- i -

i2() : core::scoring::methods::GoapRsdType
i3() : core::scoring::methods::GoapRsdType
I_PARAM() : core::scoring::APBSConfig::I_PARAM
iA() : core::scoring::TMscore
iB() : core::scoring::TMscore
iBR() : core::pack::annealer::FASTERAnnealer
icode() : core::pose::PDBInfo
icoor() : core::chemical::Orbital , core::chemical::ResidueConnection , core::chemical::ResidueType , core::conformation::Residue
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::scoring::packstat::CavityBall , core::sequence::Sequence
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_xyz() : core::chemical::Atom , core::chemical::Orbital
IdealBondLengthSet() : core::chemical::IdealBondLengthSet
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_transform() : core::kinematics::Jump , core::kinematics::RT
IdentityEval() : core::fragment::picking_old::vall::eval::IdentityEval
IdentityEvent() : core::conformation::signals::IdentityEvent
IdentityFunc() : core::scoring::func::IdentityFunc
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
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_waters() : core::io::pdb::FileDataOptions
ignore_zero_occupancy() : core::io::pdb::FileDataOptions
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_torsion_parameters() : core::scoring::methods::ResidueCartBondedParameters
in_paired_strands() : core::scoring::dssp::Dssp
in_place_copy() : core::conformation::Conformation
include_current() : core::pack::task::operation::OptH , core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
include_gly() : core::pack::task::operation::RestrictYSDesign
include_intra_res_RNA() : core::scoring::hbonds::HBondOptions
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_virtual_side_chain() : core::pack::task::ResidueLevelTask , 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::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::AtomICoor , core::chemical::ResidueConnection , core::fragment::picking_old::vall::VallSection
index2frac() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
index2symbol() : core::util::ABEGOManager
index_to_id() : core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
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::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::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::hbonds::HBondEnergy , core::scoring::interface_::DDPscore , core::scoring::loop_graph::LoopCloseEnergy , 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::CSD_TorsionEnergy , 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::FreeMoietyEnergy , core::scoring::methods::FreeResidueBonusEnergy , 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::MetalloPlacementEnergy , 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::PyContextIndependentTwoBodyEnergy , 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::ResidualDipolarCouplingEnergyRigidSegments , core::scoring::methods::RG_Energy , 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::RG_Energy_RNA , core::scoring::rna::RNA_BaseBaseEnergy , core::scoring::rna::RNA_BulgeEnergy , core::scoring::rna::RNA_DataBackboneEnergy , 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::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
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::RingConformerSet , core::conformation::membrane::MembraneInfo , core::pose::Pose , core::pose::rna::RNA_IdealCoord , core::pose::rna::RNA_SuiteName , core::scoring::electron_density::ElectronDensity , core::scoring::methods::BBDepCartBondedParameters , core::scoring::methods::IdealParametersDatabase , core::scoring::mm::MMBondAngleResidueTypeParam , core::scoring::packstat::Array2D , core::scoring::sasa::LeGrandSasa , core::scoring::sasa::SasaCalc
Init() : core::scoring::sc::MolecularSurfaceCalculator
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_for_highres() : core::conformation::membrane::MembraneInfo
init_for_lowres() : core::conformation::membrane::MembraneInfo
init_from_comand_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::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_potentials_from_rna_torsion_database_files() : core::scoring::rna::RNA_TorsionPotential
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::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::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::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::LinearChainbreakEnergy , core::scoring::methods::LKB_ResidueInfo , core::scoring::methods::LKB_ResPairMinData , core::scoring::methods::ProQ_Energy , core::scoring::ResidueNblistData , 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::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 >
initialize_carbontypes_to_linearize_fasol() : core::scoring::etable::Etable
initialize_chains() : core::membrane::MembraneProteinFactory
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::methods::EnergyMethodOptions , core::scoring::methods::NMerPSSMEnergy , core::scoring::methods::NMerRefEnergy , core::scoring::methods::NMerSVMEnergy
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::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_lips_exp() : core::membrane::MembraneProteinFactory
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_residue_type() : core::scoring::methods::LKB_ResidueInfo
initialize_resources() : core::membrane::MembraneProteinFactory
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_topology() : core::membrane::MembraneProteinFactory
initialized() : core::scoring::hbonds::HBondDatabase , core::scoring::MembraneTopology , core::scoring::methods::LKB_ResPairMinData
initializeSymmOps() : core::scoring::electron_density::ElectronDensity , core::scoring::electron_density_atomwise::ElectronDensityAtomwise
input_etable() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
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::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_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
