carbohydrates::CarbohydrateInfo
• is_using() : core::scoring::methods::GoapRsdType
• is_using_ : core::scoring::methods::GoapRsdType
• is_valid() : core::conformation::membrane::Span , core::conformation::membrane::SpanningTopology , core::fragment::FragData , core::fragment::FragID , core::fragment::Frame
• is_variant_type() : core::chemical::ResidueProperties
• is_virtual() : core::chemical::Atom , core::chemical::AtomType , core::chemical::ResidueType , core::chemical::rna::RNA_ResidueType , core::conformation::Residue , core::conformation::symmetry::SymmetryInfo
• is_virtual_ : core::chemical::Atom , core::chemical::rna::RNA_ResidueType
• is_virtual_residue() : core::chemical::ResidueType , core::conformation::Residue
• is_weight_type() : core::scoring::hbonds::HBondTypeManager
• isbb() : core::scoring::elec::ElecAtom
• isbb_ : core::scoring::elec::ElecAtom
• IsBondedToAHalogen() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• IsBondInRing() : core::chemical::Bond
• IsBondOrderKnown() : core::chemical::Bond
• isEmpty() : core::grid::CartGrid< T >
• isFiberDataLoaded() : core::scoring::fiber_diffraction::FiberDiffraction
• isFullyOccupied() : core::grid::CartGrid< T >
• isHet : core::io::pdb::AtomInformation , core::pose::PDBInfo::AtomRecord
• isLoaded : core::scoring::electron_density::ElectronDensity , core::scoring::fiber_diffraction::FiberDiffraction
• isMapLoaded() : core::scoring::electron_density::ElectronDensity , core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• isometry() : core::chemical::Bond
• isometry_ : core::chemical::Bond
• IsProteinCAPredicate() : core::scoring::IsProteinCAPredicate
• isRepacking : core::scoring::electron_density::PattersonCorrEnergy
• issue_passport() : core::environment::EnvCore
• IsUnsaturated() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• it_ : core::fragment::ConstantLengthFragSetIterator_ , core::fragment::ConstFrameIterator , core::fragment::FragID_Iterator , core::fragment::FrameListIterator_ , core::io::raw_data::RawFileData::const_iterator , core::io::raw_data::RawFileData::iterator , core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator
• iter_begin() : core::conformation::PseudoBondCollection
• iter_end() : core::conformation::PseudoBondCollection
• iterate_bump_selector() : core::pack::rotamer_set::BumpSelector
• iterate_tensor_weights() : core::scoring::ResidualDipolarCoupling
• iterator() : core::io::raw_data::RawFileData::iterator , core::io::silent::SilentFileData::iterator , core::kinematics::FoldTree , core::optimization::MinimizerMap , core::scoring::constraints::ResidueConstraints , core::scoring::dssp::StrandPairingSet , core::scoring::EMapVector
• iterator_category : core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator , core::kinematics::RT , core::kinematics::tree::Atom