inter_residue_connection_partner() : core::conformation::Conformation
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
InteractionGraphBase() : core::pack::interaction_graph::InteractionGraphBase
intercept() : core::scoring::packing::HolesParams
interchangeability_group() : core::chemical::ResidueType
interchangeability_group_map() : core::chemical::ResidueTypeSet
interface_number() : core::conformation::symmetry::SymmetryInfo
InterfaceDefinitionCalculator() : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
InterfaceDeltaEnergeticsCalculator() : core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator
InterfaceNeighborDefinitionCalculator() : core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator
InterfaceSasaDefinitionCalculator() : core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
InterGroupInterfaceByVectorSelector() : core::pack::task::residue_selector::InterGroupInterfaceByVectorSelector
IntermolEnergy() : core::scoring::methods::IntermolEnergy
internalize_new_domain_map() : core::scoring::Energies
interpolate_bbdep_nrchi_sample() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
interpolate_bins() : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::TableLookupEvaluator
interpolate_rotamers() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
interpolated_analytic_etable_evaluation() : core::scoring::etable::Etable
interres_evaluator() : core::scoring::etable::AnalyticEtableEnergy , core::scoring::etable::TableLookupEtableEnergy
intersubunit_hbond_energy() : core::scoring::symmetry::SymmetricScoreFunction
intra_elec_scale() : core::scoring::FACTSRsdTypeInfo
intra_residue_energy() : core::scoring::constraints::Constraints
intra_solv_scale() : core::scoring::FACTSRsdTypeInfo
intrares_elec_correction_scale() : core::scoring::methods::EnergyMethodOptions
intrares_evaluator() : core::scoring::etable::AnalyticEtableEnergy , core::scoring::etable::TableLookupEtableEnergy
intrares_upper_atom_neighbors() : core::scoring::NeighborList
inv_die() : core::scoring::FACTSPotential
inv_dist6() : core::scoring::constraints::AmbiguousNMRDistanceConstraint
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
is_acc_chem_type() : core::scoring::hbonds::HBondTypeManager
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_aro() : core::scoring::rna::RNA_FullAtomStackingEnergy
is_aromatic() : core::chemical::AtomType , core::chemical::ResidueType , core::conformation::Residue
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_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_branch_lower_terminus() : core::chemical::ResidueType , core::conformation::Residue
is_bulge() : core::scoring::dssp::StrandPairing
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_chemical_bond() : core::kinematics::Edge
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_closed_atom() : core::scoring::rna::RNA_TorsionPotential
is_cutpoint_closed_torsion() : core::scoring::rna::RNA_TorsionPotential
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_DNA() : core::chemical::ResidueType , core::conformation::Residue
is_dna() : core::scoring::hbonds::hbtrie::HBAtom
is_don_chem_type() : core::scoring::hbonds::HBondTypeManager
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_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_geo_dim_type() : core::scoring::hbonds::HBondTypeManager
is_glob() : core::scoring::saxs::FormFactor
is_glycoside() : core::chemical::carbohydrates::CarbohydrateInfo
is_good() : core::sequence::ScoringScheme
is_h2o() : core::chemical::AtomType
is_haro() : core::chemical::Atom , core::chemical::AtomType
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_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_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_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_magnetic_anisotropy_source_atom() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
is_membrane() : core::conformation::Conformation , core::conformation::membrane::MembraneInfo
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_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_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_phosphate() : core::chemical::rna::RNA_ResidueType
is_polar() : core::chemical::ResidueType , core::conformation::Residue
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_protein() : core::chemical::ResidueType , core::conformation::Residue , core::scoring::hbonds::hbtrie::HBAtom
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_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_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_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_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 >
is_terminus() : core::chemical::ResidueType , core::conformation::Residue
is_tetrose() : core::chemical::carbohydrates::CarbohydrateInfo
is_torsion_exists() : core::pose::rna::RNA_IdealCoord
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_valid() : core::fragment::FragData , core::fragment::FragID , core::fragment::Frame
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_residue() : core::chemical::ResidueType , core::conformation::Residue
is_weight_type() : core::scoring::hbonds::HBondTypeManager
isbb() : core::scoring::elec::ElecAtom
IsBondedToAHalogen() : core::chemical::gasteiger::PossibleAtomTypesForAtom
IsBondInRing() : core::chemical::Bond
IsBondOrderKnown() : core::chemical::Bond
isEmpty() : core::grid::CartGrid< T >
isFullyOccupied() : core::grid::CartGrid< T >
isMapLoaded() : core::scoring::electron_density::ElectronDensity , core::scoring::electron_density_atomwise::ElectronDensityAtomwise
isometry() : core::chemical::Bond
IsProteinCAPredicate() : core::scoring::IsProteinCAPredicate
issue_passport() : core::environment::EnvCore
IsUnsaturated() : core::chemical::gasteiger::PossibleAtomTypesForAtom
